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https://www.readbyqxmd.com/read/28929751/structural-biology-inspired-discovery-of-novel-kras-pde%C3%AE-inhibitors
#1
Yan Jiang, Chunlin Zhuang, Long Chen, Junjie Lu, Guoqiang Dong, Zhenyuan Miao, Wannian Zhang, Jian Li, Chunquan Sheng
Structural biology is a powerful tool for investigating the stereospecific interactions between a protein and its ligand. Herein, an unprecedented chiral binding pattern was observed for inhibitors of KRAS-PDEδ interactions. Virtual screening and X-ray crystallography studies revealed that two enantiomers of a racemic inhibitor could bind at different sites. Fragment-based drug design was used to identify highly potent PDEδ inhibitors that can be used as promising lead compounds for target validation and antitumor drug development...
September 20, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28926711/regiocontrolled-synthesis-of-%C3%AE-sulfonylmethyl-o-nitrostyrenes-via-zni2-mediated-sulfonylation-and-agno2-pd-pph3-4-promoted-o-nitration
#2
Meng-Yang Chang, Han-Yu Chen, Heui-Sin Wang
We report herein the AgNO2/Pd(PPh3)4-promoted regiocontrolled o-nitration of α-sulfonylmethyl styrenes in MeNO2 with good yields. The o-nitration process provides a series of sulfonyl o-nitrostyrenes. Substituted α-sulfonylmethyl styrenes were synthesized from ZnI2-mediated sulfonylation of substituted α-methylstyrenes and sodium sulfinates (RSO2Na) in MeCN with good to excellent yields. The structures of the key products were confirmed by X-ray crystallography. A plausible mechanism has been proposed herein...
September 19, 2017: Journal of Organic Chemistry
https://www.readbyqxmd.com/read/28925702/environmentally-friendly-procedure-based-on-supercritical-fluid-chromatography-and-tandem-mass-spectrometry-molecular-networking-for-the-discovery-of-potent-antiviral-compounds-from-euphorbia-semiperfoliata
#3
Louis-Félix Nothias, Stéphanie Boutet-Mercey, Xavier Cachet, Erick De La Torre, Laurent Laboureur, Jean-François Gallard, Pascal Retailleau, Alain Brunelle, Pieter C Dorrestein, Jean Costa, Luis M Bedoya, Fanny Roussi, Pieter Leyssen, José Alcami, Julien Paolini, Marc Litaudon, David Touboul
A supercritical fluid chromatography-based targeted purification procedure using tandem mass spectrometry and molecular networking was developed to analyze, annotate, and isolate secondary metabolites from complex plant extract mixture. This approach was applied for the targeted isolation of new antiviral diterpene esters from Euphorbia semiperfoliata whole plant extract. The analysis of bioactive fractions revealed that unknown diterpene esters, including jatrophane esters and phorbol esters, were present in the samples...
September 19, 2017: Journal of Natural Products
https://www.readbyqxmd.com/read/28925695/nanomolar-inhibitors-of-glycogen-phosphorylase-based-on-%C3%AE-d-glucosaminyl-heterocycles-a-combined-synthetic-enzyme-kinetic-and-protein-crystallography-study
#4
Eva Bokor, Efthimios Kyriakis, Theodora Ga Solovou, Csenge Koppány, Anastassia L Kantsadi, Katalin E Szabó, Andrea Szakács, Georgios A Stravodimos, Tibor Docsa, Vassiliki T Skamnaki, Spyros E Zographos, Pál Gergely, Demetres D Leonidas, László Somsák
Aryl substituted 1-(β-D-glucosaminyl)-1,2,3-triazoles as well as C-β-D-glucosaminyl 1,2,4-triazoles and imidazoles were synthesized and tested as inhibitors against muscle and liver isoforms of glycogen phosphorylase (GP). While the N-β-D-glucosaminyl 1,2,3-triazoles showed weak or no inhibition, the C-β-D-glucosaminyl derivatives had potent activity and the best inhibitor was the 2-(β-D-glucosaminyl)-4(5)-(2-naphthyl)-imidazole with a Ki value of 143 nM against human liver GPa. An X-ray crystallography study of the rabbit muscle GPb inhibitor complexes revealed structural features of the strong binding, and offered an explanation for the differences in inhibitory potency between glucosyl and glucosaminyl derivatives and also for the differences between imidazole and 1,2,4-triazole analogues...
