I18-Microfocus Spectroscopy
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Anouk M.
Borst
,
Martin P.
Smith
,
Adrian
Finch
,
Guillaume
Estrade
,
Cristina
Villanova-de-benavent
,
Peter
Nason
,
Eva
Marquis
,
Nicola J.
Horsburgh
,
Kathryn M.
Goodenough
,
Cheng
Xu
,
Jindřich
Kynický
,
Kalotina
Geraki
Diamond Proposal Number(s):
[14793, 15903]
Open Access
Abstract: Global resources of heavy Rare Earth Elements (REE) are dominantly sourced from Chinese regolith-hosted ion-adsorption deposits in which the REE are inferred to be weakly adsorbed onto clay minerals. Similar deposits elsewhere might provide alternative supply for these high-tech metals, but the adsorption mechanisms remain unclear and the adsorbed state of REE to clays has never been demonstrated in situ. This study compares the mineralogy and speciation of REE in economic weathering profiles from China to prospective regoliths developed on peralkaline rocks from Madagascar. We use synchrotron X-ray absorption spectroscopy to study the distribution and local bonding environment of Y and Nd, as proxies for heavy and light REE, in the deposits. Our results show that REE are truly adsorbed as easily leachable 8- to 9-coordinated outer-sphere hydrated complexes, dominantly onto kaolinite. Hence, at the atomic level, the Malagasy clays are genuine mineralogical analogues to those currently exploited in China.
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Dec 2020
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Krios III-Titan Krios III at Diamond
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Diamond Proposal Number(s):
[18477]
Open Access
Abstract: Traditionally, molecular assembly pathways for viruses are inferred from high resolution structures of purified stable intermediates, low resolution images of cell sections and genetic approaches. Here, we directly visualise an unsuspected ‘single shelled’ intermediate for a mammalian orthoreovirus in cryo-preserved infected cells, by cryo-electron tomography of cellular lamellae. Particle classification and averaging yields structures to 5.6 Å resolution, sufficient to identify secondary structural elements and produce an atomic model of the intermediate, comprising 120 copies each of protein λ1 and σ2. This λ1 shell is ‘collapsed’ compared to the mature virions, with molecules pushed inwards at the icosahedral fivefolds by ~100 Å, reminiscent of the first assembly intermediate of certain prokaryotic dsRNA viruses. This supports the supposition that these viruses share a common ancestor, and suggests mechanisms for the assembly of viruses of the Reoviridae. Such methodology holds promise for dissecting the replication cycle of many viruses.
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Sep 2020
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I03-Macromolecular Crystallography
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Diamond Proposal Number(s):
[8547]
Open Access
Abstract: Complex I is the first and the largest enzyme of respiratory chains in bacteria and mitochondria. The mechanism which couples spatially separated transfer of electrons to proton translocation in complex I is not known. Here we report five crystal structures of T. thermophilus enzyme in complex with NADH or quinone-like compounds. We also determined cryo-EM structures of major and minor native states of the complex, differing in the position of the peripheral arm. Crystal structures show that binding of quinone-like compounds (but not of NADH) leads to a related global conformational change, accompanied by local re-arrangements propagating from the quinone site to the nearest proton channel. Normal mode and molecular dynamics analyses indicate that these are likely to represent the first steps in the proton translocation mechanism. Our results suggest that quinone binding and chemistry play a key role in the coupling mechanism of complex I.
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Aug 2020
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B22-Multimode InfraRed imaging And Microspectroscopy
I11-High Resolution Powder Diffraction
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Xiaolin
Li
,
Juehua
Wang
,
Xinran
Zhang
,
Xue
Han
,
Ivan
Da Silva
,
Christopher G.
Morris
,
Shaojun
Xu
,
Damian M.
Wilary
,
Yinyong
Sun
,
Yongqiang
Cheng
,
Claire A.
Murray
,
Chiu C.
Tang
,
Mark D.
Frogley
,
Gianfelice
Cinque
,
Tristan
Lowe
,
Haifei
Zhang
,
Anibal J.
Ramirez-cuesta
,
K. Mark
Thomas
,
Leslie W.
Bolton
,
Sihai
Yang
,
Martin
Schroeder
,
Nannan
Bai
Diamond Proposal Number(s):
[13247]
Open Access
Abstract: The demand for xylenes is projected to increase over the coming decades. The separation of xylene isomers, particularly p- and m-xylenes, is vital for the production of numerous polymers and materials. However, current state-of-the-art separation is based upon fractional crystallisation at 220 K which is highly energy intensive. Here, we report the discrimination of xylene isomers via refinement of the pore size in a series of porous metal–organic frameworks, MFM-300, at sub-angstrom precision leading to the optimal kinetic separation of all three xylene isomers at room temperature. The exceptional performance of MFM-300 for xylene separation is confirmed by dynamic ternary breakthrough experiments. In-depth structural and vibrational investigations using synchrotron X-ray diffraction and terahertz spectroscopy define the underlying host–guest interactions that give rise to the observed selectivity (p-xylene < o-xylene < m-xylene) and separation factors of 4.6–18 for p- and m-xylenes.
