I15-1-X-ray Pair Distribution Function (XPDF)
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Steffen
Schlicher
,
Nils
Prinz
,
Julius
Bürger
,
Andreas
Omlor
,
Christian
Singer
,
Mirijam
Zobel
,
Roland
Schoch
,
Jörg K. N.
Lindner
,
Volker
Schünemann
,
Sven
Kureti
,
Matthias
Bauer
Diamond Proposal Number(s):
[20578]
Open Access
Abstract: The replacement of noble metal catalysts by abundant iron as an active compound in CO oxidation is of ecologic and economic interest. However, improvement of their catalytic performance to the same level as state-of-the-art noble metal catalysts requires an in depth understanding of their working principle on an atomic level. As a contribution to this aim, a series of iron oxide catalysts with varying Fe loadings from 1 to 20 wt% immobilized on a γ-Al2O3 support is presented here, and a multidimensional structure–activity correlation is established. The CO oxidation activity is correlated to structural details obtained by various spectroscopic, diffraction, and microscopic methods, such as PXRD, PDF analysis, DRUVS, Mössbauer spectroscopy, STEM-EDX, and XAS. Low Fe loadings lead to less agglomerated but high percentual amounts of isolated, tetrahedrally coordinated iron oxide species, while the absolute amount of isolated species reaches its maximum at high Fe loadings. Consequently, the highest CO oxidation activity in terms of turnover frequencies can be correlated to small, finely dispersed iron oxide species with a large amount of tetrahedrally oxygen coordinated iron sites, while the overall amount of isolated iron oxide species correlates with a lower light-off temperature.
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Jun 2022
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I08-Scanning X-ray Microscopy beamline (SXM)
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Diamond Proposal Number(s):
[23540]
Open Access
Abstract: Mineral-associated organic matter is an integral part of soil carbon pool. Biological processes contribute to the formation of such organo-mineral complexes when soil microbes, and in particular soil fungi, deposit a suite of extracellular metabolic compounds and their necromass on the mineral surfaces. While studied in bulk, micro- to nanoscale fungal–mineral interactions remain elusive. Of particular interest are the mutual effects at the interface between the fungal exometabolites and proximal mineral particles. In this work, we have grown saprotrophic and symbiotic fungi in contact with two soil minerals with contrasting properties: quartz and goethite, on top of X-ray transparent silicon nitride membrane windows and analyzed fungal hyphae by synchrotron-based scanning transmission X-ray microscopy in combination with near edge X-ray fine structure spectroscopy at C(K) and Fe(L) absorption edges. In the resultant chemical maps, we were able to visualize and differentiate organic compounds constituting the fungal cells, their extracellular metabolites, and the exometabolites adsorbing on the minerals. We found that the composition of the exometabolites differed between the fungal functional guilds, particularly, in their sugar to protein ratio and potassium concentration. In samples with quartz and goethite, we observed adsorption of the exometabolic compounds on the mineral surfaces with variations in their chemical composition around the particles. Although we did not observe clear alteration in the exometabolite chemistry upon mineral encounters, we show that fungal–mineral interaction result in reduction of Fe(III) in goethite. This process has been demonstrated for bulk systems, but, to our knowledge, this is the first observation on a single hypha scale offering insight into its underlying biological mechanisms. This demonstrates the link between processes initiated at the single-cell level to macroscale phenomena. Thus, spatially resolved chemical characterization of the microbial–mineral interfaces is crucial for an increased understanding of overall carbon cycling in soil.
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Jun 2022
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B22-Multimode InfraRed imaging And Microspectroscopy
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Abstract: Breadcrust bombs are pyroclasts displaying fractured, dense surfaces enveloping expanded interiors, and are associated with Vulcanian explosions. We document pyroclasts from the 2008–2009 CE eruption of Chaitén (Chile) that are internally as well as externally breadcrusted. The pyroclasts are cut by intersecting micrometer- to millimeter-thick tuffisites with dense glassy walls, which grade into strongly inflated pumiceous material. We find H2O diffusion gradients proximal to the breadcrusted surfaces, such that H2O is depleted from far-field magma (0.68 ± 0.04 wt%) into dense, fractured vein walls (0.2–0.3 wt%), indicating a spatial association between H2O mass transfer within the pyroclast interior and both suppressed vesiculation and breadcrusting. We experimentally confirm that diffusive H2O depletion suppresses bubble growth at shallow conduit conditions. Therefore, we interpret the breadcrust formation to be induced by H2O diffusion and the associated rise in viscosity rather than by cooling in the classical breadcrust-formation models. We posit that a “dehydration quench” is important as degassing continues to very low H2O contents in shallow-conduit magma that continues to vesiculate.
