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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E02-JEM ARM 300CF
I15-1-X-ray Pair Distribution Function (XPDF)
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Jingwei
Hou
,
Christopher W.
Ashling
,
Sean M.
Collins
,
Andraž
Krajnc
,
Chao
Zhou
,
Louis
Longley
,
Duncan N.
Johnstone
,
Philip
Chater
,
Shichun
Li
,
Marie-vanessa
Coulet
,
Philip L.
Llewellyn
,
François-xavier
Coudert
,
David
Keen
,
Paul A.
Midgley
,
Gregor
Mali
,
Vicki
Chen
,
Thomas D.
Bennett
Diamond Proposal Number(s):
[171151, 19130, 16983]
Open Access
Abstract: The majority of research into metal-organic frameworks (MOFs) focuses on their crystalline nature. Recent research has revealed solid-liquid transitions within the family, which we use here to create a class of functional, stable and porous composite materials. Described herein is the design, synthesis, and characterisation of MOF crystal-glass composites, formed by dispersing crystalline MOFs within a MOF-glass matrix. The coordinative bonding and chemical structure of a MIL-53 crystalline phase are preserved within the ZIF-62 glass matrix. Whilst separated phases, the interfacial interactions between the closely contacted microdomains improve the mechanical properties of the composite glass. More significantly, the high temperature open pore phase of MIL-53, which spontaneously transforms to a narrow pore upon cooling in the presence of water, is stabilised at room temperature in the crystal-glass composite. This leads to a significant improvement of CO2 adsorption capacity.
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Jun 2019
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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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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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I13-2-Diamond Manchester Imaging
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Diamond Proposal Number(s):
[4022]
Abstract: Microstructures and pore systems in shales are key to understanding the role of shale in many energy applications. This study proposes a novel multi-stage upscaling procedure to comprehensively investigate the heterogeneous and complex microstructures and pore systems in a laminated and microfractured shale, utilizing 3D multi-scale imaging data. Five imaging techniques were used for characterisation from sub-nanoscale to macroscale (core-scale), spanning four orders of magnitude. Image data collected using X-ray tomography, Focused Ion Beam, and Electron Tomography techniques range in voxel size from 0.6 nm to 13 μm.
Prior to upscaling, a novel two-step analysis was performed to ensure sub-samples were representative. Following this, a three-step procedure, based on homogenising descriptors and computed volume coefficients, was used to upscale the quantified microstructure and pore system. At the highest resolution (nanoscale), four distinct pore types were identified. At the sub-micron scale equations were derived for three pore-associated phases. At the microscale, the volume coefficients were recalculated to upscale the pore system to the macroscale (millimetre). The accuracy of the upscaling methodology was verified, predicting the total porosity within 7.2% discrepancy. The results provide a unique perspective to understand heterogeneous rock types, breaking though prior scale limitations in the pore system.
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Jun 2019
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K.
Saksl
,
Z.
Molčanová
,
J.
Durisin
,
S.
Michalik
,
L.
Temleitner
,
B.
Balloková
,
V.
Girman
,
Y.
Katuna
,
M.
Sulikova
,
K.
Sulova
,
M.
Fejercak
,
M.
Lisnichuk
,
A.
Lachová
,
L.
Kapuscinský
Abstract: Very low density eutectic Ca72Mg28 at.% alloy is a precursor of complex biodegradable alloys with potential use as bioresorbable alloy for orthopaedic applications. The structure of the amorphous alloy was investigated by using X-ray, neutron diffraction and reverse Monte Carlo (RMC) modelling. The RMC configuration was decomposed into polyhedral holes whose faces are all triangles consisting of chemical bonds. Free volumes in the respective polyhedral holes were evaluated with reference to the packing efficiency of crystalline CaMg2 HCP phase. The tetrahedral holes, accounting for about 55% of the whole space, are regarded as densely packed units because the average packing efficiency of them is approximately equal to that of the corresponding crystal phase. At the same time, various types of polyhedral holes which have a certain free volume have been observed, and some of them are connected with each other. The densely packed coordination polyhedra consisting only of tetrahedral holes tend to be clustered.
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Jun 2019
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I04-Macromolecular Crystallography
I24-Microfocus Macromolecular Crystallography
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Diamond Proposal Number(s):
[14980]
Open Access
Abstract: The suppressor of cytokine signaling 2 (SOCS2) acts as substrate recognition subunit of a Cullin5 E3 ubiquitin ligase complex. SOCS2 binds to phosphotyrosine-modified epitopes as degrons for ubiquitination and proteasomal degradation, yet the molecular basis of substrate recognition has remained elusive. Here, we report co-crystal structures of SOCS2-ElonginB-ElonginC in complex with phosphorylated peptides from substrates growth hormone receptor (GHR-pY595) and erythropoietin receptor (EpoR-pY426) at 1.98 Å and 2.69 Å, respectively. Both peptides bind in an extended conformation recapitulating the canonical SH2 domain-pY pose, but capture different conformations of the EF loop via specific hydrophobic interactions. The flexible BG loop is fully defined in the electron density, and does not contact the substrate degron directly. Cancer-associated SNPs located around the pY pocket weaken substrate-binding affinity in biophysical assays. Our findings reveal insights into substrate recognition and specificity by SOCS2, and provide a blueprint for small molecule ligand design.
