I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
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Justina
Briliūtė
,
Paulina A.
Urbanowicz
,
Ana S.
Luis
,
Arnaud
Basle
,
Neil
Paterson
,
Osmond
Rebello
,
Jenifer
Hendel
,
Didier A.
Ndeh
,
Elisabeth C.
Lowe
,
Eric C.
Martens
,
Daniel I. R.
Spencer
,
David N.
Bolam
,
Lucy I.
Crouch
Diamond Proposal Number(s):
[13587, 18598]
Abstract: Glycans are the major carbon sources available to the human colonic microbiota. Numerous N-glycosylated proteins are found in the human gut, from both dietary and host sources, including immunoglobulins such as IgA that are secreted into the intestine at high levels. Here, we show that many mutualistic gut Bacteroides spp. have the capacity to utilize complex N-glycans (CNGs) as nutrients, including those from immunoglobulins. Detailed mechanistic studies using transcriptomic, biochemical, structural and genetic techniques reveal the pathway employed by Bacteroides thetaiotaomicron (Bt) for CNG degradation. The breakdown process involves an extensive enzymatic apparatus encoded by multiple non-adjacent loci and comprises 19 different carbohydrate-active enzymes from different families, including a CNG-specific endo-glycosidase activity. Furthermore, CNG degradation involves the activity of carbohydrate-active enzymes that have previously been implicated in the degradation of other classes of glycan. This complex and diverse apparatus provides Bt with the capacity to access the myriad different structural variants of CNGs likely to be found in the intestinal niche.
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Jun 2019
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B18-Core EXAFS
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Diamond Proposal Number(s):
[10306, 15151]
Open Access
Abstract: The structure of a highly active pyridine-alkoxide iridium water oxidation catalyst (WOC) is examined by X-ray absorption spectroscopy (XAS). A detailed comparison with IrO2 points to a rigid molecular unit of low nuclearity, with the best analysis suggesting the existence of a novel tetrameric iridium-oxo cubane as the resting state.
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Jun 2019
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B18-Core EXAFS
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Diamond Proposal Number(s):
[15151]
Abstract: UV activated photocatalysts deposited using chemical vapour deposition have found commercial success as self-cleaning coatings. However, only limited work has been conducted on the use of the more recently discovered visible light activated photocatalysis for this application. Tantalum oxynitride is an established visible light photocatalyst, and in this paper we have investigated the ability of thin films of tantalum oxynitride to photocatalytically degrade a model organic pollutant, stearic acid, and therefore assess the coatings potential for self-cleaning applications. Thin films of tantalum oxide were formed using aerosol assisted chemical vapour deposition (AACVD) of tantalum ethoxide, and then converted into tantalum oxynitride through ammonolysis at temperatures between 550 °C and 750 °C. Investigation of the films using XRD, UV-vis spectroscopy and XAFS identify that amorphous tantalum oxynitride is formed during the ammonolysis, with complete conversion to TaON under conditions of 700 °C for 24 hours. The self-cleaning ability of this film was assessed using stearic acid as the model pollutant, with a degradation rate of 2.5(2) × 1013 molecules per min per cm2 when exposed to a 5-sun solar simulator, equipped with a UV cut-off filter. We therefore conclude that tantalum oxynitride thin films are able to act as self-cleaning coatings through visible light photocatalysis and that films of tantalum oxynitride can be synthesized using a scalable chemical vapour deposition route.
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Jun 2019
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I23-Long wavelength MX
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Open Access
Abstract: The ribosome, the largest RNA-containing macromolecular machinery in cells, requires metal ions not only to maintain its three-dimensional fold but also to perform protein synthesis. Despite the vast biochemical data regarding the importance of metal ions for efficient protein synthesis and the increasing number of ribosome structures solved by X-ray crystallography or cryo-electron microscopy, the assignment of metal ions within the ribosome remains elusive due to methodological limitations. Here we present extensive experimental data on the potassium composition and environment in two structures of functional ribosome complexes obtained by measurement of the potassium anomalous signal at the K-edge, derived from long-wavelength X-ray diffraction data. We elucidate the role of potassium ions in protein synthesis at the three-dimensional level, most notably, in the environment of the ribosome functional decoding and peptidyl transferase centers. Our data expand the fundamental knowledge of the mechanism of ribosome function and structural integrity.
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Jun 2019
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Krios I-Titan Krios I at Diamond
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Rana
Abdelnabi
,
James A.
Geraets
,
Yipeng
Ma
,
Carmen
Mirabelli
,
Justin W.