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Jun 2022
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Krios I-Titan Krios I at Diamond
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Diamond Proposal Number(s):
[20287]
Open Access
Abstract: Although amyloid fibres are highly stable protein aggregates, a specific combination of human Hsp70 system chaperones can disassemble them, including fibres formed of α-synuclein, huntingtin, or Tau. Disaggregation requires the ATPase activity of the constitutively expressed Hsp70 family member, Hsc70, together with the J domain protein DNAJB1 and the nucleotide exchange factor Apg2. Clustering of Hsc70 on the fibrils appears to be necessary for disassembly. Here we use atomic force microscopy to show that segments of in vitro assembled α-synuclein fibrils are first coated with chaperones and then undergo bursts of rapid, unidirectional disassembly. Cryo-electron tomography and total internal reflection fluorescence microscopy reveal fibrils with regions of densely bound chaperones, preferentially at one end of the fibre. Sub-stoichiometric amounts of Apg2 relative to Hsc70 dramatically increase recruitment of Hsc70 to the fibres, creating localised active zones that then undergo rapid disassembly at a rate of ~ 4 subunits per second. The observed unidirectional bursts of Hsc70 loading and unravelling may be explained by differences between the two ends of the polar fibre structure.
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Jun 2022
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B21-High Throughput SAXS
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Open Access
Abstract: Biotherapeutic development presents a myriad of challenges in relation to delivery, in particular for protein therapeutics. Protein delivery is complicated due to hydrophilicity, size, rate of degradation in vivo, low permeation through biological barriers, pH and temperature sensitivity, as well as the need to conserve its quaternary structure to retain function. To preserve therapeutic levels in vivo, proteins require frequent administration due to their short half-lives. Formulation strategies combining proteins with lipid carriers for parenteral administration show potential for improving bioavailability, while preserving protein activity and bypassing the mucosal barriers of the body. Encapsulating protein in long acting injectable delivery systems can improve therapeutic indices by prolonging and controlling protein release and reducing the need for repeat interventions. Two lyotropic crystal forming lipids, monoolein and phytantriol, have been formulated to produce lipidic cubic phases and assessed for their use as long acting protein eluting injectables. Three soluble proteins, cytochrome c, glyceraldehyde-3-phosphate dehydrogenase and aldehyde dehydrogenase and one membrane protein, cytochrome c oxidase, were incorporated into bulk cubic phase formulations of each lipid system to comparatively assess protein release kinetics. The activity of the soluble proteins was measured upon release from a phytantriol bulk cubic phase and phytantriol cubosomes, produced using a liquid precursor method.
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Jun 2022
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B18-Core EXAFS
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Open Access
Abstract: Layered oxides for Na-ion batteries containing Fe have attracted strong interest mainly due to their low cost. However, full oxidation of Fe3+ to Fe4+ is rarely seen before O-redox sets in and is typically accompanied by voltage and capacity fade on cycling. On charging P2-Na0.67[Fe0.5Mn0.5]O2, Fe3+ is oxidized to only ≈Fe3.3+ before the onset of O-redox. O-redox occurs when the Na content is sufficiently low (Na ≈0.3) to permit the transition from P-type to O-type stacking, thus enabling Fe3+ migration to the Na layer. Fe3+ migration generates cation vacancies in the transition metal layer, forming □-O-□ configurations, which trigger the onset of O-redox. In contrast, doping this material with Mg2+ to form P2-Na0.67[Fe0.25Mn0.6Mg0.15]O2 allows full oxidation of Fe3+ to Fe4+ before the Na content is low enough to favor O-type stacking. During O-redox, Mg2+ is displaced into the Na layers instead of Fe. Mg substitution enables greater reversibility of the Fe3+/Fe4+ redox couple and significantly suppresses Fe migration, which is responsible for the voltage and capacity fade observed for P2-Na0.67Fe0.5Mn0.5O2.
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Jun 2022
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I24-Microfocus Macromolecular Crystallography
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Diamond Proposal Number(s):
[13775]
Open Access
Abstract: Solution and solid-state NMR spectroscopy are highly complementary techniques for studying structure and dynamics in very high molecular weight systems. Here we have analysed the dynamics of HIV-1 capsid (CA) assemblies in presence of the cofactors IP6 and ATPγS and the host-factor CPSF6 using a combination of solution state and cross polarisation magic angle spinning (CP-MAS) solid-state NMR. In particular, dynamical effects on ns to µs and µs to ms timescales are observed revealing diverse motions in assembled CA.
Using CP-MAS NMR, we exploited the sensitivity of the amide/Cα-Cβ backbone chemical shifts in DARR and NCA spectra to observe the plasticity of the HIV-1 CA tubular assemblies and also map the binding of cofactors and the dynamics of cofactor-CA complexes. In solution, we measured how the addition of host- and co-factors to CA -hexamers perturbed the chemical shifts and relaxation properties of CA-Ile and -Met methyl groups using transverse-relaxation-optimized NMR spectroscopy to exploit the sensitivity of methyl groups as probes in high-molecular weight proteins. These data show how dynamics of the CA protein assembly over a range of spatial and temporal scales play a critical role in CA function. Moreover, we show that binding of IP6, ATPγS and CPSF6 results in local chemical shift as well as dynamic changes for a significant, contiguous portion of CA, highlighting how allosteric pathways communicate ligand interactions between adjacent CA protomers.
