I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[26998, 22717, 28172]
Open Access
Abstract: NSP14 is a dual function enzyme containing an N-terminal exonuclease domain (ExoN) and C-terminal Guanine-N7-methyltransferase (N7-MTase) domain. Both activities are essential for the viral life cycle and may be targeted for anti-viral therapeutics. NSP14 forms a complex with NSP10, and this interaction enhances the nuclease but not the methyltransferase activity. We have determined the structure of SARS-CoV-2 NSP14 in the absence of NSP10 to 1.7 Å resolution. Comparisons with NSP14/NSP10 complexes reveal significant conformational changes that occur within the NSP14 ExoN domain upon binding of NSP10, including helix to coil transitions that facilitate the formation of the ExoN active site and provide an explanation of the stimulation of nuclease activity by NSP10. We have determined the structure of NSP14 in complex with cap analogue 7MeGpppG, and observe conformational changes within a SAM/SAH interacting loop that plays a key role in viral mRNA capping offering new insights into MTase activity. We perform an X-ray fragment screen on NSP14, revealing 72 hits bound to sites of inhibition in the ExoN and MTase domains. These fragments serve as excellent starting point tools for structure guided development of NSP14 inhibitors that may be used to treat COVID-19 and potentially other future viral threats.
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Jan 2023
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Open Access
Abstract: Enzymes with iron-containing active sites play crucial roles in catalysing a myriad of oxidative reactions essential to aerobic life. Defining the three-dimensional structures of iron enzymes in resting, oxy-bound intermediate and substrate-bound states is particularly challenging, not least because of the extreme susceptibility of the Fe(III) and Fe(IV) redox states to radiation-induced chemistry caused by intense X-ray or electron beams. The availability of novel sources such as X-ray free electron lasers has enabled structures that are effectively free of the effects of radiation-induced chemistry and allows time-resolved structures to be determined. Important to both applications is the ability to obtain in crystallo spectroscopic data to identify the redox state of the iron in any particular structure or timepoint.
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Dec 2022
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I15-1-X-ray Pair Distribution Function (XPDF)
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Diamond Proposal Number(s):
[29757]
Open Access
Abstract: Aqueous phase reforming (APR) of waste oxygenates offers the potential for sustainable hydrogen production. However, catalyst stability remains elusive, due to the aggressive hydrothermal conditions employed. Herein, we show that the catalytic performance and stability of Pt supported on LaAlO3 catalysts for glycerol APR is strongly influenced by the phase purity of LaAlO3. Calcination of the support at 700 °C produces the LaAlO3 perovskite phase and an amorphous lanthanum carbonate phase, which can be removed by calcination at higher temperature. Catalysts comprised of phase pure LaAlO3 were notably more active, with a support calcination temperature of 1100 °C resulting in 20.4% glycerol conversion (TOF 686 h−1) in a 2 h batch reaction. Interestingly, all the catalysts, regardless of LaAlO3 phase purity, eventually transform into Pt/LaCO3OH-AlO(OH) during reaction, but only in the presence of evolved carbon dioxide, itself produced from glycerol reforming. Studies using simulated reaction products showed that organic acid products (lactic acid), in the absence of CO2, facilitated La leaching and loss of crystallinity. A carbonate source (CO2) is essential to limit La leaching and form stable Pt/LaCO3OH. Pt supported on LaCO3OH and AlO(OH) are stable and active catalysts during APR reactions. Yet, the rate of perovskite phase decomposition strongly influences the final catalyst performance, with the initially phase impure LaAlO3 decomposing too quickly to facilitate Pt redistribution. LaAlO3 calcined at higher temperatures evolved more slowly and consequently produced more active catalysts.
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Dec 2022
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I03-Macromolecular Crystallography
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Silvia
Gaggero
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Jonathan
Martinez-Fabregas
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Adeline
Cozzani
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Paul K.
Fyfe
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Malo
Leprohon
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Jie
Yang
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F. Emil
Thomasen
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Hauke
Winkelmann
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Romain
Magnez
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Alberto G.