September 19, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28925040/thermal-melt-circular-dichroism-spectroscopic-studies-for-identifying-stabilising-amphipathic-molecules-for-the-voltage-gated-sodium-channel-navms
#5
Sam M Ireland, Altin Sula, B A Wallace
Purified integral membrane proteins require amphipathic molecules to maintain their solubility in aqueous solutions. These complexes, in turn, are used in studies to characterise the protein structures by a variety of biophysical and structural techniques, including spectroscopy, crystallography, and cryo-electron microscopy. Typically the amphilphiles used have been detergent molecules, but more recently they have included amphipols, which are polymers of different sizes and compositions designed to create smaller, more well-defined solubilised forms of the membrane proteins...
September 19, 2017: Biopolymers
https://www.readbyqxmd.com/read/28924211/hydrogen-bonds-to-au-atoms-in-coordinated-gold-clusters
#6
Md Abu Bakar, Mizuho Sugiuchi, Mitsuhiro Iwasaki, Yukatsu Shichibu, Katsuaki Konishi
It is well known that various transition elements can form M···H hydrogen bonds. However, for gold, there has been limited decisive experimental evidence of such attractive interactions. Herein we demonstrate an example of spectroscopically identified hydrogen bonding interaction of C-H units to Au atoms in divalent hexagold clusters ([Au6](2+)) decorated by diphosphine ligands. X-ray crystallography reveals substantially short Au-H/Au-C distances to indicate the presence of attractive interactions involving unfunctionalized C-H moieties...
September 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28921970/tris-heteroleptic-iridium-complexes-based-on-cyclometalated-ligands-with-different-cores
#7
Yanouk Cudré, Felipe Franco de Carvalho, Gregory R Burgess, Louise Male, Simon J A Pope, Ivano Tavernelli, Etienne Baranoff
A series of tris-heteroleptic iridium complexes of the form [Ir(C^N(1))(C^N(2))(acac)] combining 2-phenylpyridine (ppy), 2-(2,4-difluorophenyl)pyridine (dFppy), 1-phenylpyrazole (ppz), and 1-(2,4-difluorophenyl)pyrazole (dFppz) as the C^N ligands have been synthesized and fully characterized by NMR, X-ray crystallography, UV-vis absorption and emission spectroscopy, and electrochemical methods. It is shown that "static properties" (e.g., absorption and emission spectra and redox potentials) are primarily dictated by the overall architecture of the complex, while "dynamic properties" (e...
September 18, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28921782/estimate-your-dose-raddose-3d
#8
Charles S Bury, Jonathan C Brooks-Bartlett, Steven P Walsh, Elspeth F Garman
We present the current status of RADDOSE-3D, a software tool allowing the estimation of the dose absorbed in a macromolecular crystallography diffraction experiment. The code allows a temporal and spatial dose contour map to be calculated for a crystal of any geometry and size as it is rotated in an X-ray beam, and gives several summary dose values: among them diffraction weighted dose. This allows experimenters to plan data collections which will minimise radiation damage effects by spreading the absorbed dose more homogeneously, and thus to optimise the use of their crystals...
September 16, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28920698/correlating-bridging-ligand-with-properties-of-ligand-templated-mn-ii-3x3-3-clusters-x-br-cl-h-meo
#9
Kevin J Anderton, David M Ermert, Pedro A Quintero, Mackenzie W Turvey, Majed S Fataftah, Khalil A Abboud, Mark W Meisel, Erik Čižmár, Leslie J Murray
Polynuclear manganese compounds have garnered interest as mimics and models of the water oxidizing complex (WOC) in photosystem II and as single molecule magnets. Molecular systems in which composition can be correlated to physical phenomena, such as magnetic exchange interactions, remain few primarily because of synthetic limitations. Here, we report the synthesis of a family of trimanganese(II) complexes of the type Mn3X3L (X = Cl(-), H(-), and MeO(-)) where L(3-) is a tris(β-diketiminate) cyclophane. The tri(chloride) complex (2) is structurally similar to the reported tri(bromide) complex (1) with the Mn3X3 core having a ladder-like arrangement of alternating M-X rungs, whereas the tri(μ-hydride) (3) and tri(μ-methoxide) (4) complexes contain planar hexagonal cores...
September 18, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28920692/roseochelin-b-an-algaecidal-natural-product-synthesized-by-the-roseobacter-phaeobacter-inhibens-in-response-to-algal-sinapic-acid
#10
Rurun Wang, Mohammad R Seyedsayamdost
The secondary metabolome of the representative Roseobacter, Phaeobacter inhibens, was examined in response to algal sinapic acid. In addition to roseobacticides, sinapic acid induced the production of two new natural products, roseochelin A and B, which were characterized by NMR and X-ray crystallography. Functional assays showed that roseochelin B binds iron and is algaecidal against the algal host Emiliania huxleyi. It appears to be produced by a rarely observed combination of nonenzymatic and enzymatic transformations...
