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Han-Xiao Wang, Shu-Zhen Hu, Qiang Shi, Chuan-Feng Chen
With an expanded electron-rich cavity and a fixed conformation, macrocycle H was found to encapsulate π-extended viologens G1-G4 to form the first case of pseudo[3]rotaxanes based on oxacalixarenes. The complexation was investigated in detail both in solution and in the solid state using NMR spectroscopy and X-ray crystallography. Due to the three-dimensional nonsymmetric structure of H, three orientational isomers of the pseudorotaxanes could be expected theoretically. However, as the crystal structure analysis revealed, only one of the three isomers was obtained with either G1 or G3...
October 20, 2016: Organic & Biomolecular Chemistry
Daniel R Ripoll, Ilja Khavrutskii, Anders Wallqvist, Sidhartha Chaudhury
Cryo-electron-microscopy (cryo-EM) structures of flaviviruses reveal significant variation in epitope occupancy across different monoclonal antibodies that have largely been attributed to epitope-level differences in conformation or accessibility that affect antibody binding. The consequences of these variations for macroscopic properties such as antibody binding and neutralization are the results of the law of mass action-a stochastic process of innumerable binding and unbinding events between antibodies and the multiple binding sites on the flavivirus in equilibrium-that cannot be directly imputed from structure alone...
October 18, 2016: Biophysical Journal
Yang Yu, Igor Petrik, Kelly N Chacón, Parisa Hosseinzadeh, Honghui Chen, Ninian J Blackburn, Yi Lu
Type 1 copper (T1Cu) proteins are electron transfer (ET) proteins involved in many important biological processes. While the effects of changing primary and secondary coordination spheres in the T1Cu ET function have been extensively studied, no report has explored the effect of the overall protein structural perturbation on active site configuration or reduction potential of the protein, even though the protein scaffold has been proposed to play a critical role in enforcing the entatic or "rack-induced" state for ET functions...
October 19, 2016: Protein Science: a Publication of the Protein Society
Young-Ho Yoon, Clive S Barker, Paula V Bulieris, Hideyuki Matsunami, Fadel A Samatey
Across bacteria, the protein that makes the flagellar hook, FlgE, has a high variability in amino acid residue composition and sequence length. We hereby present the structure of two fragments of FlgE protein from Campylobacter jejuni and from Caulobacter crescentus, which were obtained by X-ray crystallography, and a high-resolution model of the hook from Caulobacter. By comparing these new structures of FlgE proteins, we show that bacterial hook can be divided in two distinct parts. The first part comprises domains that are found in all FlgE proteins and that will make the basic structure of the hook that is common to all flagellated bacteria...
October 19, 2016: Scientific Reports
Gargi Mahapatra, Ashwathy Varughese, Qinqin Ji, Icksoo Lee, Jenney Liu, Asmita Vaishnav, Christopher Sinkler, Alexandr A Kapralov, Carlos T Moraes, Thomas H Sanderson, Timothy L Stemmler, Lawrence I Grossman, Valerian E Kagan, Joseph S Brunzelle, Arthur R Salomon, Brian F P Edwards, Maik Hüttemann
Mammalian cytochrome c (Cytc) plays a key role in cellular life and death decisions, functioning as an electron carrier in the electron transport chain (ETC) and as a trigger of apoptosis when released from the mitochondria. However, its regulation is not well understood. We show that the major fraction of Cytc isolated from kidneys is phosphorylated on Thr28, leading to a partial inhibition of respiration in the reaction with cytochrome c oxidase. To further study the effect of Cytc phosphorylation in vitro, we generated Thr28Glu phosphomimetic Cytc, revealing superior behavior regarding protein stability and its ability to degrade reactive oxygen species compared to wild-type unphosphorylated Cytc...
October 7, 2016: Journal of Biological Chemistry
Irina G Tikhonova
Five G protein-coupled receptors (GPCRs) have been identified to be activated by free fatty acids (FFA). Among them, FFA1 (GPR40) and FFA4 (GPR120) bind long-chain fatty acids, FFA2 (GPR43) and FFA3 (GPR41) bind short-chain fatty acids and GPR84 binds medium-chain fatty acids. Free fatty acid receptors have now emerged as potential targets for the treatment of diabetes, obesity and immune diseases. The recent progress in crystallography of GPCRs has now enabled the elucidation of the structure of FFA1 and provided reliable templates for homology modelling of other FFA receptors...