Conti
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Stephan
Wilmes
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Elizabeth
Pohler
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Manuel
Van Gijsel Bonnello
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Xavier
Thuru
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Bruno
Quesnel
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Fabrice
Soncin
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Jacob
Piehler
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Kresten
Lindorff-Larsen
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Rahul
Roychoudhuri
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Ignacio
Moraga
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Suman
Mitra
Abstract: Cytokines interact with their receptors in the extracellular space to control immune responses. How the physicochemical properties of the extracellular space influence cytokine signaling is incompletely elucidated. Here, we show that the activity of interleukin-2 (IL-2), a cytokine critical to T cell immunity, is profoundly affected by pH, limiting IL-2 signaling within the acidic environment of tumors. Generation of lactic acid by tumors limits STAT5 activation, effector differentiation, and antitumor immunity by CD8+ T cells and renders high-dose IL-2 therapy poorly effective. Directed evolution enabled selection of a pH-selective IL-2 mutein (Switch-2). Switch-2 binds the IL-2 receptor subunit IL-2Rα with higher affinity, triggers STAT5 activation, and drives CD8+ T cell effector function more potently at acidic pH than at neutral pH. Consequently, high-dose Switch-2 therapy induces potent immune activation and tumor rejection with reduced on-target toxicity in normal tissues. Last, we show that sensitivity to pH is a generalizable property of a diverse range of cytokines with broad relevance to immunity and immunotherapy in healthy and diseased tissues.
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Dec 2022
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I10-Beamline for Advanced Dichroism
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Peng
Chen
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Qi
Yao
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Junqi
Xu
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Qiang
Sun
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Alexander J.
Grutter
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Patrick
Quarterman
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Purnima P.
Balakrishnan
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Christy J.
Kinane
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Andrew J.
Caruana
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Sean
Langridge
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Ang
Li
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Barat
Achinuq
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Emily
Heppell
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Yuchen
Ji
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Shanshan
Liu
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Baoshan
Cui
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Jiuming
Liu
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Puyang
Huang
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Zhongkai
Liu
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Guoqiang
Yu
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Faxian
Xiu
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Thorsten
Hesjedal
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Jin
Zou
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Xiaodong
Han
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Haijun
Zhang
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Yumeng
Yang
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Xufeng
Kou
Diamond Proposal Number(s):
[30262]
Abstract: The intrinsic magnetic topological insulator MnBi2Te4 (MBT) provides a platform for the creation of exotic quantum phenomena. Novel properties can be created by modification of the MnBi2Te4 framework, but the design of stable magnetic structures remains challenging. Here we report ferromagnet-intercalated MnBi2Te4 superlattices with tunable magnetic exchange interactions. Using molecular beam epitaxy, we intercalate ferromagnetic MnTe layers into MnBi2Te4 to create [(MBT)(MnTe)m]N superlattices and examine their magnetic interaction properties using polarized neutron reflectometry and magnetoresistance measurements. Incorporation of the ferromagnetic spacer tunes the antiferromagnetic interlayer coupling of the MnBi2Te4 layers through the exchange-spring effect at MnBi2Te4/MnTe hetero-interfaces. The MnTe thickness can be used to modulate the relative strengths of the ferromagnetic and antiferromagnetic order, and the superlattice periodicity can tailor the spin configurations of the synthesized multilayers.
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Dec 2022
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I15-1-X-ray Pair Distribution Function (XPDF)
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Diamond Proposal Number(s):
[18995]
Open Access
Abstract: The formation of stacking faults and phase interstratification disorder in layered nickel(II) hydroxides during the chemical precipitation synthesis of materials using nickel(II) nitrate and potassium hydroxide solutions has been investigated in the temperature range of 5 °C to 95 °C and time intervals from 1 hour to 1 week. Stacking faulted materials were identified by broadening of the 00l reflections, while interstratified materials were identified through the splitting of the 001 into two lines. In contrast to the disorder concepts presented in previous studies of these materials, this work has shown through vibrational spectroscopy that both the alpha-phase and beta-phase hydroxides are present in materials described with stacking fault disorder, while layered hydroxysalts were additionally present in the materials considered to be interstratified. Standard mixtures of Ni3(OH)4(NO3)2 and β-Ni(OH)2 were prepared to investigate if the intensity of particular vibrational bands could be correlated with the proportion of the particular phases in mixtures. The intensities of the C2v nitrate infrared and Raman bands at 990 cm−1 and 1315 cm−1 were shown to correlate with the amount of layered hydroxynitrate incorporated in the phase, theoretically providing a method to determine the components in mixed compositions. Since disorder and phase impurities in layered nickel hydroxide materials affect both their electroactive stability and performance as cathode materials, this work has important implications in several research fields.
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Dec 2022
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I14-Hard X-ray Nanoprobe
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Diamond Proposal Number(s):
[28142]
Open Access
Abstract: The interaction of a focused X-ray beam with a sample in a scanning probe experiment can provide a variety of information about the interaction volume. In many scanning probe experiments X-ray fluorescence (XRF) is supplemented with measurements of the transmitted or scattered intensity using a pixelated detector. The automated extraction of different signals from an area pixelated detector is described, in particular the methodology for extracting differential phase contrast (DPC) is demonstrated and different processing methods are compared across a range of samples. The phase shift of the transmitted X-ray beam by the sample, extracted from DPC, is also compared with ptychography measurements to provide a qualitative and quantitative comparison. While ptychography produces a superior image, DPC can offer a simple, flexible method for phase contrast imaging which can provide fast results and feedback during an experiment; furthermore, for many science problems, such as registration of XRF in a lighter matrix, DPC can provide sufficient information to meet the experimental aims. As the DPC technique is a quantitative measurement, it can be expanded to spectroscopic studies and a demonstration of DPC for spectro-microscopy measurements is presented. Where ptychography can separate the absorption and phase shifts by the sample, quantitative interpretation of a DPC image or spectro-microscopy signal can only be performed directly when absorption is negligible or where the absorption contribution is known and the contributions can be fitted.
