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https://www.readbyqxmd.com/read/28526999/solid-film-sampling-method-for-the-determination-of-protein-secondary-structure-by-fourier-transform-infrared-spectroscopy
#1
Junting Zhang, Xiaoning Zhang, Fan Zhang, Shaoning Yu
Fourier transform infrared (FTIR) spectroscopy is one of the widely used vibrational spectroscopic methods in protein structural analysis. The protein solution sample loaded in demountable CaF2 liquid cell presents a challenge and is limited to high concentrations. Some researchers attempted the simpler solid-film sampling method for the collection of protein FTIR spectra. In this study, the solid-film sampling FTIR method was studied in detail. The secondary structure components of some globular proteins were determined by this sampling method, and the results were consistent with those data determined by the traditional solution sampling FTIR method and X-ray crystallography, indicating that this sampling method is feasible and efficient for the structural characterization of proteins...
May 19, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28526839/fluorescence-correlation-spectroscopy-reveals-a-cooperative-unfolding-of-monomeric-amyloid-%C3%AE-42-with-a-low-gibbs-free-energy
#2
Mario Schneider, Stefan Walta, Chris Cadek, Walter Richtering, Dieter Willbold
The amyloid-beta peptide (Aβ) plays a major role in the progression of Alzheimer's disease. Due to its high toxicity, the 42 amino acid long isoform Aβ42 has become of considerable interest. The Aβ42 monomer is prone to aggregation down to the nanomolar range which makes conventional structural methods such as NMR or X-ray crystallography infeasible. Conformational information, however, will be helpful to understand the different aggregation pathways reported in the literature and will allow to identify potential conditions that favour aggregation-incompetent conformations...
May 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28525272/direct-synthesis-of-an-unprecedented-stable-radical-of-nickel-ii-3-5-bis-dimedonyl-azadiisoindomethene-with-strong-and-narrow-near-infrared-absorption-at-%C3%AE-%C3%A2-1000-nm
#3
Elena A Makarova, Yuriy V Zatsikha, Kelly M E Newman, Vinod K Paidi, Valeria A Beletsky, Johan van Lierop, Evgeny A Lukyanets, Victor N Nemykin
An unprecedented stable neutral radical nickel(II) complex of 3,5-bis(dimedonyl)azadiisoindomethene (1) was prepared by the direct reaction between 1,3-diiminoisoindoline and dimedone. A new radical complex 1 has an intense and narrow absorption at 1008 nm and can be reduced to a less stable anionic [1](-) with a typical aza(dibenzo)boron dipyrromethene (aza-BODIPY) UV-vis spectrum. Complex 1, along with two other colored condensation reaction products 2 and 3, was characterized by spectroscopy and X-ray crystallography, while the paramagnetic nature of 1 was probed by EPR and SQUID methods...
May 19, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28522226/electron-crystallography-reveals-that-substrate-release-from-the-pts-iic-glucose-transporter-is-coupled-to-a-subtle-conformational-change
#4
David Kalbermatter, Po-Lin Chiu, Jean-Marc Jeckelmann, Zöhre Ucurum, Thomas Walz, Dimitrios Fotiadis
The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) is a structurally and functionally complex system that mediates sugar uptake in bacteria. Besides several soluble subunits, the glucose-specific PTS includes the integral membrane protein IICB that couples the transmembrane transport of glucose to its phosphorylation. Here, we used electron crystallography of sugar-embedded tubular crystals of the glucose-specific IIC transport domain from Escherichia coli (ecIIC(glc)) to visualize the structure of the transporter in the presence and absence of its substrate...
May 15, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28520799/nonenzymatic-glycosylation-of-human-serum-albumin-and-its-effect-on-antibodies-profile-in-patients-with-diabetes-mellitus
#5
Alok Raghav, Jamal Ahmad, Khursheed Alam
BACKGROUND: Albumin glycation and subsequent formation of advanced glycation end products (AGEs) correlate with diabetes and associated complications. METHODS: Human Serum Albumin (HSA) was modified with D-glucose for a 40 day period under sterile conditions at 37°C. Modified samples along with native HSA (unmodified) were analyzed for structural modifications by UV and fluorescence, FTIR, Liquid chromatography mass spectrometry (LCMS) and X-ray crystallography...
