I04-1-Macromolecular Crystallography (fixed wavelength)
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Chloe R.
Koulouris
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Sian E.
Gardiner
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Tessa K.
Harris
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Karen T.
Elvers
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S. Mark
Roe
,
Jason A.
Gillespie
,
Simon E.
Ward
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Olivera
Grubisha
,
Robert A.
Nicholls
,
John R.
Atack
,
Benjamin D.
Bax
Diamond Proposal Number(s):
[19990]
Open Access
Abstract: Human serine racemase (hSR) catalyses racemisation of L-serine to D-serine, the latter of which is a co-agonist of the NMDA subtype of glutamate receptors that are important in synaptic plasticity, learning and memory. In a ‘closed’ hSR structure containing the allosteric activator ATP, the inhibitor malonate is enclosed between the large and small domains while ATP is distal to the active site, residing at the dimer interface with the Tyr121 hydroxyl group contacting the α-phosphate of ATP. In contrast, in ‘open’ hSR structures, Tyr121 sits in the core of the small domain with its hydroxyl contacting the key catalytic residue Ser84. The ability to regulate SR activity by flipping Tyr121 from the core of the small domain to the dimer interface appears to have evolved in animals with a CNS. Multiple X-ray crystallographic enzyme-fragment structures show Tyr121 flipped out of its pocket in the core of the small domain. Data suggest that this ligandable pocket could be targeted by molecules that inhibit enzyme activity.
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Dec 2022
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B21-High Throughput SAXS
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Diamond Proposal Number(s):
[22113]
Abstract: This study aims to understand possible effects of flavour compounds on the structure and conformation of endogenous proteins. Using methyl anthranilate (a grape flavour compound added to drinks, confectionery, and vape-liquids) and bovine serum albumin (BSA, a model serum protein) we designed experimental investigations using analytical ultracentrifugation, size exclusion chromatography small angle X-ray scattering, and fluorescence spectroscopy to reveal that methyl anthranilate spontaneously binds to BSA (ΔG°, ca. −21 KJ mol−1) which induces a conformational compactness (ca. 10 %) in the monomer structure. Complementary molecular modelling and dynamics simulations suggested the binding occurs at Sudlow II of BSA via establishment of hydrogen bonds with arginine409, lysine413 and serine488 leading to an increased conformational order in domains IA, IIB and IIIB. This work aims to set the foundation for future research on flavour-protein interactions and offer new sets of opportunities for understanding the effects of small compounds on protein structure.
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Sep 2022
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Abstract: Manufacturing austenitic stainless steels (ASSs) using additive manufacturing is of great interest for cryogenic applications. Here, the mechanical and microstructural responses of a 316L ASS built by laser powder bed fusion were revealed by performing in situ neutron diffraction tensile tests at the low-temperature range (from 373 to 10 K). The stacking fault energy almost linearly decreased from 29.2 ± 3.1 mJm−2 at 373 K to 7.5 ± 1.7 mJm−2 at 10 K, with a slope of 0.06 mJm−2K−1, leading to the transition of the dominant deformation mechanism from strain-induced twinning to martensite formation. As a result, excellent combinations of strength and ductility were achieved at the low-temperature range.
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Sep 2022
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D.
Matras
,
T. E.
Ashton
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H.
Dong
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M.
Mirolo
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I.
Martens
,
J.
Drnec
,
J. A.
Darr
,
P. D.
Quinn
,
S. D. M.
Jacques
,
A. M.
Beale
,
A.
Vamvakeros
Abstract: Synchrotron X-ray diffraction computed tomography (XRD-CT) was employed to study a commercial 18650 cylindrical LiNi0.8Co0.15Al0.5O2 (NCA) battery under operating conditions and during seven cycles. The analysis of the spatially-resolved diffraction patterns revealed multiple chemical heterogeneities related to the lithium distribution in both the cathode and the anode. It is shown that during the charging of the battery, the anode exhibits different degrees of activity regarding the lithiation process. Explicitly, the following three regions were identified: a uniform/homogenous lithiation, a delayed lithiation and an inactive-to-lithiation region. The inactive-to-lithiation anode region was a result of the specific cell geometry (i.e. due to lack of cathode tape opposite these anode areas) and throughout the cycling experiments remained present in the form of LiC30-30+. The delayed lithiation region was seen to have a direct impact on the properties of NCA in its close proximity during the battery discharging, preventing its full lithiation. Further to this, the aluminum tab negatively affected the NCA in direct contact with it, leading to different lattice parameter a and c evolution compared to the rest of the cathode.
