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X-ray crystallography

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https://www.readbyqxmd.com/read/28937766/approach-toward-the-understanding-of-coupling-mechanism-for-edc-reagent-in-solvent-free-mechanosynthesis
#1
Aneta Wróblewska, Piotr Paluch, Ewelina Wielgus, Grzegorz Bujacz, Marta K Dudek, Marek J Potrzebowski
A unique approach in mechanosynthesis, joining solid-state NMR spectroscopy, X-ray crystallography, and theoretical calculations, is employed for the first time to study the mechanism of the formation of the C-N amide bond using EDC·HCl as a coupling reagent. It has been proved that EDC·HCl, which in the crystal lattice exists exclusively in the cyclic form (X-ray data), easily undergoes transformation to a pseudocyclic stable intermediate in reaction with carboxylic acid forming a low-melt phase (differential scanning calorimetry, solid-state NMR)...
September 22, 2017: Organic Letters
https://www.readbyqxmd.com/read/28937743/rational-design-of-an-anticalin-type-sugar-binding-protein-using-a-genetically-encoded-boronate-side-chain
#2
Selvakumar Edwardraja, Andreas Eichinger, Ina Theobald, Carina Andrea Sommer, Andreas J Reichert, Arne Skerra
The molecular recognition of carbohydrates plays a fundamental role in many biological processes. However, the development of carbohydrate-binding reagents for biomedical research and use poses a challenge due to the generally poor affinity of proteins towards sugars in aqueous solution. Here, we describe the effective molecular recognition of pyranose monosaccharides (in particular, galactose and mannose) by a rationally designed protein receptor based on the human lipocalin scaffold (Anticalin). Complexation relies on reversible covalent cis-diol boronate diester formation with a genetically encoded L-boronophenylalanine (Bpa) residue which was incorporated as a non-natural amino acid at a sterically permissive position in the binding site of the Anticalin, as confirmed by X-ray crystallography...
September 22, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28937663/a-metallo-dna-nanowire-with-uninterrupted-one-dimensional-silver-array
#3
Jiro Kondo, Yoshinari Tada, Takenori Dairaku, Yoshikazu Hattori, Hisao Saneyoshi, Akira Ono, Yoshiyuki Tanaka
The double-helix structure of DNA, in which complementary strands reversibly hybridize to each other, not only explains how genetic information is stored and replicated, but also has proved very attractive for the development of nanomaterials. The discovery of metal-mediated base pairs has prompted the generation of short metal-DNA hybrid duplexes by a bottom-up approach. Here we describe a metallo-DNA nanowire-whose structure was solved by high-resolution X-ray crystallography-that consists of dodecamer duplexes held together by four different metal-mediated base pairs (the previously observed C-Ag-C, as well as G-Ag-G, G-Ag-C and T-Ag-T) and linked to each other through G overhangs involved in interduplex G-Ag-G...
October 2017: Nature Chemistry
https://www.readbyqxmd.com/read/28936338/photochemically-active-dna-intercalating-ruthenium-and-related-complexes-insights-by-combining-crystallography-and-transient-spectroscopy
#4
Christine J Cardin, John M Kelly, Susan J Quinn
Recent research on the study of the interaction of ruthenium polypyridyl compounds and defined sequence nucleic acids is reviewed. Particular emphasis is paid to complexes [Ru(LL)2(Int)](2+) containing potentially intercalating ligands (Int) such as dipyridophenazine (dppz), which are known to display light-switching or photo-oxidising behaviour, depending on the nature of the ancillary ligands. X-ray crystallography has made a key contribution to our understanding, and the first complete survey of structural results is presented...
