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https://www.readbyqxmd.com/read/28330190/phyto-synthesis-and-structural-characterization-of-catalytically-active-gold-nanoparticles-biosynthesized-using-delonix-regia-leaf-extract
#1
Preeti Dauthal, Mausumi Mukhopadhyay
Biological methods of nanoparticles synthesis are ecologically sound and sustainable alternative to the conventional methods. On the basis of aforesaid premise, the present study deals with the optimization and fabrication of gold nanoparticles (Au-NPs) using easily available bio-resource, Delonix regia leaf extract. The use of practically nontoxic natural extracts and water allows the synthesis pathways presented to be considered as ''green'' and so permitting the synthesized Au-NPs to be used in sensitive areas, such as bioremediation...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28329912/structural-and-mechanistic-insights-into-homocysteine-degradation-by-a-mutant-of-methionine-%C3%AE-lyase-based-on-substrate-assisted-catalysis
#2
Dan Sato, Tomoo Shiba, Shunsuke Yunoto, Kazuo Furutani, Mitsuki Fukumoto, Daizou Kudou, Takashi Tamura, Kenji Inagaki, Shigeharu Harada
Methionine γ-lyse (MGL) catalyzes the α, γ-elimination of l-methionine and its derivatives as well as the α, β-elimination of l-cysteine and its derivatives to produce α-keto acids, volatile thiols, and ammonia. The reaction mechanism of MGL has been characterized by enzymological studies using several site-directed mutants. The Pseudomonas putida MGL C116H mutant showed drastically reduced degradation activity toward methionine while retaining activity toward homocysteine. To understand the underlying mechanism and to discern the subtle differences between these substrates, we analyzed the crystal structures of the reaction intermediates...
March 22, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28329765/structural-insights-into-adiponectin-receptors-suggest-ceramidase-activity
#3
Ieva Vasiliauskaité-Brooks, Remy Sounier, Pascal Rochaix, Gaëtan Bellot, Mathieu Fortier, François Hoh, Luigi De Colibus, Chérine Bechara, Essa M Saied, Christoph Arenz, Cédric Leyrat, Sébastien Granier
Adiponectin receptors (ADIPORs) are integral membrane proteins that control glucose and lipid metabolism by mediating, at least in part, a cellular ceramidase activity that catalyses the hydrolysis of ceramide to produce sphingosine and a free fatty acid (FFA). The crystal structures of the two receptor subtypes, ADIPOR1 and ADIPOR2, show a similar overall seven-transmembrane-domain architecture with large unoccupied cavities and a zinc binding site within the seven transmembrane domain. However, the molecular mechanisms by which ADIPORs function are not known...
March 22, 2017: Nature
https://www.readbyqxmd.com/read/28329756/functional-materials-discovery-using-energy-structure-function-maps
#4
Angeles Pulido, Linjiang Chen, Tomasz Kaczorowski, Daniel Holden, Marc A Little, Samantha Y Chong, Benjamin J Slater, David P McMahon, Baltasar Bonillo, Chloe J Stackhouse, Andrew Stephenson, Christopher M Kane, Rob Clowes, Tom Hasell, Andrew I Cooper, Graeme M Day
Molecular crystals cannot be designed in the same manner as macroscopic objects, because they do not assemble according to simple, intuitive rules. Their structures result from the balance of many weak interactions, rather than from the strong and predictable bonding patterns found in metal-organic frameworks and covalent organic frameworks. Hence, design strategies that assume a topology or other structural blueprint will often fail. Here we combine computational crystal structure prediction and property prediction to build energy-structure-function maps that describe the possible structures and properties that are available to a candidate molecule...
March 22, 2017: Nature
https://www.readbyqxmd.com/read/28329704/the-ifn-%C3%AE-ifn-%C3%AE-r1-il-10r%C3%AE-complex-reveals-structural-features-underlying-type-iii-ifn-functional-plasticity
#5
Juan L Mendoza, William M Schneider, Hans-Heinrich Hoffmann, Koen Vercauteren, Kevin M Jude, Anming Xiong, Ignacio Moraga, Tim M Horton, Jeffrey S Glenn, Ype P de Jong, Charles M Rice, K Christopher Garcia
Type III interferons (IFN-λs) signal through a heterodimeric receptor complex composed of the IFN-λR1 subunit, specific for IFN-λs, and interleukin-10Rβ (IL-10Rβ), which is shared by multiple cytokines in the IL-10 superfamily. Low affinity of IL-10Rβ for cytokines has impeded efforts aimed at crystallizing cytokine-receptor complexes. We used yeast surface display to engineer a higher-affinity IFN-λ variant, H11, which enabled crystallization of the ternary complex. The structure revealed that IL-10Rβ uses a network of tyrosine residues as hydrophobic anchor points to engage IL-10 family cytokines that present complementary hydrophobic binding patches, explaining its role as both a cross-reactive but cytokine-specific receptor...
