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X-ray crystallography

Bethany G Caulkins, Robert P Young, Ryan A Kudla, Chen Yang, Thomas J Bittbauer, Baback Bastin, Eduardo Hilario, Li Fan, Michael J Marsella, Michael F Dunn, Leonard J Mueller
Carbanionic intermediates play a central role in the catalytic transformations of amino acids performed by pyridoxal-5'-phosphate (PLP)-dependent enzymes. Here, we make use of NMR crystallography - the synergistic combination of solid-state nuclear magnetic resonance, X-ray crystallography, and computational chemistry - to interrogate a carbanionic/quinonoid intermediate analogue in the β-subunit active site of the PLP-requiring enzyme tryptophan synthase. The solid-state NMR chemical shifts of the PLP pyridine ring nitrogen and additional sites, coupled with first principles computational models, allow a detailed model of protonation states for ionizable groups on the cofactor, substrates, and nearby catalytic residues to be established...
October 25, 2016: Journal of the American Chemical Society
Biswaranjan Mohanty, Martin L Williams, Bradley C Doak, Mansha Vazirani, Olga Ilyichova, Geqing Wang, Wolfgang Bermel, Jamie S Simpson, David K Chalmers, Glenn F King, Mehdi Mobli, Martin J Scanlon
We describe a general approach to determine the binding pose of small molecules in weakly bound protein-ligand complexes by deriving distance constraints between the ligand and methyl groups from all methyl-containing residues of the protein. We demonstrate that using a single sample, which can be prepared without the use of expensive precursors, it is possible to generate high-resolution data rapidly and obtain the resonance assignments of Ile, Leu, Val, Ala and Thr methyl groups using triple resonance scalar correlation data...
October 24, 2016: Journal of Biomolecular NMR
Tomasz Mroczek, Tomasz Plech, Monika Wujec
Till now, three major spectroscopic techniques, fourier transform infrared (FT-IR), nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography, have been used for determination of thiol-thione tautomeric forms. Therefore, a novel analytical concept of discrimination of 1,2,4-triazole-3-thione and 3-thiol tautomers using two high-resolution mass spectrometers has been proposed. It comprises the high-performance liquid chromatography (HPLC) hyphenated with electrospray ionization (ESI)-time-of-flight mass spectrometry (ESI-TOF-MS, positive ion mode) followed by in-source collision-induced dissociation (CID) and low-energy CID-tandem mass spectrometry (MS/MS) analysis measured with a Quadruple-TOF-MS instrument...
October 24, 2016: Journal of Chromatographic Science
William A Cantara, Erik D Olson, Karin Musier-Forsyth
In addition to their role in correctly attaching specific amino acids to cognate tRNAs, aminoacyl-tRNA synthetases (aaRS) have been found to possess many alternative functions and often bind to and act on other nucleic acids. In contrast to the well-defined 3D structure of tRNA, the structures of many of the other RNAs recognized by aaRSs have not been solved. Despite advances in the use of X-ray crystallography (XRC), nuclear magnetic resonance (NMR) spectroscopy and cryo-electron microscopy (cryo-EM) for structural characterization of biomolecules, significant challenges to solving RNA structures still exist...
October 21, 2016: Methods: a Companion to Methods in Enzymology
Qi Zhang, Zhongduo Wang, Feng Hou, Rachel Harding, Xinyi Huang, Aiping Dong, John R Walker, Yufeng Tong
BACKGROUND: Seven in absentia homologs (SIAHs) comprise a family of highly conserved E3 ubiquitin ligases that play an important role in regulating signalling pathways in tumorigenesis, including the DNA damage repair and hypoxia response pathways. SIAH1 and SIAH2 have been found to function as a tumour repressor and a proto-oncogene, respectively, despite the high sequence identity of their substrate binding domains (SBDs). Ubiquitin-specific protease USP19 is a deubiquitinase that forms a complex with SIAHs and counteracts the ligase function...
