I13-2-Diamond Manchester Imaging
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G. R.
Parker
,
D. S.
Eastwood
,
M.
Storm
,
K.
Vitharana
,
E. M.
Heatwole
,
I.
Lopez-pulliam
,
R. M.
Broilo
,
P. M.
Dickson
,
A.
Martinez
,
Christoph
Rau
,
N. K.
Bourne
Diamond Proposal Number(s):
[15068, 16650, 18198]
Abstract: High-resolution synchrotron x-ray radiography with computed tomography is used to observe the evolution of porosity created by thermal exposure in two HMX-based polymer-bonded explosive compositions; LX-04 and BX-63. The measurements were made in situ, over an extended period of time, during which the samples were heated on a slow-rate thermal trajectory. The tests ended with thermal-runaway to ignition after which the samples were consumed by combustion. The primary means of damage appears to be from mechanical debonding of the HMX-binder interface with secondary contribution from chemical decomposition. Confinement and binder properties affect the amount of porosity and permeability that develops. Additionally, observations were made describing the emergence and structure of an internal ignition volume, the formation and transport of a pre-ignition melt layer, and how the early stages of combustion were affected by material morphology, mechanical confinement and melt. The contact angle between molten HMX and the fluoropolymer, Viton A, is also presented. For the first time we have time-resolved x-ray images of ignition in sufficient detail to verify the mechanism of cookoff in polymer-bonded explosive compositions.
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Apr 2021
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I12-JEEP: Joint Engineering, Environmental and Processing
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Diamond Proposal Number(s):
[19216]
Abstract: High-speed synchrotron tomography was used to investigate the nucleation and growth dynamics of Al13Fe4 intermetallic during solidification of an Al-5wt%Fe alloy, providing new insights into its formation process. The majority of Al13Fe4 intermetallics nucleated near the surface oxide of the specimen and a few nucleated at Al13Fe4 phase. Al13Fe4 crystals grew into a variety of shapes, including plate-like, hexagonal tabular, stair-like and V-shaped, which can be attributed to the crystal structure of this compound and its susceptibility to twinning. Hole-like defects filled with aluminium melt were observed within the intermetallics. Oriented particle attachment mechanism was proposed to explain the formation of the Al13Fe4 intermetallic, which needs further experiments and simulation to confirm.
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Apr 2021
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I04-Macromolecular Crystallography
I24-Microfocus Macromolecular Crystallography
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Diamond Proposal Number(s):
[15378, 19248]
Open Access
Abstract: The production of diffraction-quality protein crystals is challenging and often requires bespoke, time-consuming and expensive strategies. A system has been developed in which the BCL6 BTB domain acts as a crystallization chaperone and promiscuous assembly block that may form the basis for affinity-capture crystallography. The protein of interest is expressed with a C-terminal tag that interacts with the BTB domain, and co-crystallization leads to its incorporation within a BTB-domain lattice. This strategy was used to solve the structure of the SH3 domain of human nebulin, a structure previously solved by NMR, at 1.56 Å resolution. This approach is simple and effective, requiring only routine protein complexation and crystallization screening, and should be applicable to a range of proteins.
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Mar 2021
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E02-JEM ARM 300CF
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Diamond Proposal Number(s):
[20431, 22317]
Abstract: Electron ptychography is a 4-D STEM phase-contrast imaging technique with applications to light-element and beam-sensitive materials. Although the electron dose (electrons incident per unit area on the sample) is the primary figure of merit for imaging beam-sensitive materials, it is also necessary to consider the contrast transfer properties of the imaging technique. Here, we explore the contrast transfer properties of electron ptychography. The contrast transfer of focused-probe, non-iterative electron ptychography using the single-side-band (SSB) method is demonstrated experimentally. The band-pass nature of the phase-contrast transfer function (PCTF) for SSB ptychography places strict limitations on the probe convergence semi-angles required to resolve specific sample features with high contrast. The PCTF of the extended ptychographic iterative engine (ePIE) is broader than that for SSB ptychography, although when both high and low spatial frequencies are transferred, band-pass filtering is required to remove image artefacts. Normalisation of the transfer function with respect to the noise level shows that the transfer window is increased while avoiding noise amplification. Avoiding algorithms containing deconvolution steps may also increase the dose-efficiency of ptychographic phase reconstructions.
