B21-High Throughput SAXS
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Diamond Proposal Number(s):
[16028]
Open Access
Abstract: Long non-coding RNAs (lncRNAs) constitute a significant fraction of the transcriptome, playing important roles in development and disease. However, our understanding of structure-function relationships for this emerging class of RNAs has been limited to secondary structures. Here, we report the 3-D atomistic structural study of epigenetic lncRNA, Braveheart (Bvht), and its complex with CNBP (Cellular Nucleic acid Binding Protein). Using small angle X-ray scattering (SAXS), we elucidate the ensemble of Bvht RNA conformations in solution, revealing that Bvht lncRNA has a well-defined, albeit flexible 3-D structure that is remodeled upon CNBP binding. Our study suggests that CNBP binding requires multiple domains of Bvht and the RHT/AGIL RNA motif. We show that RHT/AGIL, previously shown to interact with CNBP, contains a highly flexible loop surrounded by more ordered helices. As one of the largest RNA-only 3-D studies, the work lays the foundation for future structural studies of lncRNA-protein complexes.
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Jan 2020
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I03-Macromolecular Crystallography
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Daniel
Del Toro
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Maria A.
Carrasquero-ordaz
,
Amy
Chu
,
Tobias
Ruff
,
Meriam
Shahin
,
Verity A.
Jackson
,
Matthieu
Chavent
,
Miguel
Berbeira-santana
,
Goenuel
Seyit-bremer
,
Sara
Brignani
,
Rainer
Kaufmann
,
Edward
Lowe
,
Rüdiger
Klein
,
Elena
Seiradake
Diamond Proposal Number(s):
[12346, 1838]
Open Access
Abstract: Teneurins are ancient metazoan cell adhesion receptors that control brain development and neuronal wiring in higher animals. The extracellular C terminus binds the adhesion GPCR Latrophilin, forming a trans-cellular complex with synaptogenic functions. However, Teneurins, Latrophilins, and FLRT proteins are also expressed during murine cortical cell migration at earlier developmental stages. Here, we present crystal structures of Teneurin-Latrophilin complexes that reveal how the lectin and olfactomedin domains of Latrophilin bind across a spiraling beta-barrel domain of Teneurin, the YD shell. We couple structure-based protein engineering to biophysical analysis, cell migration assays, and in utero electroporation experiments to probe the importance of the interaction in cortical neuron migration. We show that binding of Latrophilins to Teneurins and FLRTs directs the migration of neurons using a contact repulsion-dependent mechanism. The effect is observed with cell bodies and small neurites rather than their processes. The results exemplify how a structure-encoded synaptogenic protein complex is also used for repulsive cell guidance.
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Jan 2020
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Open Access
Abstract: A computer-aided methodology for the approximate prediction of axially textured polycrystals’ properties is presented. The input data for the developed application consist of: (a) the two-dimensional diffraction pattern of the material under investigation and (b) the tensors of the elasto-piezo-dielectric properties of the single crystal case. Program ANAELU 2.0 allows the determination of the fiber axis inverse pole figure by means of a Rietveld-type procedure. The Material Properties Open Database (MPOD, http://mpod.cimav.edu.mx) provides free access to the experimentally determined values of the tensor properties for several crystal species. Practical estimates of polycrystals’ properties may be obtained by averaging single crystals’ properties tensors, with the orientation distribution function (the symmetry-axis inverse pole figure, in fiber textures) as a weight factor. This treatment, with the application of the Voigt, Reuss and Hill approaches, requires special precautions when it comes to the coupling properties (e.g. piezoelectricity, magnetostriction, magnetoelectricity). Some key physical, mathematical and computational aspects related to the considered topic are discussed. Program GISELLE systematizes the calculation of polycrystal properties under the considered treatments. The application of the proposed methodology to real-world events is illustrated by means of a case study.