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Aug 2020
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B18-Core EXAFS
I20-Scanning-X-ray spectroscopy (XAS/XES)
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Diamond Proposal Number(s):
[20581, 15955]
Open Access
Abstract: Uranium (U) is a ubiquitous element in the Earth’s crust at ~2 ppm. In anoxic environments, soluble hexavalent uranium (U(VI)) is reduced and immobilized. The underlying reduction mechanism is unknown but likely of critical importance to explain the geochemical behavior of U. Here, we tackle the mechanism of reduction of U(VI) by the mixed-valence iron oxide, magnetite. Through high-end spectroscopic and microscopic tools, we demonstrate that the reduction proceeds first through surface-associated U(VI) to form pentavalent U, U(V). U(V) persists on the surface of magnetite and is further reduced to tetravalent UO2 as nanocrystals (~1–2 nm) with random orientations inside nanowires. Through nanoparticle re-orientation and coalescence, the nanowires collapse into ordered UO2 nanoclusters. This work provides evidence for a transient U nanowire structure that may have implications for uranium isotope fractionation as well as for the molecular-scale understanding of nuclear waste temporal evolution and the reductive remediation of uranium contamination.
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Aug 2020
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Krios III-Titan Krios III at Diamond
Krios IV-Titan Krios IV at Diamond
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Diamond Proposal Number(s):
[21062, 24924]
Open Access
Abstract: Bacillus thuringiensis Vip3 (Vegetative Insecticidal Protein 3) toxins are widely used in biotech crops to control Lepidopteran pests. These proteins are produced as inactive protoxins that need to be activated by midgut proteases to trigger cell death. However, little is known about their three-dimensional organization and activation mechanism at the molecular level. Here, we have determined the structures of the protoxin and the protease-activated state of Vip3Aa at 2.9 Å using cryo-electron microscopy. The reconstructions show that the protoxin assembles into a pyramid-shaped tetramer with the C-terminal domains exposed to the solvent and the N-terminal region folded into a spring-loaded apex that, after protease activation, drastically remodels into an extended needle by a mechanism akin to that of influenza haemagglutinin. These results provide the molecular basis for Vip3 activation and function, and serves as a strong foundation for the development of more efficient insecticidal proteins.
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Aug 2020
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I03-Macromolecular Crystallography
I04-1-Macromolecular Crystallography (fixed wavelength)
I24-Microfocus Macromolecular Crystallography
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Lucy I.
Crouch
,
Marcelo V.
Liberato
,
Paulina A.
Urbanowicz
,
Arnaud
Basle
,
Christopher A.
Lamb
,
Christopher J.
Stewart
,
Katie
Cooke
,
Mary
Doona
,
Stephanie
Needham
,
Richard R.
Brady
,
Janet E.
Berrington
,
Katarina
Madunic
,
Manfred
Wuhrer
,
Peter
Chater
,
Jeffery P.
Pearson
,
Robert
Glowacki
,
Eric C.
Martens
,
Fuming
Zhang
,
Robert J.
Linhardt
,
Daniel I. R.
Spencer
,
David N.
Bolam
Diamond Proposal Number(s):
[18598]
Open Access
Abstract: The thick mucus layer of the gut provides a barrier to infiltration of the underlying epithelia by both the normal microbiota and enteric pathogens. Some members of the microbiota utilise mucin glycoproteins as a nutrient source, but a detailed understanding of the mechanisms used to breakdown these complex macromolecules is lacking. Here we describe the discovery and characterisation of endo-acting enzymes from prominent mucin-degrading bacteria that target the polyLacNAc structures within oligosaccharide side chains of both animal and human mucins. These O-glycanases are part of the large and diverse glycoside hydrolase 16 (GH16) family and are often lipoproteins, indicating that they are surface located and thus likely involved in the initial step in mucin breakdown. These data provide a significant advance in our knowledge of the mechanism of mucin breakdown by the normal microbiota. Furthermore, we also demonstrate the potential use of these enzymes as tools to explore changes in O-glycan structure in a number of intestinal disease states.