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Feb 2021
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B21-High Throughput SAXS
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Diamond Proposal Number(s):
[23269]
Abstract: The acyl carrier protein (ACP) is an indispensable component of both fatty acid and polyketide synthases and is primarily responsible for delivering acyl intermediates to enzymatic partners. At present, increasing numbers of multidomain ACPs have been discovered with roles in molecular recognition of trans-acting enzymatic partners as well as increasing metabolic flux. Further structural information is required to provide insight into their function, yet to date, the only high-resolution structure of this class to be determined is that of the doublet ACP (two continuous ACP domains) from mupirocin synthase. Here we report the solution nuclear magnetic resonance (NMR) structure of the doublet ACP domains from PigH (PigH ACP1-ACP2), which is an enzyme that catalyzes the formation of the bipyrrolic intermediate of prodigiosin, a potent anticancer compound with a variety of biological activities. The PigH ACP1-ACP2 structure shows each ACP domain consists of three conserved helices connected by a linker that is partially restricted by interactions with the ACP1 domain. Analysis of the holo (4′-phosphopantetheine, 4′-PP) form of PigH ACP1-ACP2 by NMR revealed conformational exchange found predominantly in the ACP2 domain reflecting the inherent plasticity of this ACP. Furthermore, ensemble models obtained from SAXS data reveal two distinct conformers, bent and extended, of both apo (unmodified) and holo PigH ACP1-ACP2 mediated by the central linker. The bent conformer appears to be a result of linker–ACP1 interactions detected by NMR and might be important for intradomain communication during the biosynthesis. These results provide new insights into the behavior of the interdomain linker of multiple ACP domains that may modulate protein–protein interactions. This is likely to become an increasingly important consideration for metabolic engineering in prodigiosin and other related biosynthetic pathways.
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Jan 2021
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B18-Core EXAFS
I20-Scanning-X-ray spectroscopy (XAS/XES)
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V.
Celorrio
,
D. J.
Fermin
,
L.
Calvillo
,
A.
Leach
,
H.
Huang
,
G.
Granozzi
,
J. A.
Alonso
,
A.
Aguadero
,
R. M.
Pinacca
,
A. E.
Russell
,
D.
Tiwari
Diamond Proposal Number(s):
[10306, 15151, 16479]
Abstract: Oxygen electrocatalysis at transition metal oxides is one of the key challenges underpinning electrochemical energy conversion systems, involving a delicate interplay of the bulk electronic structure and surface coordination of the active sites. In this work, we investigate for the first time the structure–activity relationship of A2RuMnO7 (A = Dy3+, Ho3+, and Er3+) nanoparticles, demonstrating how orbital mixing of Ru, Mn, and O promotes high density of states at the appropriate energy range for oxygen electrocatalysis. The bulk structure and surface composition of these multicomponent pyrochlores are investigated by high-resolution transmission electron microscopy, X-ray diffraction, X-ray absorption spectroscopy, X-ray emission spectroscopy (XES), and X-ray photoemission spectroscopy (XPS). The materials exhibit high phase purity (cubic fcc with a space group Fd3̅m) in which variations in M–O bonds length are less than 1% upon replacing the A-site lanthanide. XES and XPS show that the mean oxidation state at the Mn-site as well as the nanoparticle surface composition was slightly affected by the lanthanide. The pyrochlore nanoparticles are significantly more active than the binary RuO2 and MnO2 toward the 4-electron oxygen reduction reaction in alkaline solutions. Interestingly, normalization of kinetic parameters by the number density of electroactive sites concludes that Dy2RuMnO7 shows twice higher activity than benchmark materials such as LaMnO3. Analysis of the electrochemical profiles supported by density functional theory calculations reveals that the origin of the enhanced catalytic activity is linked to the mixing of Ru and Mn d-orbitals and O p-orbitals at the conduction band which strongly overlap with the formal redox energy of O2 in solution. The activity enhancement strongly manifests in the case of Dy2RuMnO7 where the Ru/Mn ratio is closer to 1 in comparison with the Ho3+ and Er3+ analogs. These electronic effects are discussed in the context of the Gerischer formalism for electron transfer at the semiconductor/electrolyte junctions.
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Jan 2021
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B18-Core EXAFS
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Diamond Proposal Number(s):
[17243]
Abstract: Understanding the speciation and fate of radium during operational discharge from the offshore oil and gas industry into the marine environment is important in assessing its long term environmental impact. In the current work, 226Ra concentrations in marine sediments contaminated by produced water discharge from a site in the UK were analysed using gamma spectroscopy. Radium was present in field samples (0.1 - 0.3 Bq g-1) within International Atomic Energy Agency activity thresholds and was found to be primarily associated with micron sized radiobarite particles (≤2 μm). Experimental studies of synthetic/field produced water and seawater mixing under laboratory conditions showed that a significant proportion of radium (up to 97%) co-precipitated with barite confirming the radiobarite fate pathway. The results showed that produced water discharge into the marine environment results in the formation of radiobarite particles which incorporate a significant portion of radium and can be deposited in marine sediments.