September 18, 2017: Organic Letters
https://www.readbyqxmd.com/read/28920685/evaluation-of-the-intramolecular-charge-transfer-properties-in-solvatochromic-and-electrochromic-zinc-octa-carbazolyl-phthalocyanines
#11
Shereen A Majeed, Basma Ghazal, Dustin E Nevonen, Philip C Goff, David A Blank, Victor N Nemykin, Saad Makhseed
2,3,9,10,16,17,23·24-Octakis-(9H-carbazol-9-yl) phthalocyaninato zinc(II) (3) and 2,3,9,10,16,17,23·24-octakis-(3,6-di-tert-butyl-9H-carbazole) phthalocyaninato zinc(II) (4) complexes were prepared and characterized by NMR and UV-vis spectroscopies, magnetic circular dichroism (MCD), matrix-assisted laser desorption ionization mass spectrometry, and X-ray crystallography. UV-vis and MCD data are indicative of the interligand charge-transfer nature of the broad band observed in 450-500 nm range for 3 and 4...
September 18, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28920626/mononuclear-salen-gallium-complexes-for-iso-selective-ring-opening-polymerization-rop-of-rac-lactide
#12
David Specklin, Christophe Fliedel, Frédéric Hild, Samir Mameri, Lydia Karmazin, Corinne Bailly, Samuel Dagorne
A series of mononuclear salen-supported gallium amido/alkoxide derivatives were prepared and structurally characterized and subsequently used as initiators in rac-lactide ring-opening polymerisation (ROP). The reaction of variously substituted salen ligands (1a-1f) with 0.5 equiv. of Ga2(NMe2)6 allowed the isolation of the corresponding (salen)Ga-NMe2 chelates (2b-2d, 2f) via an amine elimination route, as poorly soluble compounds in common solvents. The (salen)Ga-OBn derivatives (3a-3e) may be readily accessed by an amine-elimination/alcoholysis sequence and the molecular structures of 3a, 3d and 3e were confirmed through X-ray crystallography diffraction analysis...
September 18, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28919419/binding-mode-of-metal-ions-to-the-bacterial-iron-import-protein-efeo
#13
Kanate Temtrirath, Kenji Okumura, Yukie Maruyama, Bunzo Mikami, Kousaku Murata, Wataru Hashimoto
The tripartite EfeUOB system functions as a low pH iron importer in Gram-negative bacteria. In the alginate-assimilating bacterium Sphingomonas sp. strain A1, an additional EfeO-like protein (Algp7) is encoded downstream of the efeUOB operon. Here we show the metal binding mode of Algp7, which carries a M_75 metallopeptidase motif. The Algp7 protein was purified from recombinant E. coli cells and was subsequently characterized using differential scanning fluorimetry, fluorescence spectrometry, atomic absorption spectroscopy, and X-ray crystallography...
September 14, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28917122/structure-determination-based-on-continuous-diffraction-from-macromolecular-crystals
#14
REVIEW
Henry N Chapman, Petra Fromme
Bright and coherent X-ray sources, such free-electron lasers, have spurred large activities in developing new methods to obtain the structures of biological macromolecules. In particular, single-molecule diffraction is highly desired, as it would abolish the need for crystallization. It provides considerably more diffraction intensity information than needed to solve a structure, unlike crystal diffraction, which is usually insufficient for direct phasing. To overcome the challenge of weak scattering signals of single molecules, the direct phasing approaches in coherent diffractive imaging have been combined with crystals in several imaginative ways...
September 13, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28915239/structural-basis-for-the-high-specificity-of-a-trypanosoma-congolense-immunoassay-targeting-glycosomal-aldolase
#15
Joar Pinto, Steven Odongo, Felicity Lee, Vaiva Gaspariunaite, Serge Muyldermans, Stefan Magez, Yann G-J Sterckx
BACKGROUND: Animal African trypanosomosis (AAT) is a neglected tropical disease which imposes a heavy burden on the livestock industry in Sub-Saharan Africa. Its causative agents are Trypanosoma parasites, with T. congolense and T. vivax being responsible for the majority of the cases. Recently, we identified a Nanobody (Nb474) that was employed to develop a homologous sandwich ELISA targeting T. congolense fructose-1,6-bisphosphate aldolase (TcoALD). Despite the high sequence identity between trypanosomatid aldolases, the Nb474-based immunoassay is highly specific for T...