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Aug 2022
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I22-Small angle scattering & Diffraction
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Diamond Proposal Number(s):
[22659]
Abstract: A multi-analytical study was performed to analyse the effect of bacterial cellulose (BCF) on the self-association of starches with different amylose content (wheat, waxy-maize), assessing macrostructural properties (rheology, gel strength) and some nano and sub-nano level features (small and wide-angle X-ray scattering). Although pasting viscosities and G′ were significantly increased by BCF in both starches, cellulose did not seem to promote the self-association of amylose in short-range retrogradation. A less elastic structure was reflected by a 2–3-fold increase in loss factor (G″/G′) at the highest BCF concentration tested. This behavior agreed with the nano and sub-nano characterisation of the samples, which showed loss of starch lamellarity and incomplete full recovery of an ordered structure after storage at 4 °C for 24 h. The gel strength data could be explained by the contribution of BCF to the mechanical response of the sample. The information gained in this work is relevant for tuning the structure of tailored starch-cellulose composites.
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Jul 2022
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B21-High Throughput SAXS
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Diamond Proposal Number(s):
[14891]
Open Access
Abstract: Calbindin-D28k is a calcium binding protein that is highly expressed in the mammalian central nervous system. It has been reported that calbindin-D28k binds to and increases the activity of inositol Monophosphatase (IMPase). This is an enzyme that is involved in the homeostasis of the Inositol trisphosphate signalling cascade by catalysing the final dephosphorylation of inositol and has been implicated in the therapeutic mechanism of lithium treatment of bipolar disorder. Previously studies have shown that calbindin-D28k can increase IMPase activity by up to 250 hundred-fold. A preliminary in silico model was proposed for the interaction.
Here, we aimed at exploring the shape and properties of the calbindin-IMPase complex to gain new insights on this biologically important interaction. We created several fusion constructs of calbindin-D28k and IMPase, connected by flexible amino acid linkers of different lengths and orientations to fuse the termini of the two proteins together. The resulting fusion proteins have activities 200%–400% higher the isolated wild-type IMPase. The constructs were characterized by small angle X-ray scattering to gain information on the overall shape of the complexes and validate the previous model. The fusion proteins form a V-shaped, elongated and less compact complex as compared to the model. Our results shed new light into this protein-protein interaction.
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Jul 2022
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I03-Macromolecular Crystallography
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Maria Giulia
Nizi
,
Mirko M.
Maksimainen
,
Sudarshan
Murthy
,
Serena
Massari
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Juho
Alaviuhkola
,
Barbara E.
Lippok
,
Sven T.
Sowa
,
Albert
Galera-Prat
,
Renata
Prunskaite-Hyyryläinen
,
Bernhard
Lüscher
,
Patricia
Korn
,
Lari
Lehtio
,
Oriana
Tabarrini
Diamond Proposal Number(s):
[19951]
Abstract: While human poly-ADP-ribose chain generating poly-ARTs, PARP1 and 2 and TNKS1 and 2, have been widely characterized, less is known on the pathophysiological roles of the mono-ADP-ribosylating mono-ARTs, partly due to the lack of selective inhibitors. In this context, we have focused on the development of inhibitors for the mono-ART PARP10, whose overexpression is known to induce cell death. Starting from OUL35 (1) and its 4-(benzyloxy)benzamidic derivative (2) we herein report the design and synthesis of new analogues from which the cyclobutyl derivative 3c rescued cells most efficiently from PARP10 induced apoptosis. Most importantly, we also identified 2,3-dihydrophthalazine-1,4-dione as a new suitable nicotinamide mimicking PARP10 inhibitor scaffold. When it was functionalized with cycloalkyl (8a-c), o-fluorophenyl (8h), and thiophene (8l) rings, IC50 values in the 130–160 nM range were obtained, making them the most potent PARP10 inhibitors reported to date. These compounds also inhibited PARP15 with low micromolar IC50s, but none of the other tested poly- and mono-ARTs, thus emerging as dual mono-ART inhibitors. Compounds 8a, 8h and 8l were also able to enter cells and rescue cells from apoptosis. Our work sheds more light on inhibitor development against mono-ARTs and identifies chemical probes to study the cellular roles of PARP10 and PARP15.