October 21, 2016: Biochimica et Biophysica Acta
Yuji Mikata, Risa Ohnishi, Risa Nishijima, Hideo Konno
The tetrakisquinoline ligand HT(6-MeO8Q)HPN (N,N,N',N'-tetrakis(6-methoxy-8-quinolylmethyl)-2-hydroxy-1,3-propanediamine) exhibited Zn(2+)-induced fluorescence enhancement with high specificity and sensitivity (IZn/I0 = 57 and ICd/IZn = 6% in the presence of 2 equiv of Zn(2+); LOD (limit of detection) = 15 nM). This ligand also exhibited fluorescence enhancement specific to inorganic phosphate (PO4(3-)) in DMF-HEPES buffer (50 mM HEPES, 100 mM KCl, pH = 7.5) (1:1) in the presence of 2 equiv of Zn(2+). The structure of the unprecedented tetranuclear zinc complex with a μ4-PO4 bridge was elucidated by X-ray crystallography as the key species responsible for fluorescence enhancement...
October 24, 2016: Inorganic Chemistry
Hong-Xu Na, Pei-Yu Yang, Zheng Yin, Yun-Hong Wang, Li-Xian Chang, Rui Si, Mohamedally Kurmoo, Ming-Hua Zeng
The square-planar monomer NiL2 (Ni1 ), L=2-ethoxy-6-(N-methyl-iminomethyl)phenolate, reacts with M(H2 O)6 (ClO4 )2 , M=Ni or Co, to form heptanuclear disks [Cox Ni7-x (OH)6 (L)6 ](ClO4 )2 ⋅2 CH3 CN (Cox Ni7-x , x=0-7) and the co-crystal [Cox Ni7-x (OH)6 L6 ][NiL2 ](ClO4 )2 ⋅2 CH3 CN (Cox Ni7-x -Ni1 ) under ambient conditions. It has proved possible to explore the bottom-up assembly process of Cox Ni7-x and Cox Ni7-x -Ni1 in real time. The final products have been characterized by thermogravimetric analysis, IR, elemental analysis, ICP-MS, and single-crystal X-ray diffraction...
October 24, 2016: Chemistry: a European Journal
Rebekka Wild, Michael Hothorn
Obtaining well-ordered crystals remains a significant challenge in protein X-ray crystallography. Carrier-driven crystallization can facilitate crystal formation and structure solution of difficult target proteins. We obtained crystals of the small and highly flexible SPX domain from the yeast vacuolar transporter chaperone 4 (Vtc4) when fused to a C-terminal, non-cleavable macro tag derived from human histone macroH2A1.1. Initial crystals diffracted to 3.3 Å resolution. Reductive protein methylation of the fusion protein yielded a new crystal form diffracting to 2...
October 24, 2016: Protein Science: a Publication of the Protein Society
Larisa Kordyukova
Two enveloped virus families, Orthomyxoviridae and Paramyxoviridae, comprise a large number of dangerous pathogens that enter the host cell via fusion of their envelope with a target cell membrane at acidic or neutral pH. The Class I prototypic glycoproteins responsible for this reaction are the Influenza virus haemagglutinin (HA) protein or paramyxovirus fusion (F) protein. X-ray crystallography and cryoelectron microscopy data are available for the HA and F ectodomains in pre- and post-fusion conformations, revealing similar spiky architectures, albeit with clear differences in the details...
October 20, 2016: Virus Research
Mohammad Yaser Masoomi, Ali Morsali, Peter C Junk, Jun Wang
Two new isostructural coordination polymers, [Zn3(Oba)4][Me2NH2)2]·6DMF·3H2O (1) and [Cd3(Oba)4][Me2NH2)2]·2DMF·2H2O (2), were synthesized using the nonlinear dicarboxylate ligand, 4,4'-oxybis(benzoic acid) (H2oba) and characterized by IR spectroscopy and single-crystal X-ray crystallography. Single-crystal X-ray data show that 1 and 2 are two-dimensional coordination polymers that can be extended to three-dimensional supramolecular networks by CH…O interactions. These two new coordination polymers were also sonochemically synthesized while sonication time and power of irradiation influencing size and morphology of nano-structured compounds were also studied...
January 2017: Ultrasonics Sonochemistry
Dimitrios Spiliotopoulos, Amedeo Caflisch
We review the results of fragment-based high-throughput docking to the N-terminal bromodomain of BRD4 and the CREBBP bromodomain. In both docking campaigns the ALTA (anchor-based library tailoring) procedure was used to reduce the size of the initial library by selecting for flexible docking only the molecules that contain a fragment with favorable predicted binding energy. Ranking by a force field-based energy with solvation has resulted in small-molecule hits with low-micromolar affinity and favorable ligand efficiency...