March 21, 2017: Immunity
https://www.readbyqxmd.com/read/28328218/functionalized-lanthanide-iii-complexes-constructed-from-azobenzene-derivative-and-%C3%AE-diketone-ligands-luminescent-magnetic-and-reversible-trans-to-cis-photoisomerization-properties
#6
Li-Rong Lin, Hui-Hui Tang, Yun-Guang Wang, Xuan Wang, Xue-Ming Fang, Li-Hua Ma
The coordination ability of ligands functionalized by azobenzene was manipulated, and two novel chelating ligands, (E)-4-(phenyldiazenyl)-N,N-bis(pyridin-2-ylmethyl) benzohydrazide (C25H22N6O, PBPM) and (E)-4-((4-(dimethylamino)phenyl)diazenyl)-N,N-bis(pyridin-2-ylmethyl) benzohydrazide (C27H27N7O, dmPBPM), were synthesized. The ligands can offer four coordinating atoms (one oxygen and three nitrogens) to act as tetradendate ligands, together with the two β-diketonates (4,4,4-trifluoro-1-phenylbutane-1,3-dionate, tfd), and the trifluoroacetate anion presented as a ligand and a counterion to form the quaternary units with lanthanide(III) ions (La, Eu, and Gd), [Ln(tfd)2(PBPM)(CF3CO2)] (LnC47H34F9N6O7) and [Ln(tfd)2(dmPBPM)(CF3CO2)] (LnC49H39F9N7O7), where the lanthanide(III) ions are nine coordinated with N3O6 donor sets...
March 22, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28328206/ligand-induced-conformational-change-of-insulin-regulated-aminopeptidase-insights-on-catalytic-mechanism-and-active-site-plasticity
#7
Anastasia Mpakali, Emmanuel Saridakis, Karl Harlos, Yuguang Zhao, Paraskevi Kokkala, Dimitris Georgiadis, Petros Giastas, Athanasios Papakyriakou, Efstratios Stratikos
Insulin-regulated aminopeptidase (IRAP) is an enzyme with several important biological functions that is known to process a large variety of different peptidic substrates although the mechanism behind this wide specificity is not clearly understood. We describe a crystal structure of IRAP in complex with a recently developed bioactive and selective inhibitor at 2.53 Å resolution. In the presence of this inhibitor the enzyme adopts a novel conformation in which domains II and IV are juxtaposed, forming a hollow structure that excludes external solvent access to the catalytic center...
March 22, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28328154/a-symmetric-co-n5-2-h2-o-4-%C3%A2-4%C3%A2-h2-o-high-nitrogen-compound-formed-by-cobalt-ii-cation-trapping-of-a-cyclo-n5-anion
#8
Chong Zhang, Chen Yang, Bingcheng Hu, Chuanming Yu, Zhansheng Zheng, Chengguo Sun
The reactions of (N5 )6 (H3 O)3 (NH4 )4 Cl with Co(NO3 )2 ⋅6 H2 O at room temperature yielded Co(N5 )2 (H2 O)4 ⋅4 H2 O as an air-stable orange metal complex. The structure, as determined by single-crystal X-ray diffraction, has two planar cyclo-N5(-) rings and four bound water molecules symmetrically positioned around the central metal ion. Thermal analysis demonstrated the explosive properties of the material.
March 22, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28328107/chiral-exploration-of-6-12-diphenyldibenzo-b-f-1-5-diazocine-with-stable-conformation
#9
Zheng-Yi Li, Yong Pan, Lin-Lin Jin, Yue Yin, Bao-Zhu Yang, Xiao-Qiang Sun
A first optical resolution of 6,12-diphenyldibenzo[b,f][1,5]diazocine with stable boat conformation was achieved by chiral supercritical fluid chromatography (SFC). The absolute configurations of enantiomers were first assigned and determined by X-ray crystal structure based on CIP-rules. The high optical rotation and circular dichroism spectrum were well explained by electronic helix theory. Owing to the high stabilization of boat conformation, the chiral configuration could be maintained at very high temperature, more than 200 °C, which was proved by Density Functional Theory calculations...
March 22, 2017: Chirality
https://www.readbyqxmd.com/read/28327738/hydroxide-bridged-dicopper-complexes-the-influence-of-secondary-coordination-sphere-on-structure-and-catecholase-activity
#10
Deepak Bansal, Rajeev Gupta
Amide-based ligands (H2L(1-6)) with assorted functional groups appended to them have been used for the synthesis of dicopper(ii) complexes 1-6 having a Cu(μ-OH)Cu core. The crystal structures of 1-6 show that while every Cu(ii) ion is ligated within the N3 pincer cavity of a potentially multidentate ligand, two Cu(ii) centers are bridged by a hydroxide group. Notably, the Cu(μ-OH)Cu core is encased within the secondary coordination sphere intricately created by the appended groups. While complexes 1 and 2 exhibit the presence of an H-bond acceptor in the proximity of the Cu(μ-OH)Cu core, complexes 3 and 4 display the occurrence of both the H-bond donor as well as H-bond acceptor groups in the vicinity of the Cu(μ-OH)Cu core...
