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https://www.readbyqxmd.com/read/28535042/dudawalamides-a-d-antiparasitic-cyclic-depsipeptides-from-the-marine-cyanobacterium-moorea-producens
#1
Jehad Almaliti, Karla L Malloy, Evgenia Glukhov, Carmenza Spadafora, Marcelino Gutiérrez, William H Gerwick
A family of 2,2-dimethyl-3-hydroxy-7-octynoic acid (Dhoya)-containing cyclic depsipeptides, named dudawalamides A-D (1-4), was isolated from a Papua New Guinean field collection of the cyanobacterium Moorea producens using bioassay-guided and spectroscopic approaches. The planar structures of dudawalamides A-D were determined by a combination of 1D and 2D NMR experiments and MS analysis, whereas the absolute configurations were determined by X-ray crystallography, modified Marfey's analysis, chiral-phase GCMS, and chiral-phase HPLC...
May 23, 2017: Journal of Natural Products
https://www.readbyqxmd.com/read/28534525/covalently-linked-dengue-virus-envelope-glycoprotein-dimers-reduce-exposure-of-the-immunodominant-fusion-loop-epitope
#2
Alexander Rouvinski, Wanwisa Dejnirattisai, Pablo Guardado-Calvo, Marie-Christine Vaney, Arvind Sharma, Stéphane Duquerroy, Piyada Supasa, Wiyada Wongwiwat, Ahmed Haouz, Giovanna Barba-Spaeth, Juthathip Mongkolsapaya, Félix A Rey, Gavin R Screaton
A problem in the search for an efficient vaccine against dengue virus is the immunodominance of the fusion loop epitope (FLE), a segment of the envelope protein E that is buried at the interface of the E dimers coating mature viral particles. Anti-FLE antibodies are broadly cross-reactive but poorly neutralizing, displaying a strong infection enhancing potential. FLE exposure takes place via dynamic 'breathing' of E dimers at the virion surface. In contrast, antibodies targeting the E dimer epitope (EDE), readily exposed at the E dimer interface over the region of the conserved fusion loop, are very potent and broadly neutralizing...
May 23, 2017: Nature Communications
https://www.readbyqxmd.com/read/28533266/non-linearity-of-the-collagen-triple-helix-in-solution-and-implications-for-collagen-function
#3
Kenneth T Walker, Ruodan Nan, David W Wright, Jayesh Gor, Anthony C Bishop, George I Makhatadze, Barbara Brodsky, Stephen J Perkins
Collagen adopts a characteristic supercoiled triple helical conformation which requires a repeating (Xaa-Yaa-Gly)n sequence. Despite the abundance of collagen, a combined experimental and atomistic modelling approach has not so far quantitated the degree of flexibility seen experimentally in the solution structures of collagen triple helices. To address this question, we report an experimental study on the flexibility of varying lengths of collagen triple helical peptides, composed of six, eight, ten and twelve repeats of the most stable Pro-Hyp-Gly (POG) units...
May 22, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28532152/attractive-interactions-between-heteroallenes-and-the-cucurbituril-portal
#4
Ofer Reany, Amanda Li, Maayan Yefet, Michael K Gilson, Ehud Keinan
This study reports on the remarkable attractive interaction between organic azides and the portal carbonyls of cucurbiturils. Five homologous bis-α,ω-azidoethylammonium alkanes were prepared, where the number of methylene groups between the ammonium groups ranges from 4 to 8. Their interactions with cucurbit[6]uril were studied by NMR, IR and X-ray crystallography, and by computational methods. Remarkably, while the distance between the portal plane and most atoms at the guest end groups increase progressively with the molecular size, the β-nitrogen atoms maintain a constant distance from the portal plane in all homologs, pointing at a strong attractive interaction between the azide group and the portal...
May 23, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28529775/crystal-structure-and-hirshfeld-surface-analysis-of-the-new-cyclo-diphosphazane-etnp-s-nme2-2
#5
Chokri Issaoui, Hammouda Chebbi, Khaled Alouani, Abderrahmen Guesmi
The cyclic compound 2,4-bis(dimethylamino)-1,3-diethylcyclodiphosphazane-2,4-dithione [systematic name: 2,4-bis(dimethylamino)-1,3-diethyl-1,3,2λ(5),4λ(5)-diazadiphosphetidine-2,4-dithione], C8H22N4P2S2 or [EtNP(S)NMe2]2, is member of a class of mol-ecules that may be used, by virtue of their complexation properties, for the extraction of metals. This compound was characterized in solution by ((1)H and (31)P) NMR, and in the solid state by energy-dispersive X-ray spectroscopy (EDX) and by X-ray crystallography...
May 1, 2017: Acta Crystallographica. Section E, Crystallographic Communications
https://www.readbyqxmd.com/read/28528669/modulation-of-ion-channels-by-cysteine-rich-peptides-from-sequence-to-structure
#6
Mehdi Mobli, Eivind A B Undheim, Lachlan D Rash
Venom peptides are natural ligands of ion channels and have been used extensively in pharmacological characterization of various ion channels and receptors. In this chapter, we survey all known venom peptide ion-channel modulators. Our survey reveals that the majority of venom peptides characterized to date target voltage-gated sodium or potassium channels. We further find that the majority of these peptides are found in scorpion and spider venoms. We discuss the influence of the pharmacological tools available in biasing discovery and the classical "toxin-to-sequence" approach to venom peptide biodiscovery...
2017: Advances in Pharmacology
https://www.readbyqxmd.com/read/28526999/solid-film-sampling-method-for-the-determination-of-protein-secondary-structure-by-fourier-transform-infrared-spectroscopy
#7
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
#8
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
#9
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/28520799/nonenzymatic-glycosylation-of-human-serum-albumin-and-its-effect-on-antibodies-profile-in-patients-with-diabetes-mellitus
#10
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
#11
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
#12
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
#13
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
#14
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/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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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