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Crystallography

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https://www.readbyqxmd.com/read/28437446/solid-state-characterization-and-theoretical-study-of-non-linear-optical-properties-of-a-fluoro-n-acylhydrazide-derivative
#1
Rosemberg F N Rodrigues, Leonardo R Almeida, Florisberto G Dos Santos, Paulo S Carvalho, Wanderson C de Souza, Kleber S Moreira, Gilberto L B de Aquino, Clodoaldo Valverde, Hamilton B Napolitano, Basílio Baseia
In this work we determine the linear and non-linear optical properties of a Fluoro-N-Acylhydrazide derivative (FBHZ), using a combined supermolecule approach and an iterative scheme of electrostatic polarization, where the atoms of neighbouring molecules are represented by point charges. Our results for non-linear optics (NLO) are comparable to those found experimentally, suggesting that FBHZ constitutes an attractive object for future studies and for use as an interesting material for third-order NLO applications...
2017: PloS One
https://www.readbyqxmd.com/read/28436967/microtubule-minus-end-regulation-at-spindle-poles-by-an-aspm-katanin-complex
#2
Kai Jiang, Lenka Rezabkova, Shasha Hua, Qingyang Liu, Guido Capitani, A F Maarten Altelaar, Albert J R Heck, Richard A Kammerer, Michel O Steinmetz, Anna Akhmanova
ASPM (known as Asp in fly and ASPM-1 in worm) is a microcephaly-associated protein family that regulates spindle architecture, but the underlying mechanism is poorly understood. Here, we show that ASPM forms a complex with another protein linked to microcephaly, the microtubule-severing ATPase katanin. ASPM and katanin localize to spindle poles in a mutually dependent manner and regulate spindle flux. X-ray crystallography revealed that the heterodimer formed by the N- and C-terminal domains of the katanin subunits p60 and p80, respectively, binds conserved motifs in ASPM...
April 24, 2017: Nature Cell Biology
https://www.readbyqxmd.com/read/28436701/two-cytotoxic-6-7-seco-spiro-lacton-ent-kauranoids-from-isodon-rubescens
#3
Guo-Yong Luo, Rui Deng, Jing-Jie Zhang, Jiang-Hai Ye, Lu-Tai Pan
The present study was performed to investigate the chemical components of the branches and leaves of Isodon rubescens. Two 6,7-seco-spiro-lacton-ent-kauranoids were obtained. Based on the extensive spectroscopic analyses, their structures were elucidated as 6-epi-11-O-acetylangustifolin (1) and 11-O-acetylangustifolin (2), respectively. The structure of 2 was further comfirmed by X-ray crystallography analysis. MTT method was employed to evaluate their cytotoxity against human lung cancer cell lines A549 and leukemia cell lines K562...
April 24, 2017: Journal of Asian Natural Products Research
https://www.readbyqxmd.com/read/28436492/a-multi-crystal-method-for-extracting-obscured-crystallographic-states-from-conventionally-uninterpretable-electron-density
#4
Nicholas M Pearce, Tobias Krojer, Anthony R Bradley, Patrick Collins, Radosław P Nowak, Romain Talon, Brian D Marsden, Sebastian Kelm, Jiye Shi, Charlotte M Deane, Frank von Delft
In macromolecular crystallography, the rigorous detection of changed states (for example, ligand binding) is difficult unless signal is strong. Ambiguous ('weak' or 'noisy') density is experimentally common, since molecular states are generally only fractionally present in the crystal. Existing methodologies focus on generating maximally accurate maps whereby minor states become discernible; in practice, such map interpretation is disappointingly subjective, time-consuming and methodologically unsound. Here we report the PanDDA method, which automatically reveals clear electron density for the changed state-even from inaccurate maps-by subtracting a proportion of the confounding 'ground state'; changed states are objectively identified from statistical analysis of density distributions...
April 24, 2017: Nature Communications
https://www.readbyqxmd.com/read/28434999/smfret-experiments-of-the-rna-polymerase-ii-transcription-initiation-complex
#5
REVIEW
Nicole Malkusch, Thilo Dörfler, Julia Nagy, Tobias Eilert, Jens Michaelis
Single-molecule fluorescence and in particular single-molecule Förster Resonance Energy Transfer (smFRET(1)) is a powerful tool to provide real-time information on the dynamic architecture of large macromolecular structures such as eukaryotic transcription initiation complexes. In contrast to other structural biology methods, not only structural details, but dynamics transitions are revealed thus closing in on the underlying molecular mechanisms. Here, we describe a comprehensive quantitative biophysical toolbox which can be used for rigorous analysis of dynamic protein-nucleic acid complexes and is applied to the study of eukaryotic transcription initiation...