2017: PloS One
https://www.readbyqxmd.com/read/28513917/fragment-screening-against-the-ethr-dna-interaction-by-native-mass-spectrometry
#6
Daniel Shiu-Hin Chan, Vitor Mendes, Sherine E Thomas, Brendan N McConnell, Dijana Matak-Vinković, Anthony G Coyne, Tom L Blundell, Christopher Abell
Native nanoelectrospray ionization mass spectrometry is an underutilized technique for fragment screening. In this study, the first demonstration is provided of the use of native mass spectrometry for screening fragments against a protein-DNA interaction. EthR is a transcriptional repressor of EthA expression in Mycobacterium tuberculosis (Mtb) that reduces the efficacy of ethionamide, a second-line anti-tubercular drug used to combat multidrug resistant Mtb strains. A small-scale fragment screening campaign was conducted against the EthR-DNA interaction using native mass spectrometry, and results were compared with those from differential scanning fluorimetry, a commonly used primary screening technique...
May 17, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28513734/strained-alkynes-derived-from-2-2-dihydroxy-1-1-biaryls-synthesis-and-copper-free-cycloaddition-with-azides
#7
Alessandro Del Grosso, Lavrentis-Dimitrios Galanopoulos, Cookson K C Chiu, Guy J Clarkson, Peter B O Connor, Martin Wills
A series of strained alkynes were prepared from 2,2'-dihydroxy-biaryls. Several were characterised by X-ray crystallography, revealing strained C(sp)-C(sp)-C(sp(3)) bond angles in the range of 163-167°. Their cycloadditions with azides proceed without a catalyst. Functionalised versions of these reagents have potential applications to materials synthesis and bioconjugations.
May 17, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28512574/crystallographic-and-saxs-studies-of-s-adenosyl-l-homocysteine-hydrolase-from-bradyrhizobium-elkanii
#8
Tomasz Manszewski, Kamil Szpotkowski, Mariusz Jaskolski
S-Adenosyl-l-homocysteine hydrolase (SAHase) from the symbiotic bacterium Bradyrhizobium elkanii (BeSAHase) was crystallized in four ligand complexes with (i) mixed adenosine (Ado) and cordycepin (Cord; 3'-deoxyadenosine), (ii) adenine (Ade), (iii) Ado and (iv) mixed 2'-deoxyadenosine (2'-dAdo) and Ade. The crystal structures were solved at resolutions of 1.84, 1.95, 1.95 and 1.54 Å, respectively. Only the Ade complex crystallized with a dimer in the asymmetric unit, while all of the other complexes formed a crystallographically independent tetrameric assembly...
May 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/28512570/the-structure-of-denisovite-a-fibrous-nanocrystalline-polytypic-disordered-very-complex-silicate-studied-by-a-synergistic-multi-disciplinary-approach-employing-methods-of-electron-crystallography-and-x-ray-powder-diffraction
#9
Ira V Rozhdestvenskaya, Enrico Mugnaioli, Marco Schowalter, Martin U Schmidt, Michael Czank, Wulf Depmeier, Andreas Rosenauer
Denisovite is a rare mineral occurring as aggregates of fibres typically 200-500 nm diameter. It was confirmed as a new mineral in 1984, but important facts about its chemical formula, lattice parameters, symmetry and structure have remained incompletely known since then. Recently obtained results from studies using microprobe analysis, X-ray powder diffraction (XRPD), electron crystallography, modelling and Rietveld refinement will be reported. The electron crystallography methods include transmission electron microscopy (TEM), selected-area electron diffraction (SAED), high-angle annular dark-field imaging (HAADF), high-resolution transmission electron microscopy (HRTEM), precession electron diffraction (PED) and electron diffraction tomography (EDT)...
May 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/28512569/unprecedented-phase-transition-sequence-in-the-perovskite-li0-2na0-8nbo3
#10
Charlotte A L Dixon, Jason A McNulty, Steven Huband, Pamela A Thomas, Philip Lightfoot
The perovskite Li0.2Na0.8NbO3 is shown, by powder neutron diffraction, to display a unique sequence of phase transitions at elevated temperature. The ambient temperature polar phase (rhombohedral, space group R3c) transforms via a first-order transition to a polar tetragonal phase (space group P42mc) in the region 150-300°C; these two phases correspond to Glazer tilt systems a(-)a(-)a(-) and a(+)a(+)c(-), respectively. At 500°C a ferroelectric-paraelectric transition takes place from P42mc to P42/nmc, retaining the a(+)a(+)c(-) tilt...