March 22, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28327704/preparation-and-phase-transition-of-feooh-nanorods-strain-effects-on-catalytic-water-oxidation
#11
Gisang Park, Yong-Il Kim, Young Heon Kim, Mira Park, Kyu Yeon Jang, Hyunjoon Song, Ki Min Nam
The evolution of the phase and morphology of FeOOH nanorods prepared by a hydrothermal method is studied via X-ray diffraction (XRD) and in situ transmission electron microscopy. The FeOOH nanorod with a tetragonal structure (β-FeOOH) is gradually converted into a rhombohedral Fe2O3 nanorod by a simple thermal treatment. The existence of an intermediate FeOOH structure with high lattice strains during the phase transition is identified by Rietveld analysis using XRD. The electrochemical properties of the nanorods are investigated based on the crystal phases to elucidate their relative catalytic activities...
March 22, 2017: Nanoscale
https://www.readbyqxmd.com/read/28327547/iron-based-magnetic-superhalogens-with-pseudohalogens-as-ligands-an-unbiased-structure-search
#12
Li Ping Ding, Peng Shao, Cheng Lu, Fang Hui Zhang, Li Ya Wang
We have performed an unbiased structure search for a series of neutral and anionic FeL4 (L = BO2, CN, NO2, NO3, OH, CH3, NH2, BH4 and Li2H3) clusters using the CALYPSO (Crystal structure Analysis by Particle Swarm Optimization) structure search method. To probe the superhalogen properties of neutral and anionic FeL4 clusters, we used density-functional theory with the B3LYP functional to examine three factors, including distribution of extra electron, pattern of bonding and the nature of the ligands. Theoretical results show that Fe(BO2)4, Fe(NO3)4 and Fe(NO2)4 can be classified as magnetic superhalogen due to that their electron affinities even exceed those of the constituent ligands...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28327307/discovery-characterization-and-biological-evaluation-of-a-novel-r-4-4-difluoropiperidine-scaffold-as-dopamine-receptor-4-d4r-antagonists
#13
Daniel E Jeffries, Jonathan O Witt, Andrea L McCollum, Kayla J Temple, Miguel A Hurtado, Joel M Harp, Anna L Blobaum, Craig W Lindsley, Corey R Hopkins
Herein, we report the synthesis and structure-activity relationship of a novel series of (R)-4,4-difluoropiperidine core scaffold as dopamine receptor 4 (D4) antagonists. A series of compounds from this scaffold are highly potent against the D4 receptor and selective against the other dopamine receptors. In addition, we were able to confirm the active isomer as the (R)-enantiomer via an X-ray crystal structure.
December 1, 2016: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28326781/the-berkeleylactones-antibiotic-macrolides-from-fungal-coculture
#14
Andrea A Stierle, Donald B Stierle, Daniel Decato, Nigel D Priestley, Jeremy B Alverson, John Hoody, Kelly McGrath, Dorota Klepacki
A carefully timed coculture fermentation of Penicillium fuscum and P. camembertii/clavigerum yielded eight new 16-membered-ring macrolides, berkeleylactones A-H (1, 4, 6-9, 12, 13), as well as the known antibiotic macrolide A26771B (5), patulin, and citrinin. There was no evidence of the production of the berkeleylactones or A26771B (5) by either fungus when grown as axenic cultures. The structures were deduced from analyses of spectral data, and the absolute configurations of compounds 1 and 9 were determined by single-crystal X-ray crystallography...
March 22, 2017: Journal of Natural Products
https://www.readbyqxmd.com/read/28326671/shape-assisted-self-organization-in-highly-disordered-liquid-crystal-phases
#15
Keiki Kishikawa, Yusuke Yamamoto, Go Watanabe, Ayaka Kawamura, Michinari Kohri, Tatsuo Taniguchi
In achiral rod-like molecules, a nematic phase is the most disordered liquid crystal phase, which only has one-directional order in the direction of the molecular long axis. A dumbbell-shaped molecule (compound 3: R-C6 H10 -CH=CH-C6 H4 -CH=CH-C6 H10 -R, (R=nC5 H11 )), and its liquid crystal phase (X phase) are reported, which exhibit high scattering without thermal fluctuation between two nematic phases under a polarized light optical microscope. The X phase was investigated by X-ray diffraction, scanning electron microscopy, atomic force microscopy, and molecular dynamics simulation...