April 18, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28434915/x-ray-crystallography-and-electron-microscopy-of-cross-and-multi-module-nonribosomal-peptide-synthetase-proteins-reveal-a-flexible-architecture
#6
Michael J Tarry, Asfarul S Haque, Khanh Huy Bui, T Martin Schmeing
Nonribosomal peptide synthetases (NRPS) are macromolecular machines that produce peptides with diverse activities. Structural information exists for domains, didomains, and even modules, but little is known about higher-order organization. We performed a multi-technique study on constructs from the dimodular NRPS DhbF. We determined a crystal structure of a cross-module construct including the adenylation (A) and peptidyl carrier protein (PCP) domains from module 1 and the condensation domain from module 2, complexed with an adenosine-vinylsulfonamide inhibitor and an MbtH-like protein (MLP)...
April 17, 2017: Structure
https://www.readbyqxmd.com/read/28434186/new-thiourea-and-1-3-thiazolidin-4-one-derivatives-effective-on-the-hiv-1-virus
#7
Anna Bielenica, Giuseppina Sanna, Silvia Madeddu, Marta Struga, Michał Jóźwiak, Anna E Kozioł, Aleksandra Sawczenko, Ilona B Materek, Alessandra Serra, Gabriele Giliberti
Thiourea derivatives have been reported to possess many biological activities, among them antiviral and antitumoral properties. As part of our continuing effort to develop new active compounds, we report the synthesis and the evaluation of new fifteen thiourea derivatives with 1,3-benzothiazol-2-yl moiety, among them a group of biologically active (1-7) also underwent cyclisation to 1,3-thiazolidin-4-ones. Molecular structure of four compounds (4, 13, 15 and 3a) was determined by an X-ray crystallography. We here report the evaluation of their cytotoxicity against human leukaemia/lymphoma- and solid tumour-derived cell lines and of their antiviral activity against HIV-1 and representatives of ssRNA and dsDNA viruses...
April 23, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28433015/probing-the-effects-of-surface-hydrophobicity-and-tether-orientation-on-antibody-antigen-binding
#8
Derek B Bush, Thomas A Knotts
Antibody microarrays have the potential to revolutionize molecular detection for many applications, but their current use is limited by poor reliability, and efforts to change this have not yielded fruitful results. One difficulty which limits the rational engineering of next-generation devices is that little is known, at the molecular level, about the antibody-antigen binding process near solid surfaces. Atomic-level structural information is scant because typical experimental techniques (X-ray crystallography and NMR) cannot be used to image proteins bound to surfaces...
April 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28432354/structural-and-functional-analysis-of-lysozyme-after-treatment-with-dielectric-barrier-discharge-plasma-and-atmospheric-pressure-plasma-jet
#9
Sooho Choi, Pankaj Attri, Inhwan Lee, Jeongmin Oh, Ji-Hye Yun, Ji Hoon Park, Eun Ha Choi, Weontae Lee
The variation in the biological function of proteins plays an important role in plasma medicine and sterilization. Several non-thermal plasma sources with different feeding gases are used worldwide for plasma treatment, including dielectric barrier discharge (DBD) and atmospheric-pressure plasma jet (APPJ) as the most commonly used sources. Therefore, in the present work, we used both DBD and APPJ plasma sources with N2 and air as feeding gases to evaluate the effects on the structural, thermodynamic, and activity changes of enzymes...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28432302/a-bacterial-abc-transporter-enables-import-of-mammalian-host-glycosaminoglycans
#10
Sayoko Oiki, Bunzo Mikami, Yukie Maruyama, Kousaku Murata, Wataru Hashimoto
Glycosaminoglycans (GAGs), such as hyaluronan, chondroitin sulfate, and heparin, constitute mammalian extracellular matrices. The uronate and amino sugar residues in hyaluronan and chondroitin sulfate are linked by 1,3-glycoside bond, while heparin contains 1,4-glycoside bond. Some bacteria target GAGs as means of establishing colonization and/or infection, and bacterial degradation mechanisms of GAGs have been well characterized. However, little is known about the bacterial import of GAGs. Here, we show a GAG import system, comprised of a solute-binding protein (Smon0123)-dependent ATP-binding cassette (ABC) transporter, in the pathogenic Streptobacillus moniliformis...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28432121/the-lon-protease-like-domain-in-the-bacterial-reca-paralog-rada-is-required-for-dna-binding-and-repair
#11
Masao Inoue, Kenji Fukui, Yuki Fujii, Noriko Nakagawa, Takato Yano, Seiki Kuramitsu, Ryoji Masui
Homologous recombination (HR) plays an essential role in the maintenance of genome integrity. RecA/Rad51 paralogs have been recognized as an important factor of HR. Among them, only one bacterial RecA/Rad51 paralog - RadA - is involved in HR as an accessory factor of RecA recombinase. RadA has a unique Lon protease-like domain (LonC) at its C-terminus, in addition to a RecA-like ATPase domain. Unlike Lon protease, RadA's LonC domain does not show protease activity but is still essential for RadA-mediated DNA repair...
