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Acta Crystallographica. Section D, Structural Biology

Jill Trewhella
No abstract text is available yet for this article.
January 1, 2019: Acta Crystallographica. Section D, Structural Biology
Jonathan A G Cox, Rebecca C Taylor, Alistair K Brown, Samuel Attoe, Gurdyal S Besra, Klaus Fütterer
The intracellular pathogen Mycobacterium tuberculosis is the causative agent of tuberculosis, which is a leading cause of mortality worldwide. The survival of M. tuberculosis in host macrophages through long-lasting periods of persistence depends, in part, on breaking down host cell lipids as a carbon source. The critical role of fatty-acid catabolism in this organism is underscored by the extensive redundancy of the genes implicated in β-oxidation (∼100 genes). In a previous study, the enzymology of the M...
January 1, 2019: Acta Crystallographica. Section D, Structural Biology
Marie Josée Haglund Halsør, Ulli Rothweiler, Bjørn Altermark, Inger Lin Uttakleiv Raeder
N-Acetylglucosamine 2-epimerases (AGEs) catalyze the interconversion of N-acetylglucosamine and N-acetylmannosamine. They can be used to perform the first step in the synthesis of sialic acid from N-acetylglucosamine, which makes the need for efficient AGEs a priority. This study presents the structure of the AGE from Nostoc sp. KVJ10 collected in northern Norway, referred to as nAGE10. It is the third AGE structure to be published to date, and the first one in space group P42 21 2. The nAGE10 monomer folds as an (α/α)6 barrel in a similar manner to that of the previously published AGEs, but the crystal did not contain the dimers that have previously been reported...
January 1, 2019: Acta Crystallographica. Section D, Structural Biology
Vladimir Y Lunin, Natalia L Lunina, Tatiana E Petrova, Manfred W Baumstark, Alexandre G Urzhumtsev
A new type of mask-selection criterion is suggested for mask-based phasing. In this phasing approach, a large number of connected molecular masks are randomly generated. Structure-factor phases corresponding to a trial mask are accepted as an admissible solution of the phase problem if the mask satisfies some specified selection rules that are key to success. The admissible phase sets are aligned and averaged to give a preliminary solution of the phase problem. The new selection rule is based on the likelihood of the generated mask...
January 1, 2019: Acta Crystallographica. Section D, Structural Biology
Alexandra Males, Gideon J Davies
The enzyme O-GlcNAcase catalyses the removal of the O-GlcNAc co/post-translational modification in multicellular eukaryotes. The enzyme has become of acute interest given the intimate role of O-GlcNAcylation in tau modification and stability; small-molecular inhibitors of human O-GlcNAcase are under clinical assessment for the treatment of tauopathies. Given the importance of structure-based and mechanism-based inhibitor design for O-GlcNAcase, it was sought to test whether different crystal forms of the human enzyme could be achieved by surface mutagenesis...
January 1, 2019: Acta Crystallographica. Section D, Structural Biology
Mi Li, Jaroslav Srp, Alla Gustchina, Zbigniew Dauter, Michael Mares, Alexander Wlodawer
Structures of a recombinant Kunitz-type serine protease inhibitor from Bauhinia bauhinioides (BbKI) complexed with bovine trypsin were determined in two crystal forms. The crystal structure with the L55R mutant of BbKI was determined in space group P64 at 1.94 Å resolution and that with native BbKI in the monoclinic space group P21 at 3.95 Å resolution. The asymmetric unit of the latter crystals contained 44 independent complexes, thus representing one of the largest numbers of independent objects deposited in the Protein Data Bank...
January 1, 2019: Acta Crystallographica. Section D, Structural Biology
A V Chandran, R Srikalaivani, A Paul, M Vijayan
LexA is a protein that is involved in the SOS response. The protein from Mycobacterium tuberculosis and its mutants have been biochemically characterized and the structures of their catalytic segments have been determined. The protein is made up of an N-terminal segment, which includes the DNA-binding domain, and a C-terminal segment encompassing much of the catalytic domain. The two segments are defined by a cleavage site. Full-length LexA, the two segments, two point mutants involving changes in the active-site residues (S160A and K197A) and another mutant involving a change at the cleavage site (G126D) were cloned and purified...
January 1, 2019: Acta Crystallographica. Section D, Structural Biology
Caixia Hou, Oleg V Tsodikov
The experimental phase determination of crystal structures of nucleic acids and nucleic acid-ligand complexes would benefit from a facile method. Even for double-stranded DNA, software-generated models are generally insufficiently accurate to serve as molecular replacement search models, necessitating experimental phasing. Here, it is demonstrated that Zn2+ ions coordinated to the N7 atom of guanine bases generate sufficient anomalous signal for single-wavelength anomalous diffraction (SAD) phasing of DNA crystal structures...
