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Chemical crystallography

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https://www.readbyqxmd.com/read/28346776/proton-exchange-in-a-paramagnetic-chemical-exchange-saturation-transfer-agent-from-experimental-studies-and-ab-initio-metadynamics-simulation
#1
Rodolphe Pollet, Célia S Bonnet, Pascal Retailleau, Philippe Durand, Éva Tóth
The proton-exchange process between water and a carbamate has been studied experimentally and theoretically in a lanthanide-based paramagnetic chemical exchange saturation transfer agent endowed with potential multimodality detection capabilities (optical imaging, or T1 MRI for the Gd(III) analogue). In addition to an in-depth structural analysis by a combined approach (using X-ray crystallography, NMR, and molecular dynamics), our ab initio simulation in aqueous solution sheds light on the reaction mechanism for this proton exchange, which involves structural Grotthuss diffusion...
March 27, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28345709/a-study-of-asymmetrical-mixed-valent-mo2-mo2-complexes-in-the-class-iii-regime
#2
Suman Mallick, Tao Cheng, Lu Chen, Miao Meng, Yu Yu Zhang, Chun Y Liu
Three novel asymmetrical dimolybdenum dimers, [Mo2(DAniF)3]2(μ-OOCCOS) (DAniF = N,N'-di(p-anisyl)formamidinate) ([OO-OS]), [Mo2(DAniF)3]2(μ-S2CCO2) ([SS-OO]), and [Mo2(DAniF)3]2(μ-SSCCOS) ([SS-OS]), have been synthesized and characterized by either single-crystal X-ray crystallography or (1)H NMR spectroscopy. The structural asymmetry for these compounds gives rise to a redox asymmetry, which enlarges the potential separation (ΔE1/2) between the two [Mo2] units. The mixed-valance (MV) species [OO-OS](+), [SS-OO](+) and [SS-OS](+), prepared by one-electron chemical oxidation of the neutral precursors, exhibit an intense and symmetrical intervalence charge transfer (IVCT) absorption band in the near-IR region, along with the high energy metal (δ) to ligand (π*) (ML) and ligand (π) to metal (δ) charge transfer (LMCT) absorptions...
March 27, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28338136/investigation-of-the-complexation-of-nat-zr-iv-and-89-zr-iv-by-hydroxypyridinones-for-the-development-of-chelators-for-pet-imaging-applications
#3
F Guérard, M Beyler, Y-S Lee, R Tripier, J-F Gestin, M W Brechbiel
Three hydroxypyridinone (HOPO) positional isomers - 1,2-HOPO (L1H) and its water soluble analogue (L1'H), 3,2-HOPO (L2H) and 3,4-HOPO (L3H) have been investigated for the complexation of Zr(iv). Potentiometric and UV-Vis spectrometric studies show a higher thermodynamic stability for the formation of Zr(L1')4 in comparison with Zr(L2)4 and Zr(L3)4 as well as a higher kinetic inertness in competition studies with EDTA or Fe(3+) at a radiotracer concentration with (89)Zr. Besides the low pKa of L1H or L1'H (pKa = 5...
March 24, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28319851/-31-p-dephased-13-c-detected-redor-for-nmr-crystallography-at-natural-isotopic-abundance
#4
Alexander I Greenwood, Mary C Clay, Chad M Rienstra
Typically, the process of NMR-based structure determination relies on accurately measuring a large number of internuclear distances to serve as restraints for simulated annealing calculations. In solids, the rotational-echo double-resonance (REDOR) experiment is a widely used approach to determine heteronuclear dipolar couplings corresponding to distances usually in the range of 1.5-8Å. A challenge in the interpretation of REDOR data is the degeneracy of symmetric subunits in an oligomer or equivalent molecules in a crystal lattice, which produce REDOR trajectories that depend explicitly on two or more distances instead of one...
February 28, 2017: Journal of Magnetic Resonance
https://www.readbyqxmd.com/read/28318239/trapping-experiments-on-a-trichlorosilanide-anion-a-key-intermediate-of-halogenosilane-chemistry
#5
Julian Teichmann, Markus Bursch, Benedikt Köstler, Michael Bolte, Hans-Wolfram Lerner, Stefan Grimme, Matthias Wagner
Treatment of Si2Cl6 with [Et4N][BCl4] in CH2Cl2 furnished the known products of a chloride-induced disproportionation reaction of the disilane, such as SiCl4, [Si(SiCl3)3](-), and [Si6Cl12·2Cl](2-). No Si-B-bonded products were detectable. In contrast, the addition of Si2Cl6 to [Et4N][BI3Cl] afforded the Si-B adduct [Et4N][I3SiBI3]. Thus, a quantitative Cl/I exchange at the silicon atom accompanies the trihalogenosilanide formation. [Et4N][I3SiBI3] was also accessible from a mixture of Si2I6, [Et4N]I, and BI3...