April 21, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28430420/a-thorium-chalcogenolate-series-generated-by-atom-insertion-into-thorium-carbon-bonds
#12
Nicholas S Settineri, Mary E Garner, John Arnold
A new thorium monoalkyl complex, Th(CH2SiMe3)(L3) (L = MeC(N(i)Pr)2) (2), undergoes insertion of chalcogen atoms resulting in a series of thorium chalcogenolate complexes, Th(ECH2SiMe3)(L3) (E = S, SS, Se, Te; 5-8). Complex 6 represents the first alkyl disulfide thorium species and illustrates the ability of 2 to undergo controllable, stoichiometric atom insertion. All complexes have been characterized by (1)H and (13)C NMR spectroscopy, FTIR, EA, and melting point, and in the case of 1, 2, and 4-8, X-ray crystallography...
April 21, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28429156/crystallization-and-preliminary-x-ray-diffraction-analysis-of-a-mammal-inositol-1-3-4-5-6-pentakisphosphate-2-kinase
#13
Elsa Franco-Echevarría, Julia Sanz-Aparicio, Nathalie Troffer-Charlier, Arnaud Poterszman, Beatriz González
Inositol 1,3,4,5,6-pentakisphosphate 2-kinase (IP5 2-K) is an enzyme that catalyses the formation of phytic acid (IP6) from IP5 and ATP. In mammals, IP6 is involved in multiple events such as DNA repair and mRNA edit and it is the precursor of inositol pyrophosphates, emerging compounds shown to have an essential role in apoptosis. In addition, IP5 2-K have functions in cells independently of its catalytic activity, for example in rRNA biogenesis. We pursue the structure determination of a mammal IP5 2-K by Protein Crystallography...
April 21, 2017: Protein Journal
https://www.readbyqxmd.com/read/28428974/perspective-a-toolbox-for-protein-structure-determination-in-physiological-environment-through-oriented-2d-ordered-site-specific-immobilization
#14
M Altissimo, M Kiskinova, R Mincigrucci, L Vaccari, C Guarnaccia, C Masciovecchio
Revealing the structure of complex biological macromolecules, such as proteins, is an essential step for understanding the chemical mechanisms that determine the diversity of their functions. Synchrotron based X-ray crystallography and cryo-electron microscopy have made major contributions in determining thousands of protein structures even from micro-sized crystals. They suffer from some limitations that have not been overcome, such as radiation damage, the natural inability to crystallize a number of proteins, and experimental conditions for structure determination that are incompatible with the physiological environment...
July 2017: Structural Dynamics (Melville, N.Y.)
https://www.readbyqxmd.com/read/28425294/reactivity-of-a-base-stabilized-germanium-i-dimer-toward-group-9-metal-i-chloride-and-dimanganese-decacarbonyl
#15
Muhammad Luthfi Bin Ismail, Fu-Quan Liu, Wai-Leung Yim, Rakesh Ganguly, Yongxin Li, Cheuk-Wai So
The reactivity of the 2-imino-5,6-methylenedioxylphenylgermanium(I) dimer toward group 9 metal(I) chloride and dimanganese decacarbonyl is described. [LGe:]2 (1, L = 2-imino-5,6-methylenedioxylphenyl) underwent a disproportionation reaction with 1.5 equiv of group 9 metal(I) chloride [MCl(cod)]2 (M = Rh, Ir) in toluene to afford a mixture of the group 9 metallogermylene-chlorometal(I) complexes [LGeμ-{M(cod)}2Cl] (M = Rh (2), Ir (4)) and chlorogermylene-chlorometal(I) complexes [L(Cl)GeM(cod)Cl] (M = Rh (3), Ir (5)), respectively...
