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https://www.readbyqxmd.com/read/28103425/efficient-synthesis-of-%C3%AE-galactosyl-oligosaccharides-using-a-mutant-bacteroides-thetaiotaomicron-retaining-%C3%AE-galactosidase-btgh97b
#1
Masayuki Okuyama, Kana Matsunaga, Ken-Ichi Watanabe, Keitaro Yamashita, Takayoshi Tagami, Asako Kikuchi, Min Ma, Patcharapa Klahan, Haruhide Mori, Min Yao, Atsuo Kimura
The preparation of a glycosynthase, a catalytic nucleophile mutant of a glycosidase, is a well-established strategy for the effective synthesis of glycosidic linkages. However, glycosynthases derived from α-glycosidases can give poor yields of desired products because they require generally unstable β-glycosyl fluoride donors. Here, we investigate a transglycosylation catalyzed by a catalytic nucleophile mutant derived from a glycoside hydrolase family (GH) 97 α-galactosidase, using more stable β-galactosyl azide and α-galactosyl fluoride donors...
January 19, 2017: FEBS Journal
https://www.readbyqxmd.com/read/28102938/low-energy-catalytic-electrolysis-for-simultaneously-hydrogen-evolution-and-lignin-depolymerization
#2
Xu Du, Wei Liu, Zhe Zhang, Arie Mulyadi, Alex Brittain, Jian Gong, Yulin Deng
Hereby we present a novel proton exchange membrane (PEM) electrolysis process in which lignin was used as the hydrogen source at anode for hydrogen production. Either polyoxometalate (POM) or FeCl3 was used as the catalysts and charge transfer agents in anode. Over 90% Faraday efficiency was achieved. In a thermal insulation reactor, the heat energy can be maintained at a very low stage for continuous operation. Compared to the best alkaline water electrolysis reported in literature, the electrical energy consumption could be 40% lower with novel lignin electrolysis method...
January 19, 2017: ChemSusChem
https://www.readbyqxmd.com/read/28100776/crystallographic-snapshots-of-class-a-%C3%AE-lactamase-catalysis-reveal-structural-changes-that-facilitate-%C3%AE-lactam-hydrolysis
#3
Xuehua Pan, Yunjiao He, Jinping Lei, Xuhui Huang, Yanxiang Zhao
β-lactamases confer resistance to β-lactam-based antibiotics. There is great interest in understanding their mechanisms to enable the development of β-lactamase-specific inhibitors. The mechanism of Class A β-lactamases has been studied extensively, revealing Lys73 and Glu166 as general bases that assist the catalytic residue Ser70. However, the specific roles of these two residues within the catalytic cycle remains not fully understood. To help resolve this question, we first identified a Glu166His mutant that is functional but kinetically slowed...
January 18, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28100692/insights-into-the-recq-helicase-mechanism-revealed-by-the-structure-of-the-helicase-domain-of-human-recql5
#4
Joseph A Newman, Hazel Aitkenhead, Pavel Savitsky, Opher Gileadi
RecQ helicases are important maintainers of genome integrity with distinct roles in almost every cellular process requiring access to DNA. RECQL5 is one of five human RecQ proteins and is particularly versatile in this regard, forming protein complexes with a diverse set of cellular partners in order to coordinate its helicase activity to various processes including replication, recombination and DNA repair. In this study, we have determined crystal structures of the core helicase domain of RECQL5 both with and without the nucleotide ADP in two distinctly different ('Open' and 'Closed') conformations...
January 18, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28098499/inhibition-of-leishmania-infantum-trypanothione-reductase-by-diaryl-sulfide-derivatives
#5
Francesco Saccoliti, Gabriella Angiulli, Giovanni Pupo, Luca Pescatori, Valentina Noemi Madia, Antonella Messore, Gianni Colotti, Annarita Fiorillo, Luigi Scipione, Marina Gramiccia, Trentina Di Muccio, Roberto Di Santo, Roberta Costi, Andrea Ilari
The study presented here aimed at identifying a new class of compounds acting against Leishmania parasites, the causative agent of Leishmaniasis. For this purpose, the thioether derivatives of our in-house library have been evaluated in whole-cell screening assays in order to determine their in vitro activity against Leishmania protozoan. Among them, promising results have been achieved with compound RDS 777 (6-(sec-butoxy)-2-((3-chlorophenyl)thio)pyrimidin-4-amine) (IC50 = 29.43 µM), which is able to impair the mechanism of the parasite defence against the reactive oxygen species by inhibiting the trypanothione reductase (TR) with high efficiency (Ki 0...
