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https://www.readbyqxmd.com/read/29145059/binding-of-naringin-and-naringenin-with-hen-egg-white-lysozyme-a-spectroscopic-investigation-and-molecular-docking-study
#1
Sourav Das, Pooja Ghosh, Sudipta Koley, Atanu Singha Roy
The interactions of naringenin (NG) and naringin (NR) with Hen Egg White Lysozyme (HEWL) in aqueous medium have been investigated using UV-vis spectroscopy, steady-state fluorescence, circular dichroism (CD), Fourier Transform infrared spectroscopy (FT-IR) and molecular docking analyses. Both NG and NR can quench the intrinsic fluorescence of HEWL via static quenching mechanism. At 300K, the value of binding constant (Kb) of HEWL-NG complex (5.596±0.063×10(4)M(-1)) was found to be greater than that of HEWL-NR complex (3...
November 8, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/29142789/catalytic-depolymerization-of-lignin-and-woody-biomass-in-supercritical-ethanol-influence-of-reaction-temperature-and-feedstock
#2
Xiaoming Huang, Ceylanpinar Atay, Jiadong Zhu, Sanne W L Palstra, Tamás I Korányi, Michael D Boot, Emiel J M Hensen
The one-step ethanolysis approach to upgrade lignin to monomeric aromatics using a CuMgAl mixed oxide catalyst is studied in detail. The influence of reaction temperature (200-420 °C) on the product distribution is investigated. At low temperature (200-250 °C), recondensation is dominant, while char-forming reactions become significant at high reaction temperature (>380 °C). At preferred intermediate temperatures (300-340 °C), char-forming reactions are effectively suppressed by alkylation and Guerbet and esterification reactions...
November 6, 2017: ACS Sustainable Chemistry & Engineering
https://www.readbyqxmd.com/read/29141528/engineering-clostridium-absonum-7%C3%AE-hydroxysteroid-dehydrogenase-for-enhancing-thermostability-based-on-flexible-site-and-%C3%AE-%C3%AE-g-prediction
#3
Deshuai Lou, Jun Tan, Liancai Zhu, Shunlin Ji, Shijin Tang, Kaiyi Yao, Jingxuan Han, Bochu Wang
Enhancing thermostability of the 7α-Hydroxysteroid dehydrogenases (7α-HSDHs) is beneficial to its industrial application broadly. Based on unfolding free energy changes (ΔΔG) prediction seven mutations of Clostridium absonum (CA) 7α-HSDH were selected and experimentally verified, and these mutants fitted three-state denaturation model well, among which S22L located in the αA possessed the greatest TmN→I increase (>8 °C). Mutants P124L, L197E, N171L and Y259E also became more stable than wild type CA 7α-HSDH with different ranges...
November 12, 2017: Protein and Peptide Letters
https://www.readbyqxmd.com/read/29140090/qm-mm-simulations-identify-the-ring-opening-mechanism-of-creatininase
#4
Jitrayut Jitonnom, Joni Mujika, Marc W van der Kamp, Adrian J Mulholland
Creatininase catalyzes the conversion of creatinine (a biosensor for kidney function) to creatine via a two-step mechanism: water-addition followed by ring-opening. Water-addition is common to other known cyclic amidohydrolases, but the precise mechanism for ring-opening is still under debate. The proton donor in this step is either His178, or a water molecule bound to one of metal ions, and the roles of His178 and Glu122 are unclear. Here, the two possible reaction pathways have been fully examined by means of combined quantum mechanics/molecular mechanics simulations at the SCC-DFTB/CHARMM22 level of theory...
November 15, 2017: Biochemistry
https://www.readbyqxmd.com/read/29139533/at-the-very-beginning-of-life-on-earth-the-thiol-rich-peptide-trp-world-hypothesis
#5
Yannick Vallee, Ibrahim Shalayel, Kieu-Dung Ly, K V Raghavendra Rao, Gael De Paëpe, Katharina Märker, Anne Milet
Life developed on Earth probably about 3.8 billion years ago, on a planet that was already largely covered by oceans and where the atmosphere was very humid. The reactions, which may have led to the formation of the first polymers, particularly to the first peptides and nucleic acids, must have been compatible with these conditions. This is the case of the reaction of nitriles with aminothiols, such as cysteine and homocysteine. Since aminonitriles are the probable precursors of amino acids, this condensation reaction has been able to rapidly yield dipeptides, tripeptides, oligomers and even true polymers, each containing thiol functions...