January 1, 2019: Acta Crystallographica. Section D, Structural Biology
Caroline Langley, Octavia Goodwin, John V Dzimianski, Courtney M Daczkowski, Scott D Pegan
Bats have long been observed to be the hosts and the origin of numerous human diseases. Bats, like all mammals, rely on a number of innate immune mechanisms to combat invading pathogens, including the interferon type I, II and III responses. Ubiquitin-like interferon-stimulated gene product 15 (ISG15) is a key modulator of these interferon responses. Within these pathways, ISG15 can serve to stabilize host proteins modulating innate immune responses and act as a cytokine. Post-translational modifications of viral proteins introduced by ISG15 have also been observed to directly affect the function of numerous viral proteins...
January 1, 2019: Acta Crystallographica. Section D, Structural Biology
Nigel W Moriarty, Paul D Adams
Accurate geometric restraints are vital in the automation of macromolecular crystallographic structure refinement. A set of restraints for the Fe4 S4 cubane-type cluster was created using the Cambridge Structural Database (CSD) and high-resolution structures from the Protein Data Bank. Geometries from each source were compared and pairs of refinements were performed to validate these new restraints. In addition to the restraints internal to the cluster, the CSD was mined to generate bond and angle restraints to be applied to the most common linking motif for Fe4 S4 : coordination of the four Fe atoms to the side-chain sulfurs of four cysteine residues...
January 1, 2019: Acta Crystallographica. Section D, Structural Biology
Thi Hong Van Nguyen, Julie Lichière, Bruno Canard, Nicolas Papageorgiou, Sarah Attoumani, François Ferron, Bruno Coutard
Middle East respiratory syndrome coronavirus (MERS-CoV) is a human pathogen responsible for a severe respiratory illness that emerged in 2012. Structural information about the proteins that constitute the viral particle is scarce. In order to contribute to a better understanding of the nucleoprotein (N) in charge of RNA genome encapsidation, the structure of the C-terminal domain of N from MERS-CoV obtained using single-crystal X-ray diffraction is reported here at 1.97 Å resolution. The molecule is present as a dimer in the crystal structure and this oligomerization state is confirmed in solution, as measured by additional methods including small-angle X-ray scattering measurements...
January 1, 2019: Acta Crystallographica. Section D, Structural Biology
Jon Agirre, Olga Moroz, Sebastian Meier, Jesper Brask, Astrid Munch, Tine Hoff, Carsten Andersen, Keith S Wilson, Gideon J Davies
α-Amylases are glycoside hydrolases that break the α-1,4 bonds in starch and related glycans. The degradation of starch is rendered difficult by the presence of varying degrees of α-1,6 branch points and their possible accommodation within the active centre of α-amylase enzymes. Given the myriad industrial uses for starch and thus also for α-amylase-catalysed starch degradation and modification, there is considerable interest in how different α-amylases might accommodate these branches, thus impacting on the potential processing of highly branched post-hydrolysis remnants (known as limit dextrins) and societal applications...
January 1, 2019: Acta Crystallographica. Section D, Structural Biology
Olga B Florek, Luke A Clifton, Marleen Wilde, Thomas Arnold, Rebecca J Green, Richard A Frazier
The creation of effective fungal membrane models for neutron and X-ray reflectometry experiments is a key step in the development of new antifungal pharmaceuticals and agrochemicals to allow in vitro investigation of their mode of interaction with target cells. The structure of the obtained models depends on the properties of the lipids used and the final composition of the leaflets, and can be subject to the spontaneous translocation of phospholipids across the bilayer. The effect of phospholipid acyl-chain unsaturation and the presence of steroids in the membrane on the bilayer asymmetry were examined by means of neutron reflectometry...
December 1, 2018: Acta Crystallographica. Section D, Structural Biology
David P Hoogerheide, Sergei Yu Noskov, Adam J Kuszak, Susan K Buchanan, Tatiana K Rostovtseva, Hirsh Nanda
Neutron reflectivity (NR) has emerged as a powerful technique to study the structure and behavior of membrane proteins at planar lipid interfaces. Integral membrane proteins (IMPs) remain a significant challenge for NR owing to the difficulty of forming complete bilayers with sufficient protein density for scattering techniques. One strategy to achieve high protein density on a solid substrate is the capture of detergent-stabilized, affinity-tagged IMPs on a nitrilotriacetic acid (NTA)-functionalized self-assembled monolayer (SAM), followed by reconstitution into the lipids of interest...