March 20, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28277547/backbone-assignment-of-perdeuterated-proteins-by-solid-state-nmr-using-proton-detection-and-ultrafast-magic-angle-spinning
#6
Pascal Fricke, Veniamin Chevelkov, Maximilian Zinke, Karin Giller, Stefan Becker, Adam Lange
Solid-state NMR (ssNMR) is a technique that allows the study of protein structure and dynamics at atomic detail. In contrast to X-ray crystallography and cryo-electron microscopy, proteins can be studied under physiological conditions-for example, in a lipid bilayer and at room temperature (0-35 °C). However, ssNMR requires considerable amounts (milligram quantities) of isotopically labeled samples. In recent years, (1)H-detection of perdeuterated protein samples has been proposed as a method of alleviating the sensitivity issue...
April 2017: Nature Protocols
https://www.readbyqxmd.com/read/28261207/investigating-substitutions-in-antibody-antigen-complexes-using-molecular-dynamics-a-case-study-with-broad-spectrum-influenza-a-antibodies
#7
William D Lees, Lenka Stejskal, David S Moss, Adrian J Shepherd
In studying the binding of host antibodies to the surface antigens of pathogens, the structural and functional characterization of antibody-antigen complexes by X-ray crystallography and binding assay is important. However, the characterization requires experiments that are typically time consuming and expensive: thus, many antibody-antigen complexes are under-characterized. For vaccine development and disease surveillance, it is often vital to assess the impact of amino acid substitutions on antibody binding...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28257017/ab-initio-crystal-structure-prediction-of-magnesium-poly-sulfides-and-calculation-of-their-nmr-parameters
#8
Gregor Mali
Ab initio prediction of sensible crystal structures can be regarded as a crucial task in the quickly-developing methodology of NMR crystallography. In this contribution, an evolutionary algorithm was used for the prediction of magnesium (poly)sulfide crystal structures with various compositions. The employed approach successfully identified all three experimentally detected forms of MgS, i.e. the stable rocksalt form and the metastable wurtzite and zincblende forms. Among magnesium polysulfides with a higher content of sulfur, the most probable structure with the lowest formation energy was found to be MgS2, exhibiting a modified rocksalt structure, in which S(2-) anions were replaced by S2(2-) dianions...
March 1, 2017: Acta Crystallographica. Section C, Structural Chemistry
https://www.readbyqxmd.com/read/28257008/single-crystal-x-ray-diffraction-and-nmr-crystallography-of-a-1-1-cocrystal-of-dithianon-and-pyrimethanil
#9
Ann Christin Pöppler, Emily K Corlett, Harriet Pearce, Mark P Seymour, Matthew Reid, Mark G Montgomery, Steven P Brown
A single-crystal X-ray diffraction structure of a 1:1 cocrystal of two fungicides, namely dithianon (DI) and pyrimethanil (PM), is reported [systematic name: 5,10-dioxo-5H,10H-naphtho[2,3-b][1,4]dithiine-2,3-dicarbonitrile-4,6-dimethyl-N-phenylpyrimidin-2-amine (1/1), C14H4N2O2S2·C12H13N2]. Following an NMR crystallography approach, experimental solid-state magic angle spinning (MAS) NMR spectra are presented together with GIPAW (gauge-including projector augmented wave) calculations of NMR chemical shieldings...
March 1, 2017: Acta Crystallographica. Section C, Structural Chemistry
https://www.readbyqxmd.com/read/28252044/understanding-surface-structure-and-chemistry-of-single-crystal-lanthanum-aluminate
#10
Stevin S Pramana, Andrea Cavallaro, Jiahui Qi, Chris L Nicklin, Mary P Ryan, Stephen J Skinner
The surface crystallography and chemistry of a LaAlO3 single crystal, a material mainly used as a substrate to deposit technologically important thin films (e.g. for superconducting and magnetic devices), was analysed using surface X-ray diffraction and low energy ion scattering spectroscopy. The surface was determined to be terminated by Al-O species, and was significantly different from the idealised bulk structure. Termination reversal was not observed at higher temperature (600 °C) and chamber pressure of 10(-10) Torr, but rather an increased Al-O occupancy occurred, which was accompanied by a larger outwards relaxation of Al from the bulk positions...