Flatt
,
Ausra
Domanska
,
Leen
Delang
,
Dirk
Jochmans
,
Timiri Ajay
Kumar
,
Venkatesan
Jayaprakash
,
Barij Nayan
Sinha
,
Pieter
Leyssen
,
Sarah
Butcher
,
Johan
Neyts
Diamond Proposal Number(s):
[1973]
Open Access
Abstract: Rhino- and enteroviruses are important human pathogens, against which no antivirals are available. The best-studied inhibitors are “capsid binders” that fit in a hydrophobic pocket of the viral capsid. Employing a new class of entero-/rhinovirus inhibitors and by means of cryo–electron microscopy (EM), followed by resistance selection and reverse genetics, we discovered a hitherto unknown druggable pocket that is formed by viral proteins VP1 and VP3 and that is conserved across entero-/rhinovirus species. We propose that these inhibitors stabilize a key region of the virion, thereby preventing the conformational expansion needed for viral RNA release. A medicinal chemistry effort resulted in the identification of analogues targeting this pocket with broad-spectrum activity against Coxsackieviruses B (CVBs) and compounds with activity against enteroviruses (EV) of groups C and D, and even rhinoviruses (RV). Our findings provide novel insights in the biology of the entry of entero-/rhinoviruses and open new avenues for the design of broad-spectrum antivirals against these pathogens.
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Jun 2019
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I24-Microfocus Macromolecular Crystallography
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Diamond Proposal Number(s):
[8015]
Abstract: RPEL proteins, which contain the G-actin-binding RPEL motif, coordinate cytoskeletal processes with actin dynamics. We show that the ArhGAP12- and ArhGAP32-family GTPase-activating proteins (GAPs) are RPEL proteins. We determine the structure of the ArhGAP12/G-actin complex, and show that G-actin contacts the RPEL motif and GAP domain sequences. G-actin inhibits ArhGAP12 GAP activity, and this requires the G-actin contacts identified in the structure. In B16 melanoma cells, ArhGAP12 suppresses basal Rac and Cdc42 activity, F-actin assembly, invadopodia formation and experimental metastasis. In this setting, ArhGAP12 mutants defective for G-actin binding exhibit more effective downregulation of Rac GTP loading following HGF stimulation and enhanced inhibition of Rac-dependent processes, including invadopodia formation. Potentiation or disruption of the G-actin/ArhGAP12 interaction, by treatment with the actin-binding drugs latrunculin B or cytochalasin D, has corresponding effects on Rac GTP loading. The interaction of G-actin with RPEL-family rhoGAPs thus provides a negative feedback loop that couples Rac activity to actin dynamics.
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Jun 2019
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I11-High Resolution Powder Diffraction
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Diamond Proposal Number(s):
[17673]
Abstract: Solid solutions of 0.35(Ba,Ca)(Zr,Ti)O3-0.65(K0.5Bi0.5)TiO3 (BCZT-KBT) having various Ca and Zr contents were synthesized by solid state reaction. The sintered ceramics exhibited interesting features comprising core-shell type microstructures and relaxor ferroelectric behaviour. The influence of air-quenching on structure and electrical properties has been systematically investigated. The results indicate that the compositional heterogeneity in the shell regions, for the slow-cooled state, was reduced by air quenching. Improvements are evident in ferroelectric tetragonal phase content, accompanied by increased polarisation values and depolarisation temperatures. Comparing the results obtained for two BCZT compositions, it was demonstrated that the stability of the ferroelectric tetragonal phase in slow-cooled BCZT-KBT samples was improved for the ceramic with lower Ca and Zr concentrations, denoted x = 0.06, comparing with that for higher levels, denoted x = 0.15. Furthermore, the electric field-induced ferroelectric state in the quenched ceramic with x = 0.06 was found to be more stable during heating, yielding an enhanced depolarisation temperature.
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Jun 2019
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I12-JEEP: Joint Engineering, Environmental and Processing
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Diamond Proposal Number(s):
[12606]
Abstract: In-situ fracture tests were carried out on the I12 beamline at the Diamond Light Source. Four Al-Ti metal-matrix composites (MMCs), with two crack lengths, were studied to assess for the impact of in-plane constraint. Synchrotron X-ray computed tomography and synchrotron X-ray diffraction were used to measure total strain and elastic strain respectively. In this work, the measured elastic strains in the samples are detailed as a function of applied load and compared against those predicted from a 3D elastic-plastic finite element model. The modelled strains increased asymptotically towards the tip of the electro discharge machined notch. The experimental results do not highlight the same response, which is due to a combination of blunting and low experimental spatial resolution. Far field experimental and measured strain fields converged, notably in the test piece containing a long notch (
a/W
= 0.5) and higher levels of constraint.