July 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28934505/combining-asymmetric-13c-labeling-and-isotopic-filter-edit-noesy-a-novel-strategy-for-rapid-and-logical-rna-resonance-assignment
#5
Regan M LeBlanc, Andrew P Longhini, Stuart F J Le Grice, Bruce A Johnson, Theodore K Dayie
Although ∼98% of the human genomic output is transcribed as non-protein coding RNA, <2% of the protein data bank structures comprise RNA. This huge structural disparity stems from combined difficulties of crystallizing RNA for X-ray crystallography along with extensive chemical shift overlap and broadened linewidths associated with NMR of RNA. While half of the deposited RNA structures in the PDB were solved by NMR methods, the usefulness of NMR is still limited by the high cost of sample preparation and challenges of resonance assignment...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28933304/survey-of-predictors-of-propensity-for-protein-production-and-crystallization-with-application-to-predict-resolution-of-crystal-structures
#6
Jian-Zhao Gao, Zhonghua Wu, Gang Hu, Kui Wang, Jiangning Song, Andrzej Joachimiak, Lukasz Kurgan
Selection of proper targets for the X-ray crystallography will benefit biological research community immensely. Several computational models were proposed to predict propensity of successful protein production and diffraction quality crystallization from protein sequences. We reviewed a comprehensive collection of 22 such predictors that were developed in the last decade. We found that almost all of these models are easily accessible as webservers and/or standalone software and we demonstrated that some of them are widely used by the research community...
September 20, 2017: Current Protein & Peptide Science
https://www.readbyqxmd.com/read/28932839/the-fluorescence-properties-of-tiara-like-structural-thiolated-palladium-clusters
#7
Jishi Chen, Yanze Pan, Zonghua Wang, Peng Zhao
A series of tiara like structural Pdn(SR)2n (5 ≤ n ≤ 20) nanoclusters were synthesized by using a modified Brust-Schiffrin route and isolated via thin layer chromatography, and further measured using MALDI-MS. A new crystal structure of tiara like structural Pd6(SC2H4Ph)12 was determined by single-crystal X-ray crystallography. The atomic distance of PdPd increased and the Pd-S bond length decreased with the increase in the n value in the optimized structure of Pdn(SR)2n (5 ≤ n ≤ 10), which were optimized by density functional theory at the B3LYP level...
September 21, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28932427/polymorphism-in-the-structure-of-n-5-methyl-thia-zol-2-yl-4-oxo-4h-chromene-3-carboxamide
#8
Ligia R Gomes, John Nicolson Low, Fernando Cagide, Fernanda Borges
Chromone derivatives have been extensively studied recently because of to their promising biological activities. The new title chromone-thia-zole hybrid presented here, C14H10N2O3S, is a candidate as a selective ligand for adenosine receptors. The compound has been synthesized and characterized by the usual spectroscopic means (NMR and EM/IE) and its structure elucidated by X-ray crystallography, which revealed the presence of packing polymorphism. The two polymorphs (one with space group P21/n and one with P21/c) show slightly different conformations and the major change induced by crystallization regards the intra-molecular contacts defining the supra-molecular structure...
July 1, 2017: Acta Crystallographica. Section E, Crystallographic Communications
https://www.readbyqxmd.com/read/28931607/direct-observation-of-conformational-population-shifts-in-crystalline-human-hemoglobin
#9
Naoya Shibayama, Mio Ohki, Jeremy Rh Tame, Sam-Yong Park
Although X-ray crystallography is the most commonly used technique for studying the molecular structure of proteins, it is not generally able to monitor the dynamic changes or global domain motions that often underlie allostery. These motions often prevent crystal growth or reduce crystal order. We have recently discovered a crystal form of human hemoglobin that contains three protein molecules allowed to express a full range of quaternary structures, while maintaining strong X-ray diffraction. Here we use this crystal form to investigate the effects of two allosteric effectors, phosphate and bezafibrate, by tracking the structures and functions of the three hemoglobin molecules following the addition of each effector...
September 20, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28929751/structural-biology-inspired-discovery-of-novel-kras-pde%C3%AE-inhibitors
#10
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
#11
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
#12
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
#13
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/28924211/hydrogen-bonds-to-au-atoms-in-coordinated-gold-clusters
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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