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Jun 2022
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B21-High Throughput SAXS
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Diamond Proposal Number(s):
[30822]
Open Access
Abstract: Botulinum Neurotoxins (BoNT) are the most potent toxins currently known. However, they also have therapeutic applications for an increasing number of motor related conditions due to their specificity, and low diffusion into the system. Although the start- and end- points for the BoNT mechanism of action are well-studied, a critical step remains poorly understood. It is theorised that BoNTs undergo a pH-triggered conformational shift, activating the neurotoxin by priming it to form a transmembrane (TM) channel. To test this hypothesis, we combined molecular dynamic (MD) simulations and small-angle x-ray scattering (SAXS), revealing a new conformation of BoNT/E. This conformation was exclusively observed in simulations below pH 5.5, as determined by principal component analysis (PCA), and its theoretical SAXS profile matched an experimental SAXS profile obtained at pH 4. Additionally, a localised secondary structural change was observed in MD simulations below pH 5.5, in a region previously identified as instrumental for membrane insertion for BoNT/A. These changes were found at a critical pH value for BoNTs in vivo, and may be relevant for their therapeutic use.
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Jun 2022
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I13-2-Diamond Manchester Imaging
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Diamond Proposal Number(s):
[20274]
Open Access
Abstract: Integrating physiology with structural insights of the same neuronal circuit provides a unique approach to understanding how the mammalian brain computes information. However, combining the techniques that provide both streams of data represents an experimental challenge. When studying glomerular column circuits in the mouse olfactory bulb, this approach involves e.g., recording the neuronal activity with in vivo 2-photon (2P) calcium imaging, retrieving the circuit structure with synchrotron X-ray computed tomography with propagation-based phase contrast (SXRT) and/or serial block-face scanning electron microscopy (SBEM) and correlating these datasets. Sample preparation and dataset correlation are two key bottlenecks in this correlative workflow. Here, we first quantify the occurrence of different artefacts when staining tissue slices with heavy metals to generate X-ray or electron contrast. We report improvements in the staining procedure, ultimately achieving perfect staining in ∼67% of the 0.6 mm thick olfactory bulb slices that were previously imaged in vivo with 2P. Secondly, we characterise the accuracy of the spatial correlation between functional and structural datasets. We demonstrate that direct, single-cell precise correlation between in vivo 2P and SXRT tissue volumes is possible and as reliable as correlating between 2P and SBEM. Altogether, these results pave the way for experiments that require retrieving physiology, circuit structure and synaptic signatures in targeted regions. These correlative function-structure studies will bring a more complete understanding of mammalian olfactory processing across spatial scales and time.
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Jun 2022
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NONE-No attached Diamond beamline
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Charles J.
Buchanan
,
Ben
Gaunt
,
Peter J.
Harrison
,
Yun
Yang
,
Jiwei
Liu
,
Aziz
Khan
,
Andrew M.
Giltrap
,
Audrey
Le Bas
,
Philip N.
Ward
,
Kapil
Gupta
,
Maud
Dumoux
,
Tiong Kit
Tan
,
Lisa
Schimaski
,
Sergio
Daga
,
Nicola
Picchiotti
,
Margherita
Baldassarri
,
Elisa
Benetti
,
Chiara
Fallerini
,
Francesca
Fava
,
Annarita
Giliberti
,
Panagiotis I.
Koukos
,
Matthew J.
Davy
,
Abirami
Lakshminarayanan
,
Xiaochao
Xue
,
Georgios
Papadakis
,
Lachlan P.
Deimel
,
Virgínia
Casablancas-Antràs
,
Timothy D. W.
Claridge
,
Alexandre M. J. J.
Bonvin
,
Quentin J.
Sattentau
,
Simone
Furini
,
Marco
Gori
,
Jiandong
Huo
,
Raymond J.
Owens
,
Christiane
Schaffitzel
,
Imre
Berger
,
Alessandra
Renieri
,
James H.
Naismith
,
Andrew J.
Baldwin
,
Benjamin G.
Davis
Open Access
Abstract: Many pathogens exploit host cell-surface glycans. However, precise analyses of glycan ligands binding with heavily-modified pathogen proteins can be confounded by overlapping sugar signals and/or compound with known experimental constraints. ‘Universal saturation transfer analysis’ (uSTA) builds on existing nuclear magnetic resonance spectroscopy to provide an automated workflow for quantitating protein-ligand interactions. uSTA reveals that early-pandemic, B-origin lineage SARS-CoV-2 spike trimer binds sialoside sugars in an ‘end-on’ manner. uSTA-guided modelling and a high-resolution cryo-electron microscopy structure implicate the spike N-terminal domain (NTD) and confirm end-on binding. This finding rationalizes the effect of NTD mutations that abolish sugar-binding in SARS CoV 2 variants of concern. Together with genetic variance analyses in early pandemic patient cohorts, this binding implicates a sialylated polylactosamine motif found on tetraantennary N-linked glycoproteins in deeper human lung as potentially relevant to virulence and/or zoonosis.
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Jun 2022
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