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Dec 2022
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I13-2-Diamond Manchester Imaging
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Diamond Proposal Number(s):
[16205]
Open Access
Abstract: Methane (CH4) hydrate dissociation and CH4 release are potential geohazards currently investigated using X-ray computed tomography (XCT). Image segmentation is an important data processing step for this type of research. However, it is often time consuming, computing resource-intensive, operator-dependent, and tailored for each XCT dataset due to differences in greyscale contrast. In this paper, an investigation is carried out using U-Nets, a class of Convolutional Neural Network, to segment synchrotron XCT images of CH4-bearing sand during hydrate formation, and extract porosity and CH4 gas saturation. Three U-Net deployments previously untried for this task are assessed: (1) a bespoke 3D hierarchical method, (2) a 2D multi-label, multi-axis method and (3) RootPainter, a 2D U-Net application with interactive corrections. U-Nets are trained using small, targeted hand-annotated datasets to reduce operator time. It was found that the segmentation accuracy of all three methods surpass mainstream watershed and thresholding techniques. Accuracy slightly reduces in low-contrast data, which affects volume fraction measurements, but errors are small compared with gravimetric methods. Moreover, U-Net models trained on low-contrast images can be used to segment higher-contrast datasets, without further training. This demonstrates model portability, which can expedite the segmentation of large datasets over short timespans.
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Dec 2022
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Krios I-Titan Krios I at Diamond
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Open Access
Abstract: Gene transcription is carried out by RNA polymerase (RNAP) and requires the conversion of the initial closed promoter complex, where DNA is double stranded, to a transcription-competent open promoter complex, where DNA is opened up. In bacteria, RNAP relies on σ factors for its promoter specificities. Using a special form of sigma factor (σ54), which forms a stable closed complex and requires its activator that belongs to the AAA+ ATPases (ATPases associated with diverse cellular activities), we obtained cryo–electron microscopy structures of transcription initiation complexes that reveal a previously unidentified process of DNA melting opening. The σ54 amino terminus threads through the locally opened up DNA and then becomes enclosed by the AAA+ hexameric ring in the activator-bound intermediate complex. Our structures suggest how ATP hydrolysis by the AAA+ activator could remove the σ54 inhibition while helping to open up DNA, using σ54 amino-terminal peptide as a pry bar.
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Dec 2022
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B21-High Throughput SAXS
I22-Small angle scattering & Diffraction
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Tamara
Ehm
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Hila
Shinar
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Guy
Jacoby
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Sagi
Meir
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Gil
Koren
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Merav
Segal Asher
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Joanna
Korpanty
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Matthew P.
Thompson
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Nathan C.
Gianneschi
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Michael M.
Kozlov
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Salome
Azoulay-Ginsburg
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Roey J.
Amir
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Joachim O.
Rädler
,
Roy
Beck
Diamond Proposal Number(s):
[21971, 24693, 29428, 28723, 28010]
Open Access
Abstract: Intrinsically disordered peptide amphiphiles (IDPAs) present a novel class of synthetic conjugates that consist of short hydrophilic polypeptides anchored to hydrocarbon chains. These hybrid polymer-lipid block constructs spontaneously self-assemble into dispersed nanoscopic aggregates or ordered mesophases in aqueous solution due to hydrophobic interactions. Yet, the possible sequence variations and their influence on the self-assembly structures are vast and have hardly been explored. Here, we measure the nanoscopic self-assembled structures of four IDPA systems that differ by their amino acid sequence. We show that permutations in the charge pattern along the sequence remarkably alter the headgroup conformation and consequently alter the pH-triggered phase transitions between spherical, cylindrical micelles and hexagonal condensed phases. We demonstrate that even a single amino acid mutation is sufficient to tune structural transitions in the condensed IDPA mesophases, while peptide conformations remain unfolded and disordered. Furthermore, alteration of the peptide sequence can render IDPAs to become susceptible to enzymatic cleavage and induce enzymatically activated phase transitions. These results hold great potential for embedding multiple functionalities into lipid nanoparticle delivery systems by incorporating IDPAs with the desired properties.
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Dec 2022
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