I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[23620]
Open Access
Abstract: The cell cycle checkpoint kinase Mec1ATR and its integral partner Ddc2ATRIP are vital for the DNA damage and replication stress response. Mec1–Ddc2 “senses” single-stranded DNA (ssDNA) by being recruited to the ssDNA binding Replication Protein A (RPA) via Ddc2. In this study, we show that a DNA damage–induced phosphorylation circuit modulates checkpoint recruitment and function. We demonstrate that Ddc2–RPA interactions modulate the association between RPA and ssDNA and that Rfa1-phosphorylation aids in the further recruitment of Mec1–Ddc2. We also uncover an underappreciated role for Ddc2 phosphorylation that enhances its recruitment to RPA-ssDNA that is important for the DNA damage checkpoint in yeast. The crystal structure of a phosphorylated Ddc2 peptide in complex with its RPA interaction domain provides molecular details of how checkpoint recruitment is enhanced, which involves Zn2+. Using electron microscopy and structural modeling approaches, we propose that Mec1–Ddc2 complexes can form higher order assemblies with RPA when Ddc2 is phosphorylated. Together, our results provide insight into Mec1 recruitment and suggest that formation of supramolecular complexes of RPA and Mec1–Ddc2, modulated by phosphorylation, would allow for rapid clustering of damage foci to promote checkpoint signaling.
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Apr 2023
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B21-High Throughput SAXS
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Diamond Proposal Number(s):
[28806, 28287]
Abstract: Bioinspired de novo self-assembling peptides have been widely used for the development of soft biomaterials for a wide variety of biomedical and pharmaceutical applications, such as cell scaffolding for tissue engineering1, controlled and localised drug delivery2, biosensing3, and many others. The meticulous control of peptide-based nanomaterial properties over the length scale, by molecular design, remains the main challenge for tailoring biomaterials properties to meet the application needs. In our group, we have recently adopted a minimalistic molecular engineering approach for the development of Ultrashort Ionic-complementary Constrained Peptides (UICPs), which were rationally designed to self-assemble into amphiphilic β-sheet nanofibers with unique hydrogelation properties and surface activity.4 We have previously demonstrated the crucial role played by aromatic stacking for the formation and thermodynamic stabilisation of UICP β-sheet structures. Herein, we will show how charge interactions can be manipulated for fine tuning molecular self-assembly, morphology and size of nanofibrous structures formation and viscoelasticity of UICP hydrogels.
A library of 18 peptide sequences (4-5 residues long) was developed to study the effect of the sequence net charge, charge density distribution, reversal of charge order and ionic self-complementarity on their propensity towards self-assembly and gelation. Interestingly, 12 of these peptides self-assembled into β-sheet nanofibrous structures forming hydrogels at pH 4.5-5, as confirmed by ATR-FTIR, SEM, TEM, SAXS and oscillatory rheology. Full control over β-sheet content (ranging from ~30-80%), fibre morphology (thin fibrils, thick straight fibre bundles, twisted helical nanofibres, flat nanoribbons and nanotubes) and sizes (~4-67 nm in diameter), as well as gelation (critical gelation concentrations ranging from <7.5 to >100 mM) and viscoelastic properties (storage moduli G’ ~0.1-100 KPa) was achieved by the careful positioning of both Glu and Lys residues at both C- and N-termini, in the sequence core and on both the hydrophilic and hydrophobic faces of the peptide chain. In essence, this design approach enabled/disabled lateral growth along the β-sheet ladder via electrostatic attraction (counter charge, anion-pi and cation-pi)/repulsion, hence controlling fibre thickness, morphology, entanglement, and the resulting viscoelasticity of the system. Our UICPs platform thus provides the flexibility in peptide molecular design for the manufacturing of soft biomaterials with versatile properties that can be in future tailored to the relevant biomedical application.
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Apr 2023
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I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[9306, 12346]
Open Access
Abstract: Structurally complex genomic regions, such as centromeres, are inherently difficult to duplicate. The mechanism behind centromere inheritance is not well understood, and one of the key questions relates to the reassembly of centromeric chromatin following DNA replication. Here, we define ERCC6L2 as a key regulator of this process. ERCC6L2 accumulates at centromeres and promotes deposition of core centromeric factors. Interestingly, ERCC6L2−/− cells show unrestrained replication of centromeric DNA, likely caused by the erosion of centromeric chromatin. Beyond centromeres, ERCC6L2 facilitates replication at genomic repeats and non-canonical DNA structures. Notably, ERCC6L2 interacts with the DNA-clamp PCNA through an atypical peptide, presented here in a co-crystal structure. Finally, ERCC6L2 also restricts DNA end resection, acting independently of the 53BP1-REV7-Shieldin complex. We propose a mechanistic model, which reconciles seemingly distinct functions of ERCC6L2 in DNA repair and DNA replication. These findings provide a molecular context for studies linking ERCC6L2 to human disease.
