I04-1-Macromolecular Crystallography (fixed wavelength)
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Chloe R.
Koulouris
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Sian E.
Gardiner
,
Tessa K.
Harris
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Karen T.
Elvers
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S. Mark
Roe
,
Jason A.
Gillespie
,
Simon E.
Ward
,
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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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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I03-Macromolecular Crystallography
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Maria Giulia
Nizi
,
Mirko M.
Maksimainen
,
Sudarshan
Murthy
,
Serena
Massari
,
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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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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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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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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B21-High Throughput SAXS
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Diamond Proposal Number(s):
[23041, 27887]
Open Access
Abstract: Nanodiscs are used to stabilize membrane proteins in a lipid environment and enable investigations of the function and structure of these. Membrane proteins are often only available in small amounts, and thus the stability and ease of use of the nanodiscs are essential. We have recently explored circularizing and supercharging membrane scaffolding proteins (MSPs) for nanodisc formation and found increased temporal stability at elevated temperatures. In the present study, we investigate six different supercharged MSPs and their ability to form nanodiscs: three covalently circularized and the three non-circularized, linear versions. Using standard reconstitution protocols using cholate as the reconstitution detergent, we found that two of the linear constructs formed multiple lipid-protein species, whereas adding n-Dodecyl-B-D-maltoside (DDM) with the cholate in the reconstitution gave rise to single-species nanodisc formation for these MSPs. For all MSPs, the formed nanodiscs were analyzed by small-angle X-ray scattering (SAXS), which showed similar structures for each MSP, respectively, suggesting that the structures of the formed nanodiscs are independent of the initial DDM content, as long as cholate is present. Lastly, we incorporated the membrane protein proteorhodopsin into the supercharged nanodiscs and observed a considerable increase in incorporation yield with the addition of DDM. For the three circularized MSPs, a single major species appeared in the size exclusion chromatography (SEC) chromatogram, suggesting monodisperse nanodiscs with proteorhodopsin incorporated, which is in strong contrast to the samples without DDM showing almost no incorporation and high polydispersity.
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Jun 2022
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B18-Core EXAFS
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Hongman
Sun
,
Yu
Zhang
,
Chunfen
Wang
,
Mark A.
Isaacs
,
Ahmed I.
Osman
,
Yehong
Wang
,
David
Rooney
,
Youhe
Wang
,
Zifeng
Yan
,
Christopher M. A.
Parlett
,
Feng
Wang
,
Chunfei
Wu
Diamond Proposal Number(s):
[19850]
Abstract: Integrated carbon capture and utilization (ICCU) presents an ideal solution to address anthropogenic carbon dioxide (CO2) emissions from industry and energy sectors, facilitating CO2 capture and subsequent utilization through conversion into high-value chemicals, as opposed to current release into the atmosphere. Herein, we report the synergistic coupling of porous CaO, as a sorbent for CO2 capture, and Ni doped CeO2 nanorods, as catalytic sites for CO2 reduction. It is found that ceria is shown to possess the capacity for CO2 utilization, however, critically it only results in the generation of CO due to the weak CO-ceria bonding. The addition of Ni active sites gives rise to CH4 being the predominant product, via the strong interaction between Ni species and CO, which facilitates further reduction. Through tuning Ni loadings, we have evaluated the role of catalytic active site size, with a Ni loading of only 0.5 wt% providing optimal performance through the formation of sub-nanometer sized clusters. This near-atomic active site dispersion gives rise to CH4 productivity and selectivity of 1540 mmol g−1 Ni and 85.8%, respectively, with this optimal combination of catalyst and sorbent demonstrating high stability over 10 cycles of ICCU process. These observations in parallel with the synergistic coupling of earth-abundant, low-cost materials (CaO and Ni) will have broad implications on the design and implementation of high efficiency, cost-effective ICCU materials and processes.
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Jun 2022
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B22-Multimode InfraRed imaging And Microspectroscopy
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Diamond Proposal Number(s):
[25407]
Abstract: Mechanofluorochromic materials are of great significance for the fabrication of innovative sensors and optoelectronics. However, efficient mechanofluorochromic materials are rarely explored due to the deficiency of existing design strategies. Here, we demonstrate the incarceration of aggregation-induced emission (AIE) materials within metal-organic framework (MOF) single crystals to construct a composite system with turn-on mechanofluorochromism. A new type of AIE@MOF material was designed: integrating a zeolitic MOF (ZIF-71) and tetraphenylethylene (TPE, a topical AIE material) to generate a TPE@ZIF-71 system with exceptional turn-on type mechanofluorochromism. Using terahertz vibrational spectroscopy, we show the unique fluorochromism mainly emanates from the enhanced nanoconfinement effect exerted by ZIF-71 host on TPE guest under pressure. Compared with pure TPE, we demonstrate the nanoconfinement in AIE@MOF not only changes the TPE's turn-off type sensing behavior to a turn-on type, but boosts the original sensitivity markedly by tenfold. Significantly, because ZIF-71 prevents the spontaneous recrystallization of TPE upon unloading, this allows TPE@ZIF-71 to record the stress history. This is the first demonstration of the Guest@MOF system combining the concepts of AIE and MOF; its promising properties and potential engineering applications will stimulate new directions pertaining to luminescent stress sensors and smart optics.
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Jun 2022
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