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Jan 2021
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I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
I04-Macromolecular Crystallography
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Declan A.
Gray
,
Joshua B. R.
White
,
Abraham O.
Oluwole
,
Parthasarathi
Rath
,
Amy J.
Glenwright
,
Adam
Mazur
,
Michael
Zahn
,
Arnaud
Basle
,
Carl
Morland
,
Sasha L.
Evans
,
Alan
Cartmell
,
Carol V.
Robinson
,
Sebastian
Hiller
,
Neil A.
Ranson
,
David N.
Bolam
,
Bert
Van Den Berg
Diamond Proposal Number(s):
[13587, 18598]
Open Access
Abstract: In Bacteroidetes, one of the dominant phyla of the mammalian gut, active uptake of large nutrients across the outer membrane is mediated by SusCD protein complexes via a “pedal bin” transport mechanism. However, many features of SusCD function in glycan uptake remain unclear, including ligand binding, the role of the SusD lid and the size limit for substrate transport. Here we characterise the β2,6 fructo-oligosaccharide (FOS) importing SusCD from Bacteroides thetaiotaomicron (Bt1762-Bt1763) to shed light on SusCD function. Co-crystal structures reveal residues involved in glycan recognition and suggest that the large binding cavity can accommodate several substrate molecules, each up to ~2.5 kDa in size, a finding supported by native mass spectrometry and isothermal titration calorimetry. Mutational studies in vivo provide functional insights into the key structural features of the SusCD apparatus and cryo-EM of the intact dimeric SusCD complex reveals several distinct states of the transporter, directly visualising the dynamics of the pedal bin transport mechanism.
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Jan 2021
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I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[19800]
Open Access
Abstract: Dye‐decolorizing peroxidases (DyPs) constitute a superfamily of heme‐containing peroxidases that are related neither to animal nor to plant peroxidase families. These are divided into four classes (types A, B, C, and D) based on sequence features. The active site of DyPs contains two highly conserved distal ligands, an aspartate and an arginine, the roles of which are still controversial. These ligands have mainly been studied in class A‐C bacterial DyPs, largely because no effective recombinant expression systems have been developed for the fungal (D‐type) DyPs. In this work, we employ ancestral sequence reconstruction (ASR) to resurrect a D‐type DyP ancestor, AncDyPD‐b1. Expression of AncDyPD‐b1 in Escherichia coli results in large amounts of a heme‐containing soluble protein and allows for the first mutagenesis study on the two distal ligands of a fungal DyP. UV‐Vis and resonance Raman (RR) spectroscopic analyses, in combination with steady‐state kinetics and the crystal structure, reveal fine pH‐dependent details about the heme active site structure and show that both the aspartate (D222) and the arginine (R390) are crucial for hydrogen peroxide reduction. Moreover, the data indicate that these two residues play important but mechanistically different roles on the intraprotein long‐range electron transfer process.
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Jan 2021
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I03-Macromolecular Crystallography
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Samuel L.
Rose
,
Svetlana V.
Antonyuk
,
Daisuke
Sasaki
,
Keitaro
Yamashita
,
Kunio
Hirata
,
Go
Ueno
,
Hideo
Ago
,
Robert R.
Eady
,
Takehiko
Tosha
,
Masaki
Yamamoto
,
S. Samar
Hasnain
Diamond Proposal Number(s):
[15991]
Open Access
Abstract: Copper-containing nitrite reductases (CuNiRs), encoded by nirK gene, are found in all kingdoms of life with only 5% of CuNiR denitrifiers having two or more copies of nirK. Recently, we have identified two copies of nirK genes in several α-proteobacteria of the order Rhizobiales including Bradyrhizobium sp. ORS 375, encoding a four-domain heme-CuNiR and the usual two-domain CuNiR (Br2DNiR). Compared with two of the best-studied two-domain CuNiRs represented by the blue (AxNiR) and green (AcNiR) subclasses, Br2DNiR, a blue CuNiR, shows a substantially lower catalytic efficiency despite a sequence identity of ~70%. Advanced synchrotron radiation and x-ray free-electron laser are used to obtain the most accurate (atomic resolution with unrestrained SHELX refinement) and damage-free (free from radiation-induced chemistry) structures, in as-isolated, substrate-bound, and product-bound states. This combination has shed light on the protonation states of essential catalytic residues, additional reaction intermediates, and how catalytic efficiency is modulated.
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Jan 2021
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