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Aug 2020
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I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[14891]
Open Access
Abstract: Cells utilise specialized polymerases from the Primase-Polymerase (Prim-Pol) superfamily to maintain genome stability. Prim-Pol’s function in genome maintenance pathways including replication, repair and damage tolerance. Mycobacteria contain multiple Prim-Pols required for lesion repair, including Prim-PolC that performs short gap repair synthesis during excision repair. To understand the molecular basis of Prim-PolC’s gap recognition and synthesis activities, we elucidated crystal structures of pre- and post-catalytic complexes bound to gapped DNA substrates. These intermediates explain its binding preference for short gaps and reveal a distinctive modus operandi called Synthesis-dependent Template Displacement (STD). This mechanism enables Prim-PolC to couple primer extension with template base dislocation, ensuring that the unpaired templating bases in the gap are ushered into the active site in an ordered manner. Insights provided by these structures establishes the molecular basis of Prim-PolC’s gap recognition and extension activities, while also illuminating the mechanisms of primer extension utilised by closely related Prim-Pols.
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Aug 2020
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B18-Core EXAFS
E01-JEM ARM 200CF
E02-JEM ARM 300CF
I11-High Resolution Powder Diffraction
I20-Scanning-X-ray spectroscopy (XAS/XES)
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Liqun
Kang
,
Bolun
Wang
,
Qiming
Bing
,
Michal
Zalibera
,
Robert
Büchel
,
Ruoyu
Xu
,
Qiming
Wang
,
Yiyun
Liu
,
Diego
Gianolio
,
Chiu C.
Tang
,
Emma K.
Gibson
,
Mohsen
Danaie
,
Christopher
Allen
,
Ke
Wu
,
Sushila
Marlow
,
Ling-dong
Sun
,
Qian
He
,
Shaoliang
Guan
,
Anton
Savitsky
,
Juan J.
Velasco-vélez
,
June
Callison
,
Christopher W. M.
Kay
,
Sotiris E.
Pratsinis
,
Wolfgang
Lubitz
,
Jing-yao
Liu
,
Feng Ryan
Wang
Diamond Proposal Number(s):
[15151, 15763, 16966, 17377, 19072, 19246, 20939, 17559, 24285, 19318, 19850]
Open Access
Abstract: Supported atomic metal sites have discrete molecular orbitals. Precise control over the energies of these sites is key to achieving novel reaction pathways with superior selectivity. Here, we achieve selective oxygen (O2) activation by utilising a framework of cerium (Ce) cations to reduce the energy of 3d orbitals of isolated copper (Cu) sites. Operando X-ray absorption spectroscopy, electron paramagnetic resonance and density-functional theory simulations are used to demonstrate that a [Cu(I)O2]3− site selectively adsorbs molecular O2, forming a rarely reported electrophilic η2-O2 species at 298 K. Assisted by neighbouring Ce(III) cations, η2-O2 is finally reduced to two O2−, that create two Cu–O–Ce oxo-bridges at 453 K. The isolated Cu(I)/(II) sites are ten times more active in CO oxidation than CuO clusters, showing a turnover frequency of 0.028 ± 0.003 s−1 at 373 K and 0.01 bar PCO. The unique electronic structure of [Cu(I)O2]3− site suggests its potential in selective oxidation.
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Aug 2020
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Krios I-Titan Krios I at Diamond
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Leifu
Chang
,
Jing
Yang
,
Chang Hwa
Jo
,
Andreas
Boland
,
Ziguo
Zhang
,
Stephen H.
Mclaughlin
,
Afnan
Abu-thuraia
,
Ryan C.
Killoran
,
Matthew J.
Smith
,
Jean-francois
Côté
,
David
Barford
Diamond Proposal Number(s):
[13708]
Open Access
Abstract: DOCK (dedicator of cytokinesis) proteins are multidomain guanine nucleotide exchange factors (GEFs) for RHO GTPases that regulate intracellular actin dynamics. DOCK proteins share catalytic (DOCKDHR2) and membrane-associated (DOCKDHR1) domains. The structurally-related DOCK1 and DOCK2 GEFs are specific for RAC, and require ELMO (engulfment and cell motility) proteins for function. The N-terminal RAS-binding domain (RBD) of ELMO (ELMORBD) interacts with RHOG to modulate DOCK1/2 activity. Here, we determine the cryo-EM structures of DOCK2−ELMO1 alone, and as a ternary complex with RAC1, together with the crystal structure of a RHOG−ELMO2RBD complex. The binary DOCK2−ELMO1 complex adopts a closed, auto-inhibited conformation. Relief of auto-inhibition to an active, open state, due to a conformational change of the ELMO1 subunit, exposes binding sites for RAC1 on DOCK2DHR2, and RHOG and BAI GPCRs on ELMO1. Our structure explains how up-stream effectors, including DOCK2 and ELMO1 phosphorylation, destabilise the auto-inhibited state to promote an active GEF.
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Jul 2020
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