2017: International Journal of Developmental Biology
https://www.readbyqxmd.com/read/29138410/pla2-like-proteins-myotoxic-mechanism-a-dynamic-model-description
#6
Rafael J Borges, Ney Lemke, Marcos R M Fontes
Phospholipase A2-like (PLA2-like) proteins contribute to the development of muscle necrosis in Viperidae snake bites and are not efficiently neutralized by current antivenom treatments. The toxic mechanisms of PLA2-like proteins are devoid of catalytic activity and not yet fully understood, although structural and functional experiments suggest a dimeric assembly and that the C-terminal residues are essential to myotoxicity. Herein, we characterized the functional mechanism of bothropic PLA2-like structures related to global and local measurements using the available models in the Protein Data Bank and normal mode molecular dynamics (NM-MD)...
November 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29137155/identification-expression-and-functional-analysis-of-the-fructokinase-gene-family-in-cassava
#7
Yuan Yao, Meng-Ting Geng, Xiao-Hui Wu, Chong Sun, Yun-Lin Wang, Xia Chen, Lu Shang, Xiao-Hua Lu, Zhan Li, Rui-Mei Li, Shao-Ping Fu, Rui-Jun Duan, Jiao Liu, Xin-Wen Hu, Jian-Chun Guo
Fructokinase (FRK) proteins play important roles in catalyzing fructose phosphorylation and participate in the carbohydrate metabolism of storage organs in plants. To investigate the roles of FRKs in cassava tuber root development, seven FRK genes (MeFRK1-7) were identified, and MeFRK1-6 were isolated. Phylogenetic analysis revealed that the MeFRK family genes can be divided into α (MeFRK1, 2, 6, 7) and β (MeFRK3, 4, 5) groups. All the MeFRK proteins have typical conserved regions and substrate binding residues similar to those of the FRKs...
November 12, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29135925/membrane-active-properties-of-an-amphitropic-peptide-from-the-cyaa-toxin-translocation-region
#8
Alexis Voegele, Orso Subrini, Nicolas Sapay, Daniel Ladant, Alexandre Chenal
The adenylate cyclase toxin CyaA is involved in the early stages of infection by Bordetella pertussis, the causative agent of whooping cough. CyaA intoxicates target cells by a direct translocation of its catalytic domain (AC) across the plasma membrane and produces supraphysiological levels of cAMP, leading to cell death. The molecular process of AC translocation remains largely unknown, however. We have previously shown that deletion of residues 375-485 of CyaA selectively abrogates AC translocation into eukaryotic cells...
November 14, 2017: Toxins
https://www.readbyqxmd.com/read/29132266/in-silico-molecular-docking-and-simulation-studies-on-novel-chalcone-and-flavone-hybrid-derivatives-with-1-2-3-triazole-linkage-as-vital-inhibitors-of-plasmodium-falciparum-dihydroorotate-dehydrogenase
#9
Mahalakshmi Thillainayagam, Kullappan Malathi, Sudha Ramaiah
The structural motifs of chalcones, flavones and triazoles with varied substitutions have been studied for the anti-malarial activity. In this study, 25 novel derivatives of chalcone and flavone hybrid derivatives with 1, 2, 3 - triazole linkage are docked with Plasmodium falciparum dihydroorotate dehydrogenase to establish their inhibitory activity against Plasmodium falciparum. The best binding conformation of the ligands at the catalytic site of dihydroorotate dehydrogenase are selected to characterize the best bound ligand using the best consensus score and the number of hydrogen bond interactions...
November 13, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29131453/mechanistic-insights-on-human-phosphoglucomutase-revealed-by-transition-path-sampling-and-molecular-dynamics-calculations
#10
Natercia Bras, Pedro Fernandes, Maria Ramos, Steven Schwartz
Human -phosphoglucomutase 1 (-PGM) catalyzes the isomerization of glucose-1-phosphate into glucose-6-phosphate (G6P) via two sequential phosphoryl transfer steps with a glucose-1,6-bisphosphate (G16P) intermediate. Given that the release of G6P in gluconeogenesis raises glucose output levels, -PGM represents a tempting pharmacological target for type 2 diabetes. Here, we provide the first theoretical study of the catalytic mechanism of human -PGM. We performed transition path sampling simulations to unveil the atomic details of the two catalytic chemical steps, which could be key for developing transition state (TS) analogue molecules with inhibitory properties...