September 15, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28915048/xfel-radiation-damage-through-the-s-state-cycle-of-the-oxygen-evolving-complex-of-photosystem-ii
#16
Muhamed Amin, Mikhail Askerka, Victor S Batista, Gary W Brudvig, Marilyn R Gunner
The oxygen-evolving complex (OEC) of photosystem II (PSII) catalyzes water-splitting through a reaction mechanism that cycles the OEC through five redox states, the 'S-state' intermediates. Understanding structure/function relations of the S-state intermediates is crucial for elucidation of the reaction mechanism and the design of biomimetic catalytic systems. Due to the limitations of conventional X-ray crystallography, serial femtosecond X-ray crystallography has been used to minimize the radiation-damage...
September 15, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28915025/structural-evidence-for-the-dopamine-first-mechanism-of-norcoclaurine-synthase
#17
Benjamin R Lichman, Altin Sula, Thomas Pesnot, Helen C Hailes, John M Ward, Nicholas H Keep
Norcoclaurine synthase (NCS) is a Pictet-Spenglerase that catalyzes the first key step in plant benzylisoquinoline alkaloid metabolism, a compound family that includes bioactive natural products such as morphine. The enzyme has also shown great potential as a biocatalyst for the formation of chiral isoquinolines. Here we present new high-resolution X-ray crystallography data describing Thalictrum flavum NCS bound to a mechanism-inspired ligand. The structure supports two key features of the NCS "dopamine-first" mechanism: the binding of dopamine catechol to Lys-122 and the position of the carbonyl substrate binding site at the active site entrance...
September 20, 2017: Biochemistry
https://www.readbyqxmd.com/read/28915017/cationic-and-anionic-disorder-in-cztsse-kesterite-compounds-a-chemical-crystallography-study
#18
Pierre Bais, Maria Teresa Caldes, Michaël Paris, Catherine Guillot-Deudon, Pierre Fertey, Bernadette Domengès, Alain Lafond
The cationic and anionic disorder in the Cu2ZnSnSe4-Cu2ZnSnS4 (CZTSe-CZTS) system has been investigated through a chemical crystallography approach including X-ray diffraction (in conventional and resonant setup), (119)Sn and (77)Se NMR spectroscopy, and high-resolution transmission electron microscopy (HRTEM) techniques. Single-crystal XRD analysis demonstrates that the studied compounds behave as a solid solution with the kesterite crystal structure in the whole S/(S + Se) composition range. As previously reported for pure sulfide and pure selenide compounds, the (119)Sn NMR spectroscopy study gives clear evidence that the level of Cu/Zn disorder in mixed S/Se compounds depends on the thermal history of the samples (slow cooled or quenched)...
September 15, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28912485/serial-millisecond-crystallography-for-routine-room-temperature-structure-determination-at-synchrotrons
#19
Tobias Weinert, Natacha Olieric, Robert Cheng, Steffen Brünle, Daniel James, Dmitry Ozerov, Dardan Gashi, Laura Vera, May Marsh, Kathrin Jaeger, Florian Dworkowski, Ezequiel Panepucci, Shibom Basu, Petr Skopintsev, Andrew S Doré, Tian Geng, Robert M Cooke, Mengning Liang, Andrea E Prota, Valerie Panneels, Przemyslaw Nogly, Ulrich Ermler, Gebhard Schertler, Michael Hennig, Michel O Steinmetz, Meitian Wang, Jörg Standfuss
Historically, room-temperature structure determination was succeeded by cryo-crystallography to mitigate radiation damage. Here, we demonstrate that serial millisecond crystallography at a synchrotron beamline equipped with high-viscosity injector and high frame-rate detector allows typical crystallographic experiments to be performed at room-temperature. Using a crystal scanning approach, we determine the high-resolution structure of the radiation sensitive molybdenum storage protein, demonstrate soaking of the drug colchicine into tubulin and native sulfur phasing of the human G protein-coupled adenosine receptor...
September 14, 2017: Nature Communications
https://www.readbyqxmd.com/read/28911097/structural-accommodation-of-ribonucleotide-incorporation-by-the-dna-repair-enzyme-polymerase-mu
#20
Andrea F Moon, John M Pryor, Dale A Ramsden, Thomas A Kunkel, Katarzyna Bebenek, Lars C Pedersen
While most DNA polymerases discriminate against ribonucleotide triphosphate (rNTP) incorporation very effectively, the Family X member DNA polymerase μ (Pol μ) incorporates rNTPs almost as efficiently as deoxyribonucleotides. To gain insight into how this occurs, here we have used X-ray crystallography to describe the structures of pre- and post-catalytic complexes of Pol μ with a ribonucleotide bound at the active site. These structures reveal that Pol μ binds and incorporates a rNTP with normal active site geometry and no distortion of the DNA substrate or nucleotide...
September 6, 2017: Nucleic Acids Research
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