May 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/28510429/copolymerization-of-carbon-dioxide-with-epoxides-catalyzed-by-structurally-well-characterized-dinickel-bis-benzotriazole-iminophenolate-complexes-influence-of-carboxylate-ligands-on-the-catalytic-performance
#11
Li-Shin Huang, Chen-Yen Tsai, Hui-Ju Chuang, Bao-Tsan Ko
A series of structurally well-defined dinickel carboxylate complexes based on the (R)BiIBTP derivatives [(R)BiIBTP = bis(benzotriazole iminophenolate), where R = 3C for the propyl-bridged backbone and 5C for the 2,2-dimethyl-1,3-propyl-bridged backbone] were synthesized and developed for copolymerization of CO2 and epoxides. The one-pot reactions of nickel perchlorate with the (R)BiIBTP-H2 proligands and an appropriate amount of carboxylic acid derivatives (CF3COOH or 4-X-C6H4CO2H; X = H, CF3, OMe) upon the addition of triethylamine in refluxing methanol (MeOH) afforded dinuclear nickel dicarboxylate complexes, which could be formulated as either [((R)BiIBTP)Ni2(O2CCF3)2] (1 and 2) or [((R)BiIBTP)Ni2(O2CC6H4-4-X)2] (3-7)...
May 16, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28510083/software-for-molecular-docking-a-review
#12
REVIEW
Nataraj S Pagadala, Khajamohiddin Syed, Jack Tuszynski
Molecular docking methodology explores the behavior of small molecules in the binding site of a target protein. As more protein structures are determined experimentally using X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy, molecular docking is increasingly used as a tool in drug discovery. Docking against homology-modeled targets also becomes possible for proteins whose structures are not known. With the docking strategies, the druggability of the compounds and their specificity against a particular target can be calculated for further lead optimization processes...
April 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/28510023/protein-rna-interactions-structural-biology-and-computational-modeling-techniques
#13
REVIEW
Susan Jones
RNA-binding proteins are functionally diverse within cells, being involved in RNA-metabolism, translation, DNA damage repair, and gene regulation at both the transcriptional and post-transcriptional levels. Much has been learnt about their interactions with RNAs through structure determination techniques and computational modeling. This review gives an overview of the structural data currently available for protein-RNA complexes, and discusses the technical issues facing structural biologists working to solve their structures...
December 2016: Biophysical Reviews
https://www.readbyqxmd.com/read/28509544/search-for-electron-delocalization-from-fe-cn-6-3-to-the-dication-of-viologen-in-dnp-3-fe-cn-6-2%C3%A2-10h2o
#14
Ahmed S Abouelwafa, Andreas Hauser, Valeriu Mereacre, Yanhua Lan, Gary J Long, Fernande Grandjean, Gernot Buth, Christopher E Anson, Annie K Powell
K3Fe(CN)6 reacts with the viologen 1,1'-bis(2,4-dinitrophenyl)-4,4'-bipyridinium dication, (DNP)(2+), to form a supramolecular complex, (DNP)3[Fe(CN)6]2·10H2O (1). The crystal structure of 1 reveals that there are two [Fe(CN)6](3-) anions within an organic framework of three (DNP)(2+) cations with the shortest Fe(III)···Fe(III) distances of ca. 9.8 Å, distances that minimize extensive long-range magnetic exchange coupling interactions between the [Fe(CN)6](3-) anions, and, thus, 1 is paramagnetic above ca...
May 16, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28509538/bis-thiosemicarbazone-complexes-of-cobalt-iii-synthesis-characterization-and-anticancer-potential
#15
A Paden King, Hendryck A Gellineau, Jung-Eun Ahn, Samantha N MacMillan, Justin J Wilson
Nine bis(thiosemicarbazone) (BTSC) cobalt(III) complexes of the general formula [Co(BTSC)(L)2]NO3 were synthesized, where BTSC = diacetyl bis(thiosemicarbazone) (ATS), pyruvaldehyde bis(thiosemicarbazone) (PTS), or glyoxal bis(thiosemicarbazone) (GTS) and L = ammonia, imidazole (Im), or benzylamine (BnA). These compounds were characterized by multinuclear NMR spectroscopy, mass spectrometry, cyclic voltammetry, and X-ray crystallography. Their stability in phosphate-buffered saline was investigated and found to be highly dependent on the nature of the axial ligand, L...