April 20, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28423995/harvesting-nutrients-from-source-separated-urine-using-powdered-rice-straw
#16
Shervin Hashemi, Mooyoung Han
As a principle of resource-oriented sanitation practice, urine should be separated from the source and utilized for other purposes such as producing fertilizer. This is because urine is rich in nutrients; therefore, sending it directly to wastewater treatment plants causes problems in the regular treatment process. The addition of solid additives such as powdered rice straw can help with harvesting nutrients from urine. In this study, the procedure and efficiency of using powdered rice straw for nutrient harvesting were investigated by tracking the reductions in ammonia, phosphate, magnesium, and calcium ions, and the harvested nutrients were identified using crystallography methods...
April 20, 2017: Environmental Technology
https://www.readbyqxmd.com/read/28422713/sel120-34a-is-a-novel-cdk8-inhibitor-active-in-aml-cells-with-high-levels-of-serine-phosphorylation-of-stat1-and-stat5-transactivation-domains
#17
Tomasz Rzymski, Michał Mikula, Eliza Żyłkiewicz, Agnieszka Dreas, Katarzyna Wiklik, Aniela Gołas, Katarzyna Wójcik, Magdalena Masiejczyk, Anna Wróbel, Izabela Dolata, Agata Kitlińska, Małgorzata Statkiewicz, Urszula Kuklinska, Krzysztof Goryca, Łukasz Sapała, Aleksandra Grochowska, Aleksandra Cabaj, Małgorzata Szajewska-Skuta, Ewelina Gabor-Worwa, Katarzyna Kucwaj, Arkadiusz Białas, Adam Radzimierski, Michał Combik, Jakub Woyciechowski, Maciej Mikulski, Renata Windak, Jerzy Ostrowski, Krzysztof Brzózka
Inhibition of oncogenic transcriptional programs is a promising therapeutic strategy. A substituted tricyclic benzimidazole, SEL120-34A, is a novel inhibitor of Cyclin-dependent kinase 8 (CDK8), which regulates transcription by associating with the Mediator complex. X-ray crystallography has shown SEL120-34A to be a type I inhibitor forming halogen bonds with the protein's hinge region and hydrophobic complementarities within its front pocket. SEL120-34A inhibits phosphorylation of STAT1 S727 and STAT5 S726 in cancer cells in vitro...
April 4, 2017: Oncotarget
https://www.readbyqxmd.com/read/28421768/synthesis-structure-and-properties-of-tetrabenzo-7-circulene
#18
Xiao Gu, Huiyan Li, Bowen Shan, Zhifeng Liu, Qian Miao
Tetrabenzo[7]circulene, a new member of aromatic saddles, was conveniently synthesized from 2-(1-naphthoyl)benzoic acid with the seven-membered ring constructed at an early stage of the synthesis. This method, upon minor modification, was also useful for synthesis of thiophene-annulated [7]circulenes. The structures of tetrabenzo[7]circulene and [7]circulene were compared in terms of symmetry, flexibility, and curvature on the basis of DFT calculations and X-ray crystallography. It was also found that tetrabenzo[7]circulene functioned as a p-type semiconductor in thin-film transistors and cocrystallized with C60...
April 19, 2017: Organic Letters
https://www.readbyqxmd.com/read/28418624/nickel-cornered-molecular-rectangles-as-polycyclic-aromatic-hydrocarbon-receptors
#19
Víctor Martínez-Agramunt, Sheila Ruiz-Botella, Eduardo Peris
Two nickel-cornered organometallic metalla-rectangles containing a pyrene-linked-di-N-heterocyclic carbene have been prepared. The dimensions of one side of the rectangle were modulated by either using pyrazine or 4,4'-bipyridine. The two molecules were tested as hosts for the recognition of seven small polycyclic aromatic hydrocarbons (PAHs) in [D6 ]acetone. By using (1) H NMR spectroscopy titrations, it could be established that the host-guest stoichiometries of the inclusion complexes formed were 1:1 for the pyrazine-based host, and 1:2 for the host containing bipyridine, in accordance with the larger dimensions of the latter...
April 18, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28418382/structure-of-the-hexagonal-surface-layer-on-caulobacter-crescentus-cells
#20
Tanmay A M Bharat, Danguole Kureisaite-Ciziene, Gail G Hardy, Ellen W Yu, Jessica M Devant, Wim J H Hagen, Yves V Brun, John A G Briggs, Jan Löwe
Many prokaryotic cells are encapsulated by a surface layer (S-layer) consisting of repeating units of S-layer proteins. S-layer proteins are a diverse class of molecules found in Gram-positive and Gram-negative bacteria and most archaea(1-5). S-layers protect cells from the outside, provide mechanical stability and also play roles in pathogenicity. In situ structural information about this highly abundant class of proteins is scarce, so atomic details of how S-layers are arranged on the surface of cells have remained elusive...
April 18, 2017: Nature Microbiology
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