December 2017: Journal of Enzyme Inhibition and Medicinal Chemistry
https://www.readbyqxmd.com/read/28098447/the-stories-tryptophans-tell-exploring-protein-dynamics-of-heptosyltransferase-i-from-escherichia-coli
#6
Joy M Cote, Carlos Andres Ramirez-Mondragon, Zarek S Siegel, Daniel Joseph Czyzyk, Jiali Gao, Yuk Yin Sham, Ishita Mukerji, Erika A Taylor
Heptosyltransferase I (HepI) catalyzes the addition of a single L-glycero-β-D-manno-heptose sugar (heptose) onto the membrane incorporated Kdo2-Lipid A as part of the biosynthesis of the core region of lipopolysaccharide (LPS). Gram-negative bacteria with gene knockouts of HepI have reduced virulence with enhanced susceptibility to hydrophobic antibiotics, making design of inhibitors against HepI of interest. Previous studies have shown that HepI protein dynamics are partially rate limiting, and therefore disruption of protein dynamics might provide a new strategy for inhibiting HepI...
January 18, 2017: Biochemistry
https://www.readbyqxmd.com/read/28097911/design-synthesis-and-docking-study-of-novel-coumarin-ligands-as-potential-selective-acetylcholinesterase-inhibitors
#7
Fatih Sonmez, Belma Zengin Kurt, Isil Gazioglu, Livia Basile, Aydan Dag, Valentina Cappello, Tiziana Ginex, Mustafa Kucukislamoglu, Salvatore Guccione
New coumaryl-thiazole derivatives with the acetamide moiety as a linker between the alkyl chains and/or the heterocycle nucleus were synthesized and in vitro tested as acetylcholinesterase (AChE) inhibitors. 2-(diethylamino)-N-(4-(2-oxo-2H-chromen-3-yl)thiazol-2-yl)acetamide (6c, IC50 value of 43 nM) was the best AChE inhibitor with a selectivity index of 4151.16 over BuChE. Kinetic study of AChE inhibition revealed that 6c was a mixed-type inhibitor. Moreover, the result of H4IIE hepatoma cell toxicity assay for 6c showed negligible cell death...
December 2017: Journal of Enzyme Inhibition and Medicinal Chemistry
https://www.readbyqxmd.com/read/28097692/structural-role-of-a-conserved-active-site-cis-proline-in-the-thermotoga-maritima-acetyl-esterase-from-the-carbohydrate-esterase-family-7
#8
Mrityunjay K Singh, Narayanan Manoj
A conserved cis proline residue located in the active site of Thermotoga maritima acetyl esterase (TmAcE) from the carbohydrate esterase family 7 (CE7) has been substituted by alanine. The residue was known to play a crucial role in determining the catalytic properties of the enzyme. To elucidate the structural role of the residue, the crystal structure of the Pro228Ala variant (TmAcEP228A ) was determined at 2.1 Å resolution. The replacement does not affect the overall secondary, tertiary and quaternary structures and moderately decreases the thermal stability...
January 18, 2017: Proteins
https://www.readbyqxmd.com/read/28097171/structural-insights-into-the-effects-of-charge-reversal-substitutions-at-the-surface-of-horseradish-peroxidase
#9
Leila Navapour, Navid Mogharrab
Horseradish peroxidase (HRP), has gained significant interests in biotechnology, especially in biosensor field and diagnostic test kits. Hence, its solvent-exposed lysine residues 174, 232, and 241 have been frequently modified with the aim of improving its stability and catalytic efficiency. In this computational study, we investigated the effects of Lys-to-Glu substitutions on HRP structure to model charge-reversal manipulations at the enzyme surface. Simulation results implied that upon these substitutions, the number of stable hydrogen bonds and α-helical content of HRP are increased and the proximal Ca2+ binding pocket becomes more integrated...
September 2016: Molecular Biology Research Communications
https://www.readbyqxmd.com/read/28096902/functional-characterization-of-the-active-mutator-like-transposable-element-muta1-from-the-mosquito-aedes-aegypti
#10
Kun Liu, Susan R Wessler
BACKGROUND: Mutator-like transposable elements (MULEs) are widespread with members in fungi, plants, and animals. Most of the research on the MULE superfamily has focused on plant MULEs where they were discovered and where some are extremely active and have significant impact on genome structure. The maize MuDR element has been widely used as a tool for both forward and reverse genetic studies because of its high transposition rate and preference for targeting genic regions. However, despite being widespread, only a few active MULEs have been identified, and only one, the rice Os3378, has demonstrated activity in a non-host organism...