November 12, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/29129932/the-vaccinia-virus-dna-polymerase-structure-provides-insights-into-the-mode-of-processivity-factor-binding
#11
Nicolas Tarbouriech, Corinne Ducournau, Stephanie Hutin, Philippe J Mas, Petr Man, Eric Forest, Darren J Hart, Christophe N Peyrefitte, Wim P Burmeister, Frédéric Iseni
Vaccinia virus (VACV), the prototype member of the Poxviridae, replicates in the cytoplasm of an infected cell. The catalytic subunit of the DNA polymerase E9 binds the heterodimeric processivity factor A20/D4 to form the functional polymerase holoenzyme. Here we present the crystal structure of full-length E9 at 2.7 Å resolution that permits identification of important poxvirus-specific structural insertions. One insertion in the palm domain interacts with C-terminal residues of A20 and thus serves as the processivity factor-binding site...
November 13, 2017: Nature Communications
https://www.readbyqxmd.com/read/29129140/effects-of-helix-and-fingertip-mutations-on-the-thermostability-of-xyn11a-investigated-by-molecular-dynamics-simulations-and-enzyme-activity-assays
#12
Thana Sutthibutpong, Triwit Rattanarojpong, Pongsak Khunrae
Local conformational changes and global unfolding pathways of wildtype xyn11A recombinant and its mutated structures were studied through a series of atomistic molecular dynamics (MD) simulations, along with enzyme activity assays at three incubation temperatures to investigate the effects of mutations at three different sites to the thermostability. The first mutation was to replace an unstable negatively charged residue at a surface beta turn near the active site (D32G) by a hydrophobic residue. The second mutation was to create a disulfide bond (S100C/N147C) establishing a strong connection between an alpha helix and a distal beta hairpin associated with the thermally sensitive Thumb loop, and the third mutation add an extra hydrogen bond (A155S) to the same alpha helix...
November 13, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29128676/how-nature-tunes-isoenzyme-activity-in-the-multifunctional-catalytic-globin-dehaloperoxidase-from-amphitrite-ornata
#13
Leiah M Carey, Roman Gavenko, Dimitri A Svistunenko, Reza A Ghiladi
The coelomic hemoglobin of Amphitrite ornata, termed dehaloperoxidase (DHP), is the first known multifunctional catalytic globin to possess biologically-relevant peroxidase and peroxygenase activities. Although the two isoenzymes of DHP, A and B, differ in sequence by only 5 amino acids out of 137 residues, DHP B consistently exhibits a greater activity than isoenzyme A. To delineate the contributions of each amino acid substitution to the activity of either isoenzyme, the substitutions of the five amino acids were systematically investigated, individually and in combination, using 22 mutants...
November 8, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29128497/replacement-of-oxidizable-residues-predicted-by-qm-mm-simulation-of-a-fungal-laccase-generates-variants-with-higher-operational-stability
#14
Mayra Avelar, Nina Pastor, Joaquin Ramirez-Ramirez, Marcela Ayala
In this work, we sought to obtain a more stable laccase with higher operational stability for the oxidation of phenols. During this reaction, phenoxy free radicals are produced that gradually inactivate the enzyme; the inactivation rate depends on the phenol chemical nature. In order to predict residues prone to oxidize within the active site, we simulated activated states of the catalytic region of a fungal laccase using QM-MM tools (Quantum Mechanics-Molecular Mechanics). After simulating the electron distribution in both the basal and activated state (plus or minus one electron) of several conformations of Coriolopsis gallica laccase, residues that could be susceptible to oxidation were identified, according to the values of spin density obtained from calculations...
October 12, 2017: Journal of Inorganic Biochemistry
https://www.readbyqxmd.com/read/29127897/highly-efficient-charge-transfer-in-co-co2p-schottky-junctions-embedded-in-nitrogen-doped-porous-carbon-for-enhancing-bioelectricity-generation
#15
Xin Xu, Shijie You, Liu Yang, Zipeng Xing, Siyu Pan, Zhuang Cai, Ying Dai, Jinlong Zou
Exploration of noble-metal free catalysts with high oxygen reduction reaction (ORR) activity and durability as alternatives for platinum/carbon (Pt/C) in microbial fuel cells (MFCs) remains a great challenge. This study reports the preparation of nitrogen-doped cobalt/cobalt phosphide/carbon (Co/Co2P/NC) catalysts via an in situ simultaneous doping/reduction method by using residual cornstalks as carbon source. Effects of carbonization temperature on structural characteristics and catalytic activity of Co/Co2P/NC catalysts are investigated...