March 2, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28250957/the-mechanism-behind-the-selection-of-two-different-cleavage-sites-in-nag-nam-polymers
#11
Marko Mihelič, Kristina Vlahoviček-Kahlina, Miha Renko, Stephane Mesnage, Andreja Doberšek, Ajda Taler-Verčič, Andreja Jakas, Dušan Turk
Peptidoglycan is a giant molecule that forms the cell wall that surrounds bacterial cells. It is composed of alternating N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) residues connected by β-(1,4)-glycosidic bonds and cross-linked with short polypeptide chains. Owing to the increasing antibiotic resistance against drugs targeting peptidoglycan synthesis, studies of enzymes involved in the degradation of peptidoglycan, such as N-acetylglucos-aminidases, may expose new, valuable drug targets. The scientific challenge addressed here is how lysozymes, muramidases which are likely to be the most studied enzymes ever, and bacterial N-acetylglucosaminidases discriminate between two glycosidic bonds that are different in sequence yet chemically equivalent in the same NAG-NAM polymers...
March 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/28250956/the-application-of-tailor-made-force-fields-and-molecular-dynamics-for-nmr-crystallography-a-case-study-of-free-base-cocaine
#12
Xiaozhou Li, Marcus A Neumann, Jacco van de Streek
Motional averaging has been proven to be significant in predicting the chemical shifts in ab initio solid-state NMR calculations, and the applicability of motional averaging with molecular dynamics has been shown to depend on the accuracy of the molecular mechanical force field. The performance of a fully automatically generated tailor-made force field (TMFF) for the dynamic aspects of NMR crystallography is evaluated and compared with existing benchmarks, including static dispersion-corrected density functional theory calculations and the COMPASS force field...
March 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/28250943/fifteen-years-of-the-protein-crystallography-station-the-coming-of-age-of-macromolecular-neutron-crystallography
#13
REVIEW
Julian C-H Chen, Clifford J Unkefer
The Protein Crystallography Station (PCS), located at the Los Alamos Neutron Scattering Center (LANSCE), was the first macromolecular crystallography beamline to be built at a spallation neutron source. Following testing and commissioning, the PCS user program was funded by the Biology and Environmental Research program of the Department of Energy Office of Science (DOE-OBER) for 13 years (2002-2014). The PCS remained the only dedicated macromolecular neutron crystallography station in North America until the construction and commissioning of the MaNDi and IMAGINE instruments at Oak Ridge National Laboratory, which started in 2012...
January 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/28250468/drop-on-demand-sample-delivery-for-studying-biocatalysts-in-action-at-x-ray-free-electron-lasers
#14
Franklin D Fuller, Sheraz Gul, Ruchira Chatterjee, E Sethe Burgie, Iris D Young, Hugo Lebrette, Vivek Srinivas, Aaron S Brewster, Tara Michels-Clark, Jonathan A Clinger, Babak Andi, Mohamed Ibrahim, Ernest Pastor, Casper de Lichtenberg, Rana Hussein, Christopher J Pollock, Miao Zhang, Claudiu A Stan, Thomas Kroll, Thomas Fransson, Clemens Weninger, Markus Kubin, Pierre Aller, Louise Lassalle, Philipp Bräuer, Mitchell D Miller, Muhamed Amin, Sergey Koroidov, Christian G Roessler, Marc Allaire, Raymond G Sierra, Peter T Docker, James M Glownia, Silke Nelson, Jason E Koglin, Diling Zhu, Matthieu Chollet, Sanghoon Song, Henrik Lemke, Mengning Liang, Dimosthenis Sokaras, Roberto Alonso-Mori, Athina Zouni, Johannes Messinger, Uwe Bergmann, Amie K Boal, J Martin Bollinger, Carsten Krebs, Martin Högbom, George N Phillips, Richard D Vierstra, Nicholas K Sauter, Allen M Orville, Jan Kern, Vittal K Yachandra, Junko Yano
X-ray crystallography at X-ray free-electron laser sources is a powerful method for studying macromolecules at biologically relevant temperatures. Moreover, when combined with complementary techniques like X-ray emission spectroscopy, both global structures and chemical properties of metalloenzymes can be obtained concurrently, providing insights into the interplay between the protein structure and dynamics and the chemistry at an active site. The implementation of such a multimodal approach can be compromised by conflicting requirements to optimize each individual method...
February 27, 2017: Nature Methods
https://www.readbyqxmd.com/read/28246390/prl3-phosphatase-active-site-is-required-for-binding-the-putative-magnesium-transporter-cnnm3
#15
Huizhi Zhang, Guennadi Kozlov, Xinlu Li, Howie Wu, Irina Gulerez, Kalle Gehring
The phosphatases of regenerating liver (PRLs) are involved in tumorigenesis and metastatic cancer yet their cellular function remains unclear. Recent reports have shown PRL phosphatases bind tightly to the CNNM family of membrane proteins to regulate magnesium efflux. Here, we characterize the interactions between the CBS-pair (Bateman) domain of CNNM3 and either PRL2 or PRL3 using X-ray crystallography, isothermal titration calorimetry, and activity assays. We report four new crystal structures of PRL proteins bound to the CNNM3 CBS-pair domain that reveal the effects of cysteine disulphide formation and nucleotide binding on complex formation...