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Jan 2020
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I03-Macromolecular Crystallography
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Diamond Proposal Number(s):
[19946]
Open Access
Abstract: Enteroviruses cause a range of human and animal diseases, some life-threatening, but there remain no licenced anti-enterovirus drugs. However, a benzene-sulfonamide derivative and related compounds have been shown recently to block infection of a range of enteroviruses by binding the capsid at a positively-charged surface depression conserved across many enteroviruses. It has also been established that glutathione is essential for the assembly of many enteroviruses, interacting with the capsid proteins to facilitate the formation of the pentameric assembly intermediate, although the mechanism is unknown. Here we show, by high resolution structure analyses of enterovirus F3, that reduced glutathione binds to the same interprotomer pocket as the benzene-sulfonamide derivative. Bound glutathione makes strong interactions with adjacent protomers, thereby explaining the underlying biological role of this druggable binding pocket and delineating the pharmacophore for potential antivirals.
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Jan 2020
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I24-Microfocus Macromolecular Crystallography
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Open Access
Abstract: With the increasing trend of using microcrystals and intense microbeams at synchrotron X-ray beamlines, radiation damage becomes a more pressing problem. Theoretical calculations show that the photoelectrons that primarily cause damage can escape microcrystals. This effect would become more pronounced with decreasing crystal size as well as at higher energies. To prove this effect, data from cryocooled lysozyme crystals of dimensions 5 × 3 × 3 and 20 × 8 × 8 µm mounted on cryo-transmission electron microscopy (cryo-TEM) grids were collected at 13.5 and 20.1 keV using a PILATUS CdTe 2M detector, which has a similar quantum efficiency at both energies. Accurate absorbed doses were calculated through the direct measurement of individual crystal sizes using scanning electron microscopy after the experiment and characterization of the X-ray microbeam. The crystal lifetime was then quantified based on the D1/2 metric. In this first systematic study, a longer crystal lifetime for smaller crystals was observed and crystal lifetime increased at higher X-ray energies, supporting the theoretical predictions of photoelectron escape. The use of detector technologies specifically optimized for data collection at energies above 20 keV allows the theoretically predicted photoelectron escape to be quantified and exploited, guiding future beamline-design choices.
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Jan 2020
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I04-1-Macromolecular Crystallography (fixed wavelength)
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Marcin
Bielecki
,
Svetlana
Antonyuk
,
Richard W.
Strange
,
Klaudia
Siemińska
,
John W.
Smalley
,
Paweł
Mackiewicz
,
Michał
Śmiga
,
Megan
Cowan
,
Michael J.
Capper
,
Paulina
Ślęzak
,
Mariusz
Olczak
,
Teresa
Olczak
Diamond Proposal Number(s):
[15991]
Open Access
Abstract: As part of the infective process, Porphyromonas gingivalis must acquire heme which is indispensable for life and enables the microorganism to survive and multiply at the infection site. This oral pathogenic bacterium uses a newly discovered novel hmu heme uptake system with a leading role played by the HmuY hemophore-like protein, responsible for acquiring heme and increasing virulence of this periodontopathogen. We demonstrated that Prevotella intermedia produces two HmuY homologs, termed PinO and PinA. Both proteins were produced at higher mRNA and protein levels when the bacterium grew under low-iron/heme conditions. PinO and PinA bound heme, but preferentially under reducing conditions, and in a manner different to that of the P. gingivalis HmuY. The analysis of the three-dimensional structures confirmed differences between apo-PinO and apo-HmuY, mainly in the fold forming the heme-binding pocket. Instead of two histidine residues coordinating heme iron in P. gingivalis HmuY, PinO and PinA could use one methionine residue to fulfil this function, with potential support of additional methionine residue/s. The P. intermedia proteins sequestered heme only from the host albumin-heme complex under reducing conditions. Our findings suggest that HmuY-like family might comprise proteins subjected during evolution to significant diversification, resulting in different heme coordination mode. The newer data presented in this manuscript on HmuY homologs produced by P. intermedia sheds more light on the novel mechanism of heme uptake, could be helpful in discovering their biological function, and in developing novel therapeutic approaches.