October 19, 2016: Handbook of Experimental Pharmacology
Petra Edlund, Heikki Takala, Elin Claesson, Léocadie Henry, Robert Dods, Heli Lehtivuori, Matthijs Panman, Kanupriya Pande, Thomas White, Takanori Nakane, Oskar Berntsson, Emil Gustavsson, Petra Båth, Vaibhav Modi, Shatabdi Roy-Chowdhury, James Zook, Peter Berntsen, Suraj Pandey, Ishwor Poudyal, Jason Tenboer, Christopher Kupitz, Anton Barty, Petra Fromme, Jake D Koralek, Tomoyuki Tanaka, John Spence, Mengning Liang, Mark S Hunter, Sebastien Boutet, Eriko Nango, Keith Moffat, Gerrit Groenhof, Janne Ihalainen, Emina A Stojković, Marius Schmidt, Sebastian Westenhoff
Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the room temperature crystal structure of the chromophore-binding domains of the Deinococcus radiodurans phytochrome at 2.1 Å resolution. The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser...
October 19, 2016: Scientific Reports
Aleš Hnízda, Jana Škerlová, Milan Fábry, Petr Pachl, Martina Šinalová, Lukáš Vrzal, Petr Man, Petr Novák, Pavlína Řezáčová, Václav Veverka
BACKGROUND: Relapsed acute lymphoblastic leukemia (ALL) is one of the main causes of mortality in childhood malignancies. Previous genetic studies demonstrated that chemoresistant ALL is driven by activating mutations in NT5C2, the gene encoding cytosolic 5´-nucleotidase (cN-II). However, molecular mechanisms underlying this hyperactivation are still unknown. Here, we present kinetic and structural properties of cN-II variants that represent 75 % of mutated alleles in patients who experience relapsed ALL (R367Q, R238W and L375F)...
October 19, 2016: BMC Biology
Gregory J O Beran, Joshua D Hartman, Yonaton N Heit
Molecular crystals occur widely in pharmaceuticals, foods, explosives, organic semiconductors, and many other applications. Thanks to substantial progress in electronic structure modeling of molecular crystals, attention is now shifting from basic crystal structure prediction and lattice energy modeling toward the accurate prediction of experimentally observable properties at finite temperatures and pressures. This Account discusses how fragment-based electronic structure methods can be used to model a variety of experimentally relevant molecular crystal properties...
October 18, 2016: Accounts of Chemical Research
Ewa Kober, Zofia Janas, Julia Jezierska
A series of oxidovanadium(V) complexes [VO(L-κ(4)O,N,N,O)(OR)] (1a, R = Et, L = L(1); 1b, R = Me, L = L(1); 2, R = Me, L = L(2); 3, R = Me, L = L(3)) were synthesized by the σ-bond metathesis reaction between [VO(OR)3] and the linear diaminebis(phenol) derivatives H2L (salans) containing different para-substituents on the phenoxo group [CMe3CH2CMe2, L(1); Me, L(2); Cl, L(3)]. As shown by X-ray crystallography complexes 1a, 1b, and 2 exhibit cis-α geometry, do have a stereogenic vanadium center, and exist as a racemic mixture of the Δ cis-α and Λ cis-α enantiomers...
October 18, 2016: Inorganic Chemistry
Xi Kang, Lin Xiong, Shuxin Wang, Haizhu Yu, Shan Jin, Yongbo Song, Tao Chen, Liwei Zheng, Chensong Pan, Yong Pei, Manzhou Zhu
The shape-controlled synthesis of metal nanoclusters (NCs) with precise atomic arrangement is crucial for tailoring the properties. In this work, we successfully control the shape of alloy NCs by altering the dopants in the alloying processes. The shape of the spherical [Pt1 Ag24 (SPhMe2 )18 ] NC is maintained when [Au(I) SR] is used as dopant. By contrast, the shape of Pt1 Ag24 is changed to be rodlike by alloying with [Au(I) (PPh3 )Br]. The structures of the trimetallic NCs were determined by X-ray crystallography and further confirmed by both DFT and far-IR measurements...