December 2017: Scientific Reports
https://www.readbyqxmd.com/read/28236662/monomer-to-dimer-transition-of-brucella-suis-type-iv-secretion-system-component-virb8-induces-conformational-changes
#16
Mahzad Sharifahmadian, Tarun Arya, Benoit Bessette, Lauriane Lecoq, Edward Ruediger, James G Omichinski, Christian Baron
Secretion systems are protein complexes essential for bacterial virulence and potential targets for anti-virulence drugs. In the intracellular pathogen Brucella suis, a type IV secretion system mediates the translocation of virulence factors into host cells and it is essential for pathogenicity. VirB8 is a core component of the secretion system and dimerization is important for functionality of the protein complex. We set out to study dimerization and possible conformational changes of VirB8 from Brucella suis (VirB8s) using nuclear magnetic resonance, X-ray crystallography and differential scanning fluorimetry...
February 25, 2017: FEBS Journal
https://www.readbyqxmd.com/read/28221042/internal-dynamics-of-the-3-pyrroline-n-oxide-ring-in-spin-labeled-proteins
#17
Philipp Consentius, Bernhard Loll, Ulrich Gohlke, Claudia Alings, Carsten Müller, Robert Müller, Christian Teutloff, Udo Heinemann, Martin Kaupp, Markus C Wahl, Thomas Risse
Site-directed spin labeling is a versatile tool to study structure as well as dynamics of proteins using EPR spectroscopy. Methanethiosulfonate (MTS) spin labels tethered through a disulfide linkage to an engineered cysteine residue were used in a large number of studies to extract structural as well as dynamic information on the protein from the rotational dynamics of the nitroxide moiety. The ring itself was always considered to be a rigid body. In this contribution, we present a combination of high-resolution X-ray crystallography and EPR spectroscopy of spin-labeled protein single crystals demonstrating that the nitroxide ring inverts fast at ambient temperature while exhibiting nonplanar conformations at low temperature...
February 23, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28194851/inversion-of-the-side-chain-stereochemistry-of-indvidual-thr-or-ile-residues-in-a-protein-molecule-impact-on-the-folding-stability-and-structure-of-the-shk-toxin
#18
Bobo Dang, Rong Shen, Tomoya Kubota, Kalyaneswar Mandal, Francisco Bezanilla, Benoit Roux, Stephen B H Kent
ShK toxin is a cysteine-rich 35-residue protein ion-channel ligand isolated from the sea anemone Stichodactyla helianthus. In this work, we studied the effect of inverting the side chain stereochemistry of individual Thr or Ile residues on the properties of the ShK protein. Molecular dynamics simulations were used to calculate the free energy cost of inverting the side-chain stereochemistry of individual Thr or Ile residues. Guided by the computational results, we used chemical protein synthesis to prepare three ShK polypeptide chain analogues, each containing either an allo-Thr or an allo-Ile residue...
March 13, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28181439/cryoem-structure-refinement-by-integrating-nmr-chemical-shifts-with-molecular-dynamics-simulations
#19
Juan R Perilla, Gongpu Zhao, Manman Lu, Jiying Ning, Guangjin Hou, In-Ja L Byeon, Angela M Gronenborn, Tatyana Polenova, Peijun Zhang
Single particle cryoEM has emerged as a powerful method for structure determination of proteins and complexes, complementing X-ray crystallography and NMR spectroscopy. Yet, for many systems, the resolution of cryoEM density map has been limited to 4-6 Å, which only allows for resolving bulky amino acids side chains, thus hindering accurate model building from the density map. On the other hand, experimental chemical shifts (CS) from solution and solid state MAS NMR spectra provide atomic level data for each amino acid within a molecule or a complex; however, structure determination of large complexes and assemblies based on NMR data alone remains challenging...
February 9, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28177309/getting-the-chemistry-right-protonation-tautomers-and-the-importance-of-h-atoms-in-biological-chemistry
#20
Ben Bax, Chun Wa Chung, Colin Edge
There are more H atoms than any other type of atom in an X-ray crystal structure of a protein-ligand complex, but as H atoms only have one electron they diffract X-rays weakly and are `hard to see'. The positions of many H atoms can be inferred by our chemical knowledge, and such H atoms can be added with confidence in `riding positions'. For some chemical groups, however, there is more ambiguity over the possible hydrogen placements, for example hydroxyls and groups that can exist in multiple protonation states or tautomeric forms...
February 1, 2017: Acta Crystallographica. Section D, Structural Biology
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