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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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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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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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: 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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I24-Microfocus Macromolecular Crystallography
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Diamond Proposal Number(s):
[22129]
Abstract: Background: The Yellow Fever virus (YFV) is transmitted by mosquitos and causes an infection with symptoms including fever, headaches and nausea. In 20–50% of the cases, the disease may evolve to a visceral stage, reaching high mortality rates. YFV NS2B-NS3 protease has been identified as an important drug target. Methods: Herein, we describe the crystal structure of the NS2B-NS3 protease from the 2017 YFV Brazilian circulating strain using X-ray crystallography. Furthermore, we used a combination of biochemical and biophysical assays to characterize the enzyme and investigate the impact of the polymorphisms observed in different YFV circulating strains. Results: Surprisingly, the crystal structure of YFV protease seems to adopt the closed conformation without the presence of a binding partner. Although D88E and K121R mutants exhibited a lower affinity for the substrate, both revealed to be more processive, resulting in a similar catalytic efficiency in relation to the WT protease. Still, both mutants showed an accentuated decrease in stability when compared with the WT. Conclusions: The crystal structure of YFV NS2B-NS3 in closed conformation might be an important tool for the development of new drugs, as well as understanding the activation mechanism of viral proteases. Biochemical analyses indicate that the NS2B-NS3 protease of the circulating strain of YFV is more stable than previous strains.
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Jan 2020
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I03-Macromolecular Crystallography
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Daniel
Del Toro
,
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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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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I22-Small angle scattering & Diffraction
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Diamond Proposal Number(s):
[20365]
Abstract: Understanding interactions between nanoparticles and model membranes is relevant to functional nano-composites and the fundamentals of nanotoxicity. In this study, the effect of polyamidoamine (PAMAM) dendrimers as model nanoparticles (NP) on the mesophase behaviour of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) has been investigated using high-pressure small-angle X-ray scattering (HP-SAXS). The pressure-temperature (
p−T
) diagrams for POPE mesophases in excess water were obtained in the absence and presence of G2 and G4 polyamidoamine (PAMAM) dendrimers (29 Å and 45 Å in diameter, respectively) at varying NP-lipid number ratio (ν = 0.0002-0.02) over the pressure range p = 1-3000 bar and temperature range T = 20–80°C. The
p−T
phase diagram of POPE exhibited the Lβ, Lα and HII phases. Complete analysis of the phase diagrams, including the relative area pervaded by different phases, phase transition temperatures (Tt) and pressures (pt), the lattice parameters (d-spacing), the pressure-dependence of d-spacing (Δd/Δp), and the structural ordering in the mesophase as gauged by the Scherrer coherence length (L) permitted insights into the size- and concentration-dependent interactions between the dendrimers and the model membrane system. The addition of dendrimers changed the phase transition pressure and temperature and resulted in the emergence of highly swollen lamellar phases, dubbed Lβ-den and Lα-den. G4 PAMAM dendrimers at the highest concentration ν = 0.02 suppressed the formation of the HII phase within the temperature range studied, whereas the addition of G2 PAMAM dendrimers at the same concentration promoted an extended mixed lamellar region in which Lα and Lβ phases coexisted.
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Jan 2020
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I11-High Resolution Powder Diffraction
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Diamond Proposal Number(s):
[19093]
Abstract: With the potential of delivering reversible capacities of up to 300 mAh/g, Li-rich transition metal oxides hold great promise as cathode materials for future Li-ion batteries. However, a cohesive synthesis-structure-electrochemistry relationship is still lacking for these materials, which impedes progress in the field. This work investigates how and why different synthesis routes, specifically solid-state and modified Pechini sol-gel methods, affect the properties of Li2MnO3, a compositionally simple member of this material system. Through a comprehensive investigation of the syn-thesis mechanism along with crystallographic, morphological and electrochemical characterization, the effects of different synthesis routes were found to predominantly influence the degree of stacking faults and particle morphology. That is, the modified Pechini method produced isotropic spherical particles with approx. 57% faulting and the solid state samples possessed heterogeneous morphology with approx. 43% faulting probability. Inevitably, these differences lead to variations in electrochemical performance. This study accentuates the importance of understanding how syn-thesis affects the electrochemistry of these materials, which is critical considering the crystallographic and electrochemical complexities of the class of materials more generally. The methodology employed here is extendable to studying synthesis-property relationships of other compositionally complex Li-rich layered oxide systems.
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Jan 2020
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