October 18, 2016: Chemistry: a European Journal
Emanuel Hupf, Ralf Kather, Matthias Vogt, Enno Lork, Stefan Mebs, Jens Beckmann
The previously reported bis(6-diphenylphosphinoacenaphth-5-yl)mercury (1) was used as ligand for the preparation of the copper(I) complexes, 1·CuCl and [1·Cu(NCMe)]BF4, which were characterized by multinuclear NMR spectroscopy and X-ray crystallography. DFT calculations employing topological analysis of the electron and electron pair densities within the AIM and ELI-D space-partitioning schemes revealed significant metallophilic Hg···Cu interactions. Evaluation of noncovalent bonding aspects according to the noncovalent interaction (NCI) index was applied not only for the Cu complexes 1·CuCl and [1·Cu(NCMe)]BF4 but also for the previously reported Ag and Au complexes, namely, [1·MCl] (M = Ag, Au) and [1·M(NCMe)n](+) (M = Ag, n = 2; M = Au, n = 0), and facilitated the assignment of attractive dispersive Hg···M interactions with the Hg···Cu contacts being comparable to the Hg···Ag but weaker than the Hg···Au interactions...
October 17, 2016: Inorganic Chemistry
John Lee
The molecular mechanisms of the bioluminescence systems of the firefly, bacteria, and those utilizing imidazopyrazinone luciferins such as coelenterazine, are gradually being uncovered using modern biophysical methods such as dynamic (ns-ps) fluorescence spectroscopy, NMR, X-ray crystallography, and computational chemistry. The chemical structures of all reactants are well defined and the spatial structures of the luciferases are providing important insight into interactions within the active cavity. It is generally accepted that the firefly and coelenterazine systems, although proceeding by different chemistries, both generate a dioxetanone high energy species that undergoes decarboxylation to form directly the product in its S1 state, the bioluminescence emitter...
October 17, 2016: Photochemistry and Photobiology
Jeannine Hess, Malay Patra, Abdul Jabbar, Vanessa Pierroz, Sandro Konatschnig, Bernhard Spingler, Stefano Ferrari, Robin B Gasser, Gilles Gasser
In this study, we present the design, synthesis, characterization and biological evaluation of structurally new ferrocenyl and ruthenocenyl derivatives of the organic anthelmintic monepantel (Zolvix(®)). All seven metallocenyl derivatives prepared (4a/b, 5a/b, 6a/b and 7) were isolated as racemates and characterized by (1)H, (13)C and (19)F NMR spectroscopies, mass spectrometry, IR spectroscopy and elemental microanalysis. The molecular structures of four compounds (4a/b, 6a and 7) were further confirmed by X-ray crystallography...
October 17, 2016: Dalton Transactions: An International Journal of Inorganic Chemistry
Frank Juvenal, Adam Langlois, Antoine Bonnot, Daniel Fortin, Pierre D Harvey
The organometallic synthon trans-[p-MeSC6H4C≡C-Pt(PMe3)2-C≡CC6H4SMe] (L1) reacts with CuX (X = Cl, Br, I) in PrCN and PhCN to form 1D- or 2D-coordination polymers (CP) with a very high degree of variability of features. The copper-halide unit can be either the rhomboids Cu2X2 fragments or the step cubane Cu4I4. The CP's may also incorporate a crystallization solvent molecule or not, which may be coordinated to copper or not. Their characterizations were performed by X-ray crystallography, thermal gravimetric analysis (TGA), and IR, absorption, and emission spectra as well as photophysical measurements in the presence and absence of solvent crystallization molecules...
October 17, 2016: Inorganic Chemistry
S Jamali, S Abedanzadeh, N K Khaledi, H Samouei, Z Hendi, S Zacchini, R Kia, H R Shahsavari
A mixture of the platinum(0) complex [Pt(P(t)Bu3)2] and tetrakis(acetonitrile)copper(i) hexafluorophosphate in acetone activated a water molecule and gave the hydride platinum(ii) complex [PtH(CH3CN)(P(t)Bu3)2]PF6, 1, and the hydroxide Cu(i) species. The crystal structure of complex 1 was determined by X-ray crystallography, indicating a distorted square planar geometry around the platinum center. Although three possible mechanisms are proposed for this transformation, monitoring of the reaction using NMR spectroscopy at low temperature reveals that a cooperative pathway involving formation of a Pt(0)-Cu(I) dative bond complex is the most probable pathway...