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Jun 2019
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I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
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Diamond Proposal Number(s):
[19301, 15433]
Abstract: Ubiquitylation, the posttranslational linkage of ubiquitin moieties to lysines in target proteins, helps regulate a myriad of biological processes. Ubiquitin, and sometimes ubiquitin-homology domains, are recognized by ubiquitin-binding domains, including CUE domains. CUE domains are thus generally thought to function by mediating interactions with ubiquitylated proteins. The chromatin remodeler, SMARCAD1, interacts with KAP1, a transcriptional corepressor. The SMARCAD1-KAP1 interaction is direct and involves the first SMARCAD1 CUE domain (CUE1) and the RBCC domain of KAP1. Here, we present a structural model of the KAP1 RBCC-SMARCAD1 CUE1 complex based on X-ray crystallography. Remarkably, CUE1, a canonical CUE domain, recognizes a cluster of exposed hydrophobic and surrounding charged/amphipathic residues on KAP1, which are presented in the context of a coiled-coil domain, not in a structure resembling ubiquitin. Together, these data suggest that CUE domains may have a wider function than simply recognizing ubiquitin and the ubiquitin-fold.
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Jun 2019
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I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
I04-Macromolecular Crystallography
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Daniel G. W.
Alanine
,
Doris
Quinkert
,
Rasika
Kumarasingha
,
Shahid
Mehmood
,
Francesca R.
Donnellan
,
Nana K.
Minkah
,
Bernadeta
Dadonaite
,
Ababacar
Diouf
,
Francis
Galaway
,
Sarah E.
Silk
,
Abhishek
Jamwal
,
Jennifer M.
Marshall
,
Kazutoyo
Miura
,
Lander
Foquet
,
Sean C.
Elias
,
Geneviève M.
Labbé
,
Alexander D.
Douglas
,
Jing
Jin
,
Ruth O.
Payne
,
Joseph J.
Illingworth
,
David J.
Pattinson
,
David
Pulido
,
Barnabas G.
Williams
,
Willem A.
De Jongh
,
Gavin J.
Wright
,
Stefan H. I.
Kappe
,
Carol V.
Robinson
,
Carole A.
Long
,
Brendan S.
Crabb
,
Paul R.
Gilson
,
Matthew
Higgins
,
Simon J.
Draper
Diamond Proposal Number(s):
[18069]
Open Access
Abstract: The Plasmodium falciparum reticulocyte-binding protein homolog 5 (PfRH5) is the leading target for next-generation vaccines against the disease-causing blood-stage of malaria. However, little is known about how human antibodies confer functional immunity against this antigen. We isolated a panel of human monoclonal antibodies (mAbs) against PfRH5 from peripheral blood B cells from vaccinees in the first clinical trial of a PfRH5-based vaccine. We identified a subset of mAbs with neutralizing activity that bind to three distinct sites and another subset of mAbs that are non-functional, or even antagonistic to neutralizing antibodies. We also identify the epitope of a novel group of non-neutralizing antibodies that significantly reduce the speed of red blood cell invasion by the merozoite, thereby potentiating the effect of all neutralizing PfRH5 antibodies as well as synergizing with antibodies targeting other malaria invasion proteins. Our results provide a roadmap for structure-guided vaccine development to maximize antibody efficacy against blood-stage malaria.
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Jun 2019
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I13-2-Diamond Manchester Imaging
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Abstract: Bird feather shafts are light, stiff, and strong, but the fine details of how their structure, mechanics and function relate to one another remains poorly understood. The missing piece in our understanding may be the various fibrous layers that make up the shaft's cortex. Detailed imaging techniques are needed to enable us to capture, analyse and quantify these layers before we can begin to unravel the relationship between their structure, mechanics and function.
We show that Serial‐Block‐Face scanning electron microscopy, scanning confocal polarised microscopy and synchrotron‐based computed tomography are three suitable techniques to investigate layer thickness and fibre orientation in the feather cortex. These techniques and other are discussed in terms of their ability to resolve the fibrous laminar structure of the feather cortex, on sample preparation, and on throughput. Annotated images are presented for each and less suitable techniques are presented in the supplement.
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Jun 2019
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