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Jul 2022
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I15-1-X-ray Pair Distribution Function (XPDF)
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Open Access
Abstract: Four different structural models, which all fit the same X-ray powder pattern, were obtained in the structure determination of 4,11-difluoroquinacridone (C20H10N2O2F2) from unindexed X-ray powder data by a global fit. The models differ in their lattice parameters, space groups, Z, Z′, molecular packing and hydrogen bond patterns. The molecules form a criss-cross pattern in models A and B, a layer structure built from chains in model C and a criss-cross arrangement of dimers in model D. Nevertheless, all models give a good Rietveld fit to the experimental powder pattern with acceptable R-values. All molecular geometries are reliable, except for model D, which is slightly distorted. All structures are crystallochemically plausible, concerning density, hydrogen bonds, intermolecular distances etc. All models passed the checkCIF test without major problems; only in model A a missed symmetry was detected. All structures could have probably been published, although 3 of the 4 structures were wrong. The investigation, which of the four structures is actually the correct one, was challenging. Six methods were used: (1) Rietveld refinements, (2) fit of the crystal structures to the pair distribution function (PDF) including the refinement of lattice parameters and atomic coordinates, (3) evaluation of the colour, (4) lattice-energy minimizations with force fields, (5) lattice-energy minimizations by two dispersion-corrected density functional theory methods, and (6) multinuclear CPMAS solid-state NMR spectroscopy (1H, 13C, 19F) including the comparison of calculated and experimental chemical shifts. All in all, model B (perhaps with some disorder) can probably be considered to be the correct one. This work shows that a structure determination from limited-quality powder data may result in totally different structural models, which all may be correct or wrong, even if they are chemically sensible and give a good Rietveld refinement. Additionally, the work is an excellent example that the refinement of an organic crystal structure can be successfully performed by a fit to the PDF, and the combination of computed and experimental solid-state NMR chemical shifts can provide further information for the selection of the most reliable structure among several possibilities.
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Jul 2022
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I20-Scanning-X-ray spectroscopy (XAS/XES)
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Diamond Proposal Number(s):
[17053]
Abstract: Background: The bioavailable supply of copper to ruminants has long been problematic. Complexities in supply exist due to interactions with other dietary elements in the rumen, most notably with iron or molybdenum in combination with sulphur, which can result in copper binding preventing its absorption. The molybdenum-sulphur-copper interaction has been extensively studied over the years. However, very little is known about the iron-sulphur-copper interaction, especially its mode of action in the gastrointestinal tract. Methods In the present work digesta from the rumen and jejunum of sheep fed a high copper, sulphur and iron diet was analysed using X-ray absorption spectroscopy (XAS). Results: X-ray absorption fine structure (XAFS) and X-ray absorption near edge structure (XANES) indicated that all of the copper and iron had changed in bonding in the rumen and that the oxidation state of the elements had been reduced into a mix of Fe2+ & Fe3+ and Cu+ with some Cu0. Conclusion: The copper compounds were most likely to be thiol co-ordinated in line with Cu+ chemistry. Changes to the copper compounds took place in the jejunum, although thiols were still highly favoured the possible existence of a copper-iron-sulphur complex which also included oxygen and chloride was also observed. This possibly has some resemblance to the crystal structure of bornite.
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Jul 2022
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I12-JEEP: Joint Engineering, Environmental and Processing
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Diamond Proposal Number(s):
[26376]
Open Access
Abstract: Three-dimensional X-ray diffraction (3DXRD) is shown to be feasible at the I12 Joint Engineering, Environmental and Processing (JEEP) beamline of Diamond Light Source. As a demonstration, a microstructually simple low-carbon ferritic steel was studied in a highly textured and annealed state. A processing pipeline suited to this beamline was created, using software already established in the 3DXRD user community, enabling grain centre-of-mass positions, orientations and strain tensor elements to be determined. Orientations, with texture measurements independently validated from electron backscatter diffraction (EBSD) data, possessed a ∼0.1° uncertainty, comparable with other 3DXRD instruments. The spatial resolution was limited by the far-field detector pixel size; the average of the grain centre of mass position errors was determined as ±∼80 µm. An average per-grain error of ∼1 × 10−3 for the elastic strains was also measured; this could be reduced in future experiments by improving sample preparation, geometry calibration, data collection and analysis techniques. Application of 3DXRD onto I12 shows great potential, where its implementation is highly desirable due to the flexible, open architecture of the beamline. User-owned or designed sample environments can be used, thus 3DXRD could be applied to previously unexplored scientific areas.
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Jul 2022
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