December 1, 2018: Acta Crystallographica. Section D, Structural Biology
Thomas Lykke Møller Sørensen, Samuel John Hjorth-Jensen, Esko Oksanen, Jacob Lauwring Andersen, Claus Olesen, Jesper Vuust Møller, Poul Nissen
Neutron macromolecular crystallography (NMX) has the potential to provide the experimental input to address unresolved aspects of transport mechanisms and protonation in membrane proteins. However, despite this clear scientific motivation, the practical challenges of obtaining crystals that are large enough to make NMX feasible have so far been prohibitive. Here, the potential impact on feasibility of a more powerful neutron source is reviewed and a strategy for obtaining larger crystals is formulated, exemplified by the calcium-transporting ATPase SERCA1...
December 1, 2018: Acta Crystallographica. Section D, Structural Biology
Jose A Gavira, Mayte Conejero-Muriel, José Manuel Delgado-López
The fragility of protein crystals plays an important role in the final quality of the diffraction data and therefore that of the derived three-dimensional structural model. The growth of protein crystals in gels of various natures has been shown to overcome this problem, facilitating the manipulation of the crystals; this is probably owing, amongst other factors, to the incorporation of the gel fibres within the body of the crystal. In this study, lysozyme crystals were grown in silica gel at a wide range of concentrations of up to 22%(v/v) to quantitatively determine the amount of gel incorporated into the crystal structure by means of thermogravimetric analysis...
December 1, 2018: Acta Crystallographica. Section D, Structural Biology
Wanatchaporn Arunmanee, Richard K Heenan, Jeremy H Lakey
Detergent micelles can solubilize membrane proteins, but there is always a need for a pool of free detergent at the critical micellar concentration to maintain the micelle-monomer equilibrium. Amphipol polymeric surfactants (APols) have been developed to replace conventional detergents in membrane-protein studies, but the role of free amphipol is unclear. It has previously been shown that the removal of free APol causes monodisperse outer membrane protein F (OmpF) to form long filaments. However, any remaining APol could not be resolved using electron microscopy...
December 1, 2018: Acta Crystallographica. Section D, Structural Biology
Nicolai Tidemand Johansen, Martin Cramer Pedersen, Lionel Porcar, Anne Martel, Lise Arleth
Small-angle neutron scattering (SANS) is maturing as a method for studying complex biological structures. Owing to the intrinsic ability of the technique to discern between 1 H- and 2 H-labelled particles, it is especially useful for contrast-variation studies of biological systems containing multiple components. SANS is complementary to small-angle X-ray scattering (SAXS), in which similar contrast variation is not easily performed but in which data with superior counting statistics are more easily obtained...
December 1, 2018: Acta Crystallographica. Section D, Structural Biology
Michael Weinrich, David L Worcester
This article reviews recent work in applying neutron and X-ray scattering towards the elucidation of the molecular mechanisms of volatile anesthetics. Experimental results on domain mixing in ternary lipid mixtures, and the influence of volatile anesthetics and hydrostatic pressure are placed in the contexts of ion-channel function and receptor trafficking at the postsynaptic density.
December 1, 2018: Acta Crystallographica. Section D, Structural Biology
Rana Ashkar, Hassina Z Bilheux, Heliosa Bordallo, Robert Briber, David J E Callaway, Xiaolin Cheng, Xiang Qiang Chu, Joseph E Curtis, Mark Dadmun, Paul Fenimore, David Fushman, Frank Gabel, Kushol Gupta, Frederick Herberle, Frank Heinrich, Liang Hong, John Katsaras, Zvi Kelman, Eugenia Kharlampieva, Gerald R Kneller, Andrey Kovalevsky, Susan Krueger, Paul Langan, Raquel Lieberman, Yun Liu, Mathias Losche, Edward Lyman, Yimin Mao, John Marino, Carla Mattos, Flora Meilleur, Peter Moody, Jonathan D Nickels, William B O'Dell, Hugh O'Neill, Ursula Perez-Salas, Judith Peters, Loukas Petridis, Alexei P Sokolov, Christopher Stanley, Norman Wagner, Michael Weinrich, Kevin Weiss, Troy Wymore, Yang Zhang, Jeremy C Smith
The scattering of neutrons can be used to provide information on the structure and dynamics of biological systems on multiple length and time scales. Pursuant to a National Science Foundation-funded workshop in February 2018, recent developments in this field are reviewed here, as well as future prospects that can be expected given recent advances in sources, instrumentation and computational power and methods. Crystallography, solution scattering, dynamics, membranes, labeling and imaging are examined. For the extraction of maximum information, the incorporation of judicious specific deuterium labeling, the integration of several types of experiment, and interpretation using high-performance computer simulation models are often found to be particularly powerful...
December 1, 2018: Acta Crystallographica. Section D, Structural Biology
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