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Apr 2023
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Open Access
Abstract: Composites of sodium-exchanged zeolite chabazite particles with attached superparamagnetic nanoparticles of Fe3O4 and CoFe2O4 ferrite spinels have been produced using a novel solvothermal route. These have been characterized by a combination of techniques, including powder x-ray diffraction, x-ray fluorescence spectroscopy, vibrating sample magnetometry, and both scanning and transmission electron microscopy. These confirm the nature of the attached nanoparticles, and the microscope images show a good dispersion of nanoparticles with a narrow size range deposited uniformly on the surface of the zeolite particles. The magnetization is of sufficient strength to allow magnetic separation from a solution. Both time and pH dependent Cs uptake experiments show that the magnetized systems are still excellent for the rapid uptake of Cs via an ion exchange process with no reduction in property due to the attached nanoparticles.
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Apr 2023
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B21-High Throughput SAXS
DL-SAXS-Offline SAXS and Sample Environment Development
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Diamond Proposal Number(s):
[27756, 29720]
Open Access
Abstract: Atherosclerosis is often described as a single disease entity; however, the morphology of each plaque is unique to the individual. The field currently lacks a technique that can discriminate stable from unstable plaques, to identify those at risk of a thromboembolic event. Small- and wide-angle X-ray scattering (SAXS/WAXS) holds the potential to be able to identify key materials present in a plaque, such as cholesterol species, collagen, low-density lipoproteins (LDLs), and hydroxyapatite. Protocols have been established for the preparation of excised human atherosclerotic tissue that are investigated herein. This includes the fixing, sectioning, and substrate selection of the sample. Through several sample preparation methods, vast improvements have been made to sample-to-noise ratio and background subtraction.
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Apr 2023
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I13-2-Diamond Manchester Imaging
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Carles
Bosch
,
Joerg
Lindenau
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Alexandra
Pacureanu
,
Christopher J.
Peddie
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Marta
Majkut
,
Andrew C.
Douglas
,
Raffaella
Carzaniga
,
Alexander
Rack
,
Lucy
Collinson
,
Andreas T.
Schaefer
,
Heiko
Stegmann
Diamond Proposal Number(s):
[20274]
Open Access
Abstract: Correlative multimodal imaging is a useful approach to investigate complex structural relations in life sciences across multiple scales. For these experiments, sample preparation workflows that are compatible with multiple imaging techniques must be established. In one such implementation, a fluorescently labeled region of interest in a biological soft tissue sample can be imaged with light microscopy before staining the specimen with heavy metals, enabling follow-up higher resolution structural imaging at the targeted location, bringing context where it is required. Alternatively, or in addition to fluorescence imaging, other microscopy methods, such as synchrotron x-ray computed tomography with propagation-based phase contrast or serial blockface scanning electron microscopy, might also be applied. When combining imaging techniques across scales, it is common that a volumetric region of interest (ROI) needs to be carved from the total sample volume before high resolution imaging with a subsequent technique can be performed. In these situations, the overall success of the correlative workflow depends on the precise targeting of the ROI and the trimming of the sample down to a suitable dimension and geometry for downstream imaging. Here, we showcase the utility of a femtosecond laser (fs laser) device to prepare microscopic samples (1) of an optimized geometry for synchrotron x-ray tomography as well as (2) for volume electron microscopy applications and compatible with correlative multimodal imaging workflows that link both imaging modalities.
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Apr 2023
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I18-Microfocus Spectroscopy
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Ivan N.
Pidchenko
,
John N.
Christensen
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Martin
Kutzschbach
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Konstantin
Ignatyev
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Ignasi
Puigdomenech
,
Eva-Lena
Tullborg
,
Nick M. W.
Roberts
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E. Troy
Rasbury
,
Paul
Northrup
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Ryan
Tappero
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Kristina O.