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Jun 2019
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I03-Macromolecular Crystallography
I24-Microfocus Macromolecular Crystallography
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Diamond Proposal Number(s):
[14739, 20229]
Open Access
Abstract: Rotavirus is the leading agent causing acute gastroenteritis in young children, with the P[8] genotype accounting for more than 80% of infections in humans. The molecular bases for binding of the VP8* domain from P[8] VP4 spike protein to its cellular receptor, the secretory H type-1 antigen (Fuc-α1,2-Gal-β1,3-GlcNAc; H1), and to its precursor lacto-N-biose (Gal-β1,3-GlcNAc; LNB) have been determined. The resolution of P[8] VP8* crystal structures in complex with H1 antigen and LNB and site-directed mutagenesis experiments revealed that both glycans bind to the P[8] VP8* protein through a binding pocket shared with other members of the P[II] genogroup (i.e.: P[4], P[6] and P[19]). Our results show that the L-fucose moiety from H1 only displays indirect contacts with P[8] VP8*. However, the induced conformational changes in the LNB moiety increase the ligand affinity by two-fold, as measured by surface plasmon resonance (SPR), providing a molecular explanation for the different susceptibility to rotavirus infection between secretor and non-secretor individuals. The unexpected interaction of P[8] VP8* with LNB, a building block of type-1 human milk oligosaccharides, resulted in inhibition of rotavirus infection, highlighting the role and possible application of this disaccharide as an antiviral. While key amino acids in the H1/LNB binding pocket were highly conserved in members of the P[II] genogroup, differences were found in ligand affinities among distinct P[8] genetic lineages. The variation in affinities were explained by subtle structural differences induced by amino acid changes in the vicinity of the binding pocket, providing a fine-tuning mechanism for glycan binding in P[8] rotavirus.
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Jun 2019
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I04-1-Macromolecular Crystallography (fixed wavelength)
I24-Microfocus Macromolecular Crystallography
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William
Farnaby
,
Manfred
Koegl
,
Michael J.
Roy
,
Claire
Whitworth
,
Emelyne
Diers
,
Nicole
Trainor
,
David
Zollman
,
Steffen
Steurer
,
Jale
Karolyi-oezguer
,
Carina
Riedmueller
,
Teresa
Gmaschitz
,
Johannes
Wachter
,
Christian
Dank
,
Michael
Galant
,
Bernadette
Sharps
,
Klaus
Rumpel
,
Elisabeth
Traxler
,
Thomas
Gerstberger
,
Renate
Schnitzer
,
Oliver
Petermann
,
Peter
Greb
,
Harald
Weinstabl
,
Gerd
Bader
,
Andreas
Zoephel
,
Alexander
Weiss-puxbaum
,
Katharina
Ehrenhöfer-wölfer
,
Simon
Wöhrle
,
Guido
Boehmelt
,
Joerg
Rinnenthal
,
Heribert
Arnhof
,
Nicola
Wiechens
,
Meng-ying
Wu
,
Tom
Owen-hughes
,
Peter
Ettmayer
,
Mark
Pearson
,
Darryl B.
Mcconnell
,
Alessio
Ciulli
Diamond Proposal Number(s):
[14980]
Abstract: Targeting subunits of BAF/PBAF chromatin remodeling complexes has been proposed as an approach to exploit cancer vulnerabilities. Here, we develop proteolysis targeting chimera (PROTAC) degraders of the BAF ATPase subunits SMARCA2 and SMARCA4 using a bromodomain ligand and recruitment of the E3 ubiquitin ligase VHL. High-resolution ternary complex crystal structures and biophysical investigation guided rational and efficient optimization toward ACBI1, a potent and cooperative degrader of SMARCA2, SMARCA4 and PBRM1. ACBI1 induced anti-proliferative effects and cell death caused by SMARCA2 depletion in SMARCA4 mutant cancer cells, and in acute myeloid leukemia cells dependent on SMARCA4 ATPase activity. These findings exemplify a successful biophysics- and structure-based PROTAC design approach to degrade high profile drug targets, and pave the way toward new therapeutics for the treatment of tumors sensitive to the loss of BAF complex ATPases.
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Jun 2019
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