March 22, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28326635/structure-enabled-discovery-of-a-stapled-peptide-inhibitor-to-target-the-oncogenic-transcriptional-repressor-tle1
#16
Sally McGrath, Marcello Tortorici, Ludovic Drouin, Savade Solanki, Lewis Vidler, Isaac Westwood, Peter Gimeson, Rob vanMontfort, Swen Hoelder
TLE1 is an oncogenic transcriptional co-repressor that exerts its repressive effects through binding of transcription factors. Inhibition of this protein-protein interaction represents a putative cancer target but no small molecule inhibitors have been published for this challenging interface. In this manuscript, we report the structure enabled design and synthesis of a constrained peptide inhibitor of TLE1. Our design featured introduction of a four carbon atom linker into the peptide epitope found in many TLE1 binding partners...
March 22, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28326629/solvent-controlled-phase-transition-of-a-co-ii-organic-framework-from-achiral-to-chiral-and-two-to-three-dimen-sion
#17
Xing-Po Wang, Wen-Miao Chen, Xiao-Yu Li, Cyril Rajnák, Zhen-Yu Feng, Mohamedally Kurmoo, Roman Boča, Chunjiang Jia, Chen-Ho Tung, Di Sun
We report an unprecedented reversible dynamic transformation in a metal-organic framework involving bond formation that is accompanied by two important structural changes, achiral to chiral and two- to three-dimension. Using two bent organic lig-ands (diimpym = 4,6-di(1H-imidazol-1-yl)pyrimidine; H2npta = 5-nitroisophthalic acid) and CoII(NO3)2*6H2O the coordination pol-ymer Co(diimpym)(npta)*CH3OH, 1*CH3OH, was obtained sol-vothermally. Its structure consisting of knitted pairs of square layers (44-sql) of five-coordinated Co, disordered methanol and crystallizing in achiral Pbca space group at room temperature undergoes a single-crystal to single-crystal (SC-SC) transfor-mation to a 3D interpenetrated framework (pcu) of six-coordinated Co and ordered methanol in chiral P212121 space group below 220 K...
March 21, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28325877/dual-utility-nls-drives-rnf169-dependent-dna-damage-responses
#18
Liwei An, Yiyang Jiang, Howin H W Ng, Ellen P S Man, Jie Chen, Ui-Soon Khoo, Qingguo Gong, Michael S Y Huen
Loading of p53-binding protein 1 (53BP1) and receptor-associated protein 80 (RAP80) at DNA double-strand breaks (DSBs) drives cell cycle checkpoint activation but is counterproductive to high-fidelity DNA repair. ring finger protein 169 (RNF169) maintains the balance by limiting the deposition of DNA damage mediator proteins at the damaged chromatin. We report here that this attribute is accomplished, in part, by a predicted nuclear localization signal (NLS) that not only shuttles RNF169 into the nucleus but also promotes its stability by mediating a direct interaction with the ubiquitin-specific protease USP7...
March 21, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28325875/ab-initio-solution-of-macromolecular-crystal-structures-without-direct-methods
#19
Airlie J McCoy, Robert D Oeffner, Antoni G Wrobel, Juha R M Ojala, Karl Tryggvason, Bernhard Lohkamp, Randy J Read
The majority of macromolecular crystal structures are determined using the method of molecular replacement, in which known related structures are rotated and translated to provide an initial atomic model for the new structure. A theoretical understanding of the signal-to-noise ratio in likelihood-based molecular replacement searches has been developed to account for the influence of model quality and completeness, as well as the resolution of the diffraction data. Here we show that, contrary to current belief, molecular replacement need not be restricted to the use of models comprising a substantial fraction of the unknown structure...
March 21, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28325822/structural-basis-for-chemokine-recognition-by-a-g-protein-coupled-receptor-and-implications-for-receptor-activation
#20
Joshua J Ziarek, Andrew B Kleist, Nir London, Barak Raveh, Nicolas Montpas, Julien Bonneterre, Geneviève St-Onge, Crystal J DiCosmo-Ponticello, Chad A Koplinski, Ishan Roy, Bryan Stephens, Sylvia Thelen, Christopher T Veldkamp, Frederick D Coffman, Marion C Cohen, Michael B Dwinell, Marcus Thelen, Francis C Peterson, Nikolaus Heveker, Brian F Volkman
Chemokines orchestrate cell migration for development, immune surveillance, and disease by binding to cell surface heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors (GPCRs). The array of interactions between the nearly 50 chemokines and their 20 GPCR targets generates an extensive signaling network to which promiscuity and biased agonism add further complexity. The receptor CXCR4 recognizes both monomeric and dimeric forms of the chemokine CXCL12, which is a distinct example of ligand bias in the chemokine family...
March 21, 2017: Science Signaling
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