Kvashnina
,
Thorsten
Schäfer
,
Yohey
Suzuki
,
Henrik
Drake
Diamond Proposal Number(s):
[28254]
Open Access
Abstract: Uptake of uranium (U) by secondary minerals, such as carbonates and iron (Fe)-sulfides, that occur ubiquitously on Earth, may be substantial in deep anoxic environments compared to surficial settings due to different environment-specific conditions. Yet, knowledge of U reductive removal pathways and related fractionation between 238U and 235U isotopes in deep anoxic groundwater systems remain elusive. Here we show bacteria-driven degradation of organic constituents that influences formation of sulfidic species facilitating reduction of geochemically mobile U(VI) with subsequent trapping of U(IV) by calcite and Fe-sulfides. The isotopic signatures recorded for U and Ca in fracture water and calcite samples provide additional insights on U(VI) reduction behaviour and calcite growth rate. The removal efficiency of U from groundwater reaching 75% in borehole sections in fractured granite, and selective U accumulation in secondary minerals in exceedingly U-deficient groundwater shows the potential of these widespread mineralogical sinks for U in deep anoxic environments.
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Apr 2023
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Swagatha
Ghosh
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Doris
Zorić
,
Peter
Dahl
,
Monika
Bjelčić
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Jonatan
Johannesson
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Emil
Sandelin
,
Per
Borjesson
,
Alexander
Bjorling
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Analia
Banacore
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Petra
Edlund
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Oskar
Aurelius
,
Mirko
Milas
,
Jie
Nan
,
Anastasya
Shilova
,
Ana
Gonzalez
,
Uwe
Mueller
,
Gisela
Branden
,
Richard
Neutze
Open Access
Abstract: Serial femtosecond crystallography was initially developed for room-temperature X-ray diffraction studies of macromolecules at X-ray free electron lasers. When combined with tools that initiate biological reactions within microcrystals, time-resolved serial crystallography allows the study of structural changes that occur during an enzyme catalytic reaction. Serial synchrotron X-ray crystallography (SSX), which extends serial crystallography methods to synchrotron radiation sources, is expanding the scientific community using serial diffraction methods. This report presents a simple flow cell that can be used to deliver microcrystals across an X-ray beam during SSX studies. This device consists of an X-ray transparent glass capillary mounted on a goniometer-compatible 3D-printed support and is connected to a syringe pump via lightweight tubing. This flow cell is easily mounted and aligned, and it is disposable so can be rapidly replaced when blocked. This system was demonstrated by collecting SSX data at MAX IV Laboratory from microcrystals of the integral membrane protein cytochrome c oxidase from Thermus thermophilus, from which an X-ray structure was determined to 2.12 Å resolution. This simple SSX platform may help to lower entry barriers for non-expert users of SSX.
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Apr 2023
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Open Access
Abstract: Bacterial chemosensory arrays have served as a model system for in-situ structure determination, clearly cataloguing the improvement of cryo-electron tomography (cryoET) over the past decade. In recent years, this has culminated in an accurately fitted atomistic model for the full-length core signalling unit (CSU) and numerous insights into the function of the transmembrane receptors responsible for signal transduction. Here, we review the achievements of the latest structural advances in bacterial chemosensory arrays and the developments which have made such advances possible.
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Apr 2023
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B16-Test Beamline
DIAD-Dual Imaging and Diffraction Beamline
E01-JEM ARM 200CF
E02-JEM ARM 300CF
I08-Scanning X-ray Microscopy beamline (SXM)
I12-JEEP: Joint Engineering, Environmental and Processing
I13-1-Coherence
I13-2-Diamond Manchester Imaging
I14-Hard X-ray Nanoprobe
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Open Access
Abstract: Hard dental tissues possess a complex hierarchical structure that is particularly evident in enamel, the most mineralised substance in the human body. Its complex and interlinked organisation at the Ångstrom (crystal lattice), nano-, micro-, and macro-scales is the result of evolutionary optimisation for mechanical and functional performance: hardness and stiffness, fracture toughness, thermal, and chemical resistance. Understanding the physical–chemical–structural relationships at each scale requires the application of appropriately sensitive and resolving probes. Synchrotron X-ray techniques offer the possibility to progress significantly beyond the capabilities of conventional laboratory instruments, i.e., X-ray diffractometers, and electron and atomic force microscopes. The last few decades have witnessed the accumulation of results obtained from X-ray scattering (diffraction), spectroscopy (including polarisation analysis), and imaging (including ptychography and tomography). The current article presents a multi-disciplinary review of nearly 40 years of discoveries and advancements, primarily pertaining to the study of enamel and its demineralisation (caries), but also linked to the investigations of other mineralised tissues such as dentine, bone, etc. The modelling approaches informed by these observations are also overviewed. The strategic aim of the present review was to identify and evaluate prospective avenues for analysing dental tissues and developing treatments and prophylaxis for improved dental health.
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Apr 2023
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