March 2016: Drug Discovery Today. Technologies
Martin Heberle, Stefanie Tschierlei, Nils Rockstroh, Mark Ringenberg, Wolfgang Frey, Henrik Junge, Matthias Beller, Stefan Lochbrunner, Michael Karnahl
A series of heteroleptic copper(I) photosensitizers of the type [(P^P)Cu(N^N)]+ with an extended π-system in the backbone of the diimine ligand have been prepared. The structures of all complexes are completely characterized by NMR spectroscopy, mass spectrometry and X-ray crystallography. These novel photosensitizers were assessed with respect to the photocatalytic reduction of protons in the presence of triethylamine and [Fe3(CO)12]. While the solid state structures and computational results show no significant impact of the π-extension on the structural properties decreased activities were observed...
October 21, 2016: Chemistry: a European Journal
Fang-Fang Shen, Kai Chen, Yun-Qian Zhang, Qian-Jiang Zhu, Zhu Tao, Hang Cong
Mono- and dihydroxylated symmetrical octamethylcucurbit[6]urils {(OH)OMeQ[6] and (OH)2OMeQ[6]} were prepared using a photochemical method to introduce limited alcohol group(s) directly to the parent symmetrical octamethylcucurbit[6]uril (OMeQ[6]), and the resulting compounds were verified by (1)H NMR, Xevo Q-TOF MS, and X-ray crystallography. Further chemical modification of mono- and dihydroxylated OMeQ[6] was also performed.
October 21, 2016: Organic Letters
Shuai Gao, Man Pan, Yong Zheng, Yichao Huang, Qingyun Zheng, Demeng Sun, Lining Lu, Xiaodan Tan, Xianglong Tan, Huan Lan, Jiaxing Wang, Tian Wang, Jiawei Wang, Lei Liu
Racemic or quasi-racemic crystallography recently emerges as a useful technology for solution of the crystal structures of biomacromolecules. It remains unclear to what extent the biomacromolecules of opposite handedness can differ from each other in racemic or quasi-racemic crystallography. Here we report a finding that monomeric d-ubiquitin (Ub) has propensity to cocrystallize with different dimers, trimers, and even a tetramer of l-Ub. In these cocrystals the unconnected monomeric d-Ubs can self-assemble to form pseudomirror images of different oligomers of l-Ub...
October 21, 2016: Journal of the American Chemical Society
Cleve Dionel Mboyi, Carine Maaliki, Amelle Mankou Makaya, Yves Canac, Carine Duhayon, Remi Chauvin
With the view to enhancing the unique coordinating ability of the known phenyl-tetrakis(diisopropylamino)dicyclopropeniophosphine (Ph-DCP), replacement of the phenyl substituent by a tert-butyl substituent was envisaged. Both α-dicationic R-DCP phosphines, with R = Ph and (t)Bu, were prepared in 54%-55% yield by substitution of RPCl2 with two equivalents of bis(diisopropylamino)-dicyclopropenylidene (BAC) and metathesis with NaBF4. This method is implicitly consistent with the representation of R-DCPs as BAC-phosphenium adducts...
October 21, 2016: Inorganic Chemistry
Zhuang Li, Ling Liu, Hong-Mei Sun, Qi Shen, Yong Zhang
A novel family of ionic iron(ii) complexes of the general formula [HL][Fe(PR'3)X3] (HL = 1,3-bis(2,6-diisopropylphenyl)imidazolium cation, HIPr, R' = Ph, X = Cl, 2; HL = HIPr, R' = Cy, X = Cl, 3; HL = HIPr, R' = Ph, X = Br, 4; HL = HIPr, R' = Cy, X = Br, 5; HL = 1,3-bis(2,4,6-trimethylphenyl)imidazolium cation, HIMes, R' = Cy, X = Br, 6) was easily prepared via a stepwise approach in 88%-92% yields. In addition, an ionic iron(ii) complex, [HIPr][Fe(C4H8O)Cl3] (1), has been isolated from the reaction of FeCl2(THF)1...
October 21, 2016: Dalton Transactions: An International Journal of Inorganic Chemistry
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
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
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
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