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Jan 2020
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I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
I04-Macromolecular Crystallography
I24-Microfocus Macromolecular Crystallography
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Abstract: Heterocycles, a class of molecules that includes oxazoles, constitute one of the most common building blocks in current pharmaceuticals and are common in medicinally important natural products. The antitumor natural product nataxazole is a model for a large class of benzoxazole containing molecules that are made by a pathway that is not characterized. We report structural, biochemical and chemical evidence that benzoxazole biosynthesis proceeds through an ester generated by an ATP dependent adenylating enzyme. The ester re‐arranges via a tetrahedral hemiorthoamide to yield an amide which is a shunt product and not, as previously thought, an intermediate in the pathway. A second zinc dependent enzyme catalyses formation of hemiorthoamide from the ester but, by shuttling protons, the enzyme eliminates water, a reverse hydrolysis reaction, to yield the benzoxazole and avoids the amide. These insights have allowed us to harness the pathway to synthesize a series of novel halogenated benzoxazoles.
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Jan 2020
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B18-Core EXAFS
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Diamond Proposal Number(s):
[14239]
Abstract: Increasing dependence on rechargeable batteries for energy storage calls for the improvement of energy density of batteries. Toward this goal, introduction of positive electrode materials with high voltage and/or high capacity is in high demand. The use of oxygen chemistry in lithium and sodium layered oxides has been of interest to achieve high capacity. Nevertheless, a complete understanding of oxygen-based redox processes remains elusive especially in sodium ion batteries. Herein, a novel P3-type Na0.67Ni0.2Mn0.8O2, synthesized at low temperature, exhibits oxygen redox activity in high potentials. Characterization using a range of spectroscopic techniques reveals the anionic redox activity is stabilized by the reduction of Ni, because of the strong Ni 3d–O 2p hybridization states created during charge. This observation suggests that different route of oxygen redox processes occur in P3 structure materials, which can lead to the exploration of oxygen redox chemistry for further development in rechargeable batteries.
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Jan 2020
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Abstract: In recent years a considerable amount of effort has been put into a better understanding of the correlation of structure and electrochemical properties in Li- and Mn-rich NCM layered oxide Li ion battery cathode materials, such as the intensely investigated Li1.2Ni0.15Co0.1Mn0.55O2 composition. A gradual transformation from a trigonal R-3m layered structure towards a cubic Fd-3m spinel structure during electrochemical cycling results in an unwanted decay of the mean charge and discharge voltages, called ‘voltage fade’. This transformation proceeds via an interim phase, which is characterized by the local de-ordering of cations and the introduction of various lattice defects after the formation of the initially well-ordered material. In this study, these structural changes are studied in detail on a long-range atomic scale by synchrotron radiation powder diffraction as well as on a very-local atomic scale by 7Li nuclear magnetic resonance and X-ray absorption spectroscopy. A structural reordering was induced by a mild thermal treatment (150 °C – 300 °C) in lithiated (discharged to 2.0 V) as well as in delithiated (charged to 4.7 V) electrodes, which results either in a partial recovery of the initial well-ordered state or in an intensification of the structural degradation towards a spinel-type cation ordering, respectively. The structural reordering thus obtained was again studied on a long-range and local atomic scale and correlated with the electrochemical properties. In order to complement the experiment an electrochemically highly fatigued electrode (300 cycles, discharged to 2.0 V) showing a pronounced voltage fade was thermally treated, which resulted again in a partial recovery of the initial well-ordered structure and its accompanying electrochemical properties. Finally, the results are summarized in a model explaining the influence of the local cation ordering, lattice defects and the oxygen sublattice on the electrochemical properties, such as the oxygen redox activity and the voltage fade.
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Jan 2020
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Abstract: Metal oxides can act as insulators, semiconductors, or metals depending on their chemical composition and crystal structure. Metal oxide semiconductors, which support equilibrium populations of electron and hole charge carriers, have widespread applications including batteries, solar cells, and display technologies. It is often difficult to predict in advance whether these materials will exhibit localized or delocalized charge carriers upon oxidation or reduction. We combine data from first-principles calculations of the electronic structure and dielectric response of 214 metal oxides to predict the energetic driving force for carrier localization and transport. We assess descriptors based on the carrier effective mass, static polaron binding energy, and Fröhlich electron–phonon coupling. Numerical analysis allows us to assign p- and n-type transport of a metal oxide to three classes: (i) band transport with high mobility; (ii) small polaron transport with low mobility; and (iii) intermediate behavior. The results of this classification agree with observations regarding carrier dynamics and lifetimes and are used to predict 10 candidate p-type oxides.
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Jan 2020
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