May 16, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28508075/fast-iodide-sad-phasing-for-high-throughput-membrane-protein-structure-determination
#16
Igor Melnikov, Vitaly Polovinkin, Kirill Kovalev, Ivan Gushchin, Mikhail Shevtsov, Vitaly Shevchenko, Alexey Mishin, Alexey Alekseev, Francisco Rodriguez-Valera, Valentin Borshchevskiy, Vadim Cherezov, Gordon A Leonard, Valentin Gordeliy, Alexander Popov
We describe a fast, easy, and potentially universal method for the de novo solution of the crystal structures of membrane proteins via iodide-single-wavelength anomalous diffraction (I-SAD). The potential universality of the method is based on a common feature of membrane proteins-the availability at the hydrophobic-hydrophilic interface of positively charged amino acid residues with which iodide strongly interacts. We demonstrate the solution using I-SAD of four crystal structures representing different classes of membrane proteins, including a human G protein-coupled receptor (GPCR), and we show that I-SAD can be applied using data collection strategies based on either standard or serial x-ray crystallography techniques...
May 2017: Science Advances
https://www.readbyqxmd.com/read/28507124/thiophene-antibacterials-that-allosterically-stabilize-dna-cleavage-complexes-with-dna-gyrase
#17
Pan F Chan, Thomas Germe, Benjamin D Bax, Jianzhong Huang, Reema K Thalji, Eric Bacqué, Anna Checchia, Dongzhao Chen, Haifeng Cui, Xiao Ding, Karen Ingraham, Lynn McCloskey, Kaushik Raha, Velupillai Srikannathasan, Anthony Maxwell, Robert A Stavenger
A paucity of novel acting antibacterials is in development to treat the rising threat of antimicrobial resistance, particularly in Gram-negative hospital pathogens, which has led to renewed efforts in antibiotic drug discovery. Fluoroquinolones are broad-spectrum antibacterials that target DNA gyrase by stabilizing DNA-cleavage complexes, but their clinical utility has been compromised by resistance. We have identified a class of antibacterial thiophenes that target DNA gyrase with a unique mechanism of action and have activity against a range of bacterial pathogens, including strains resistant to fluoroquinolones...
May 15, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28507038/high-affinity-pan-specific-monoclonal-antibodies-that-target-cysteinyl-leukotrienes-and-show-efficacy-in-an-acute-model-of-colitis
#18
Ashlee N King, Jonathan K Fleming, Stephanie S Knapik, Barbara Visentin, Jonathan M Wojciak, Tom Huxford
Cysteinyl leukotrienes (CysLTs) are a small family of biological signaling lipids produced by active leukocytes that contribute to diverse inflammatory disease states as a consequence of their engagement with dedicated G protein-coupled receptors. Immunization of mice with a CysLT-modified hapten carrier protein yielded novel monoclonal antibodies that display variable binding affinity to CysLTs. Solution binding assays indicated differing specificities among the antibodies tested, with antibody 10G4 displaying a preference for leukotriene C4 (LTC4)...
May 15, 2017: Journal of Lipid Research
https://www.readbyqxmd.com/read/28506657/understanding-pre-mrna-splicing-through-crystallography
#19
REVIEW
Sara Espinosa, Lingdi Zhang, Xueni Li, Rui Zhao
Crystallography is a powerful tool to determine the atomic structures of proteins and RNAs. X-ray crystallography has been used to determine the structure of many splicing related proteins and RNAs, making major contributions to our understanding of the molecular mechanism and regulation of pre-mRNA splicing. Compared to other structural methods, crystallography has its own advantage in the high-resolution structural information it can provide and the unique biological questions it can answer. In addition, two new crystallographic methods - the serial femtosecond crystallography and 3D electron crystallography - were developed to overcome some of the limitations of traditional X-ray crystallography and broaden the range of biological problems that crystallography can solve...
May 12, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28506635/cryoem-structure-of-an-influenza-virus-receptor-binding-site-antibody-antigen-interface
#20
Yuhang Liu, Junhua Pan, Simon Jenni, Donald D Raymond, Tim Caradonna, Khoi T Do, Aaron G Schmidt, Stephen C Harrison, Nikolaus Grigorieff
Structure-based vaccine design depends on extensive structural analyses of antigen-antibody complexes. Single-particle electron cryomicroscopy (cryoEM) can circumvent some of the problems of x-ray crystallography as a pipeline for obtaining the required structures. We have examined the potential of single-particle cryoEM for determining the structure of influenza-virus hemagglutinin (HA):single-chain Fv (scFv) complexes, by studying a complex we failed to crystallize in pursuing an extended project of the human immune response to influenza vaccines...
May 12, 2017: Journal of Molecular Biology
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