2017: Mobile DNA
https://www.readbyqxmd.com/read/28096446/the-rpn-yhga-like-proteins-of-escherichia-coli-k-12-and-their-contribution-to-reca-independent-horizontal-transfer
#11
Anthony W Kingston, Christine Ponkratz, Elisabeth A Raleigh
: Bacteria use a variety of DNA mobilizing enzymes to facilitate environmental niche adaptation via horizontal gene transfer. This has led to real world problems, like the spread of antibiotic resistance, yet many mobilization proteins remain undefined. Here, we investigate the uncharacterized family of YhgA-like "transposase_31" proteins (PF04754). Our primary focus was the genetic and biochemical properties of the five E. coli K-12 members of this family, which we designate RpnA-RpnE for recombination promoting nuclease...
January 17, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28096445/unraveling-the-stereochemical-and-dynamic-aspects-of-the-catalytic-site-of-bacterial-peptidyl-trna-hydrolase
#12
Ashish Kabra, Salman Shahid, Ravi Kant Pal, Rahul Yadav, S V S Rama Krishna Pulavarti, Anupam Jain, Sarita Tripathi, Ashish Arora
Bacterial peptidyl-tRNA hydrolase (Pth; EC 3.1.1.29) hydrolyzes the peptidyl-tRNAs accumulated in the cytoplasm and thereby prevents cell death by alleviating tRNA starvation. X-ray and NMR studies of Vibrio cholerae Pth (VcPth) and mutants of its key residues involved in catalysis show that the activity and selectivity of the protein depends on the stereochemistry and dynamics of residues H24, D97, N118, and N14. D97-H24 interaction is critical for activity because it increases the nucleophilicity of H24. The N118 and N14 have orthogonally competing interactions with H24, both of which reduce the nucleophilicity of H24 and are likely to be offset by positioning of a peptidyl-tRNA substrate...
February 2017: RNA
https://www.readbyqxmd.com/read/28096378/biosynthesis-of-the-microtubule-destabilizing-diterpene-pseudolaric-acid-b-from-golden-larch-involves-an-unusual-diterpene-synthase
#13
Sibongile Mafu, Prema Sambandaswami Karunanithi, Teresa Ann Palazzo, Bronwyn Lee Harrod, Selina Marakana Rodriguez, Iris Natalie Mollhoff, Terrence Edward O'Brien, Shen Tong, Oliver Fiehn, Dean J Tantillo, Jörg Bohlmann, Philipp Zerbe
The diversity of small molecules formed via plant diterpene metabolism offers a rich source of known and potentially new biopharmaceuticals. Among these, the microtubule-destabilizing activity of pseudolaric acid B (PAB) holds promise for new anticancer agents. PAB is found, perhaps uniquely, in the coniferous tree golden larch (Pseudolarix amabilis, Pxa). Here we describe the discovery and mechanistic analysis of golden larch terpene synthase 8 (PxaTPS8), an unusual diterpene synthase (diTPS) that catalyzes the first committed step in PAB biosynthesis...
January 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28096352/recognition-of-protein-linked-glycans-as-a-determinant-of-peptidase-activity
#14
Ilit Noach, Elizabeth Ficko-Blean, Benjamin Pluvinage, Christopher Stuart, Meredith L Jenkins, Denis Brochu, Nakita Buenbrazo, Warren Wakarchuk, John E Burke, Michel Gilbert, Alisdair B Boraston
The vast majority of proteins are posttranslationally altered, with the addition of covalently linked sugars (glycosylation) being one of the most abundant modifications. However, despite the hydrolysis of protein peptide bonds by peptidases being a process essential to all life on Earth, the fundamental details of how peptidases accommodate posttranslational modifications, including glycosylation, has not been addressed. Through biochemical analyses and X-ray crystallographic structures we show that to hydrolyze their substrates, three structurally related metallopeptidases require the specific recognition of O-linked glycan modifications via carbohydrate-specific subsites immediately adjacent to their peptidase catalytic machinery...
January 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28095694/effect-of-a-ph-gradient-on-the-protonation-states-of-cytochrome-c-oxidase-a-continuum-electrostatics-study
#15
Pedro Rafael Magalhães, A Sofia F Oliveira, Sara R R Campos, Claudio Manuel Soares, António M Baptista
Cytochrome c oxidase (CcO) couples the reduction of dioxygen to water with transmembrane proton pumping, which leads to the generation of an electrochemical gradient. In this study we analyze how one of the components of the electrochemical gradient, the difference in pH across the membrane, or ΔpH, influences the protonation states of residues in CcO. We modified our continuum electrostatics/Monte Carlo (CE/MC) method in order to include the ΔpH and applied it to the study of CcO, in what is, to our best knowledge, the first CE/MC study of CcO in the presence of a pH gradient...