November 6, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/29127553/identification-of-histidine-303-as-the-catalytic-base-of-lysyl-oxidase-via-site-directed-mutagenesis
#16
Rachel N Oldfield, Kathryn A Johnston, Jeanette Limones, Caitlin Ghilarducci, Karlo M Lopez
Lysyl oxidase (LOX) is a copper-dependent amine oxidase enzyme that catalyzes the formation of crosslinkages of collagen and elastin in connective tissues by oxidative deamination of lysine. Using site-directed mutagenesis, Histidine 303 has been shown to be a key residue that acts as the necessary catalytic base for this enzyme to function properly. Histidine 303 was mutated to isoleucine to remove catalytic activity and to aspartate and glutamate, respectively, in order to provide alternate residues that could act as a general base that could maintain catalytic activity...
November 10, 2017: Protein Journal
https://www.readbyqxmd.com/read/29127253/first-biochemical-and-crystallographic-characterization-of-a-fast-performing-ferritin-from-a-marine-invertebrate
#17
E De Meulenaere, J B Bailey, F A Tezcan, D D Deheyn
Ferritin, a multimeric cage-like enzyme, is integral to iron metabolism across all phyla through the sequestration and storage of iron through efficient ferroxidase activity. While ferritin sequences from around 900 species have been identified, crystal structures from only 50 species have been reported, the majority from bacterial origin. We recently isolated a secreted ferritin from the marine invertebrate Chaetopterus sp. (parchment tubeworm), which resides in muddy coastal seafloors. Here, we present the first ferritin from a marine invertebrate to be crystallized, and its biochemical characterization...
November 10, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/29127014/structural-insights-and-binding-of-a-natural-ligand-succinic-acid-with-serine-and-cysteine-proteases
#18
R Manohar, N H V Kutumbarao, Raghavendra Sashi Krishna Nagampalli, D Velmurugan, K Gunasekaran
In the age of growing infectious diseases, there is a great demand for new inhibitors which can exhibit minimum side effects. Owing to the importance of proteases in life cycle and invasion, they have been projected as attractive targets for structure based drug designing against microbes including viruses. Here we report the inhibitory activity of a well known natural compound succinic acid against both serine and cysteine proteases. The ligand is found co-crystallized with Bovine pancreatic trypsin in one of our crystallization trials and the diffraction data up to1...
November 7, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29123523/identification-of-an-evolutionarily-conserved-ankyrin-domain-containing-protein-caiap-which-regulates-inflammasome-dependent-resistance-to-bacterial-infection
#19
Sylwia D Tyrkalska, Sergio Candel, Ana B Pérez-Oliva, Ana Valera, Francisca Alcaraz-Pérez, Diana García-Moreno, María L Cayuela, Victoriano Mulero
Many proteins contain tandemly repeated modules of several amino acids, which act as the building blocks that form the underlying architecture of a specific protein-binding interface. Among these motifs and one of the most frequently observed is ankyrin repeats (ANK), which consist of 33 amino acid residues that are highly conserved. ANK domains span a wide range of functions, including protein-protein interactions, such as the recruitment of substrate to the catalytic domain of an enzyme, or the assembly of stable multiprotein complexes...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/29122686/an-artificially-constructed-dimer-through-deformation-of-a-short-zinc-binding-loop
#20
Jimin Park, Mi-Sun Kim, Keehyung Joo, Jooyoung Lee, Dong Hae Shin
We have analyzed the crystal structure of the dimeric form of d-glycero-d-manno-heptose-1,7-bisphosphate phosphatase from Burkholderia thailandensis (BtGmhB), catalyzing the removal of the phosphate at the 7 position of d-glycero-d-manno-heptose-1,7-bisphosphate. The crystal structure of BtGmhB revealed a dimeric form caused by a disruption of a short zinc-binding loop. The dimeric BtGmhB structure was induced by triggering the loss of Zn(2+)via the protonation of cysteine residues at pH 4.8 of the crystallization condition...
November 6, 2017: Biochimica et Biophysica Acta
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