October 17, 2016: Dalton Transactions: An International Journal of Inorganic Chemistry
Sylvie Y Doerflinger, Julia Tabatabai, Paul Schnitzler, Carlo Farah, Steffen Rameil, Peter Sander, Anna Koromyslova, Grant S Hansman
Human noroviruses are the dominant cause of outbreaks of acute gastroenteritis. These viruses are usually detected by molecular methods, including reverse transcriptase PCR (RT-PCR) and enzyme-linked immunosorbent assay (ELISA). Human noroviruses are genetically and antigenically diverse, with two main genogroups that are further subdivided into over 40 different genotypes. During the past decade, genogroup 2 genotype 4 (GII.4) has dominated in most countries, but recently, viruses belonging to GII.17 have increased in prevalence in a number of countries...
September 2016: MSphere
Ismael I Loera Fernandez, Samantha L Donaldson, Desmond E Schipper, Sohaila Andleeb, Kenton H Whitmire
Six new anionic bismuth-oxido clusters containing trifluoroacetate ligands were prepared. These include two new Bi6O8 clusters: [M(NCMe)2(H2O)4]3[Bi6(μ3-O)4(μ3-OH)4(CF3CO2)12] with an octahedral Bi6O4(OH)4 core (M = Ni, 1a; Co, 1b) and four Bi4O2 clusters, {[Co(NCMe)6][Bi4(μ3-O)2(CF3CO2)10]}n (2a), {[Co{HC(MeCO)2(MeCNH)}2][Bi4(μ3-O)2(CF3CO2)10]·2[CF3CO2]·2[CF3CO2H]·2[H2O]}n (2b), {[Cu(NCMe)4]2[Bi4(μ3-O)2(CF3CO2)10]·2[CF3CO2H]}n (2c), and {[Me4N]2[Bi4(μ3-O)2(CF3CO2)10]·2[CF3CO2H]}n (2d). These are among the first bismuth-oxido anionic clusters synthesized, and the first to have transition metal countercations...
October 14, 2016: Inorganic Chemistry
Dimuthu C Senevirathna, Victoria L Blair, Melissa V Werrett, Philip C Andrews
Eight novel bismuth(III) sulfonato compounds have been synthesized and characterized using the sonochemical reaction of Bi2O3 with a range of sulfonic acids, including 2,5-dimethylbenzenesulfonic acid (2,5-DMSH), 2,4-dinitrobenzenesulfonic acid (2,4-DNSH), 2,5-dichlorobenzenesulfonic acid (2,5-DCSH), 1,2-benzenedisulfonic acid (1,2-BDSH2), 1,3-benzenedisulfonic acid (1,3-BDSH2), 2-sulfobenzoic acid (2-SBH2), 3-sulfobenzoic acid (3-SBH2), and 2-naphthalenesulfonic acid (NPSH). Six of the complexes (1, 2, 4, and 6-8) were structurally characterized through single-crystal X-ray crystallography...
October 14, 2016: Inorganic Chemistry
Theresia Ahrens, Michael Teltewskoi, Mike Ahrens, Thomas Braun, Reik Laubenstein
The reaction of the silyl complex [Rh{Si(OEt)3}(PEt3)3] (1) with 3,3,3-trifluoropropene afforded the rhodium complex [Rh(CH2CHCF3){Si(OEt)3}(PEt3)2] (2) which features a bonded fluorinated olefin. In contrast the rhodium hydrido complex [Rh(H)(PEt3)3] (3) yielded on treatment with 3,3,3-trifluoropropene in the presence of a base the fluorido complex [Rh(F)(PEt3)3] (4) together with 1,1-difluoro-1-propene by C-F bond activation. At low temperature the intermediate fac-[Rh(H)(CH2CHCF3)(PEt3)3] (5) was detected by NMR spectroscopy...
October 14, 2016: Dalton Transactions: An International Journal of Inorganic Chemistry
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