January 18, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28093590/hydrogen-diffusion-into-the-subsurfaces-of-model-metal-catalysts-from-first-principles
#16
Xiangjian Shen, Yuanjie Li, Xianglin Liu, Dandan Zhang, Jian Gao, Tianshui Liang
Diffusion pathways of atomic hydrogen on model catalyst surfaces and into subsurfaces are of great significance in the exploration of novel catalytic hydrogenation in heterogeneous catalysis. We present in detail the diffusion pathways of hydrogen on seven different open and closed model catalyst surfaces from first principles calculations. Seven transition metal catalysts with thirteen different crystal surfaces, i.e., Co(001), Ni(100) and Ni(111), Pd(100) and (111), Pt(100) and (111), Cu(100) and (111), Ag(100) and (111) and Au(100) and (111), are taken into account...
January 17, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28093470/active-site-maturation-and-activity-of-the-copper-radical-oxidase-glxa-is-governed-by-a-tryptophan-residue
#17
Amanda K Chaplin, Dimitri A Svistunenko, Michael Hough, Michael T Wilson, Erik Vijgenboom, Jonathan Ar Worrall
GlxA from Streptomyces lividans is a mononuclear copper-radical oxidase and a member of the auxiliary activity family 5 (AA5). Its domain organisation and low sequence homology make it a distinct member of the AA5 family in which the fungal galactose 6-oxidase (Gox) is the best-characterized. GlxA is a key cuproenzyme in the copper-dependent morphological development of S. lividans with a function that is linked to the processing of an extracytoplasmic glycan. The catalytic site in GlxA and Gox contain two distinct one-electron acceptors comprising the copper ion and a 3'-(S-cysteinyl) tyrosine...
January 16, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28089447/networks-of-dynamic-allostery-regulate-enzyme-function
#18
Michael Joseph Holliday, Carlo Camilloni, Geoffrey Stuart Armstrong, Michele Vendruscolo, Elan Zohar Eisenmesser
Many protein systems rely on coupled dynamic networks to allosterically regulate function. However, the broad conformational space sampled by non-coherently dynamic systems has precluded detailed analysis of their communication mechanisms. Here, we have developed a methodology that combines the high sensitivity afforded by nuclear magnetic resonance relaxation techniques and single-site multiple mutations, termed RASSMM, to identify two allosterically coupled dynamic networks within the non-coherently dynamic enzyme cyclophilin A...
December 27, 2016: Structure
https://www.readbyqxmd.com/read/28088521/signal-peptidase-i-processed-secretory-signal-sequences-selection-for-and-against-specific-amino-acids-at-the-second-position-of-mature-protein
#19
Yaramah M Zalucki, Michael P Jennings
Signal peptides direct proteins from the cytoplasm to the periplasm. These N-terminal peptides are cleaved upon entry to the periplasm by either signal peptidase I, or signal peptidase II for lipoproteins. Signal peptidase I is a serine protease that has either a serine-lysine or serine-histidine catalytic dyad present in the active site. The recognition site for signal peptide cleavage by signal peptidase I has been defined primarily by an Ala-X-Ala motif at the C-terminal end of the signal peptide, one amino acid away from the cleavage site...
January 11, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28079168/molecular-dynamics-studies-unravel-role-of-conserved-residues-responsible-for-movement-of-ions-into-active-site-of-dhbps
#20
Ranajit Nivrutti Shinde, Subramanian Karthikeyan, Balvinder Singh
3,4-dihydroxy-2-butanone-4-phosphate synthase (DHBPS) catalyzes the conversion of D-ribulose 5-phosphate (Ru5P) to L-3,4-dihydroxy-2-butanone-4-phosphate in the presence of Mg(2+). Although crystal structures of DHBPS in complex with Ru5P and non-catalytic metal ions have been reported, structure with Ru5P along with Mg(2+) is still elusive. Therefore, mechanistic role played by Mg(2+) in the structure of DHBPS is poorly understood. In this study, molecular dynamics simulations of DHBPS-Ru5P complex along with Mg(2+) have shown entry of Mg(2+) from bulk solvent into active site...
January 12, 2017: Scientific Reports
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