I14-Hard X-ray Nanoprobe
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Open Access
Abstract: The Hard X-ray Nanoprobe beamline, I14, at Diamond Light Source is a new facility for nanoscale microscopy. The beamline was designed with an emphasis on multi-modal analysis, providing elemental mapping, speciation mapping by XANES, structural phase mapping using nano-XRD and imaging through differential phase contrast and ptychography. The 185 m-long beamline operates over a 5 keV to 23 keV energy range providing a ≤50 nm beam size for routine user experiments and a flexible scanning system allowing fast acquisition. The beamline achieves robust and stable operation by imaging the source in the vertical direction and implementing horizontally deflecting primary optics and an overfilled secondary source in the horizontal direction. This paper describes the design considerations, optical layout, aspects of the hardware engineering and scanning system in operation as well as some examples illustrating the beamline performance.
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May 2021
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I22-Small angle scattering & Diffraction
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Andrew
Smith
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S. G.
Alcock
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L. S.
Davidson
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J. H.
Emmins
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J. C.
Hiller Bardsley
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P.
Holloway
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M.
Malfois
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A. R.
Marshall
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C. L.
Pizzey
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S. E.
Rogers
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O.
Shebanova
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T.
Snow
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J. P.
Sutter
,
E. P.
Williams
,
N. J.
Terrill
Open Access
Abstract: Beamline I22 at Diamond Light Source is dedicated to the study of soft-matter systems from both biological and materials science. The beamline can operate in the range 3.7 keV to 22 keV for transmission SAXS and 14 keV to 20 keV for microfocus SAXS with beam sizes of 240 µm × 60 µm [full width half-maximum (FWHM) horizontal (H) × vertical (V)] at the sample for the main beamline, and approximately 10 µm × 10 µm for the dedicated microfocusing platform. There is a versatile sample platform for accommodating a range of facilities and user-developed sample environments. The high brilliance of the insertion device source on I22 allows structural investigation of materials under extreme environments (for example, fluid flow at high pressures and temperatures). I22 provides reliable access to millisecond data acquisition timescales, essential to understanding kinetic processes such as protein folding or structural evolution in polymers and colloids.
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May 2021
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I11-High Resolution Powder Diffraction
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Diamond Proposal Number(s):
[10038]
Open Access
Abstract: Magnesium potassium phosphate cements (MKPC) were investigated to determine their efficacy towards retardation of reactive uranium metal corrosion. Optimised low-water content, fly ash (FA) and blast furnace slag (BFS) blended MKPC formulations were developed and their fluidity, hydration behaviour, strength and phase assemblage investigated. In-situ time resolved synchrotron powder X-ray diffraction was used to detail the early age (~60 h) phase assemblage development and hydration kinetics, where the inclusion of BFS was observed to delay the formation of struvite-K by ~14 h compared to FA addition (~2 h). All samples set within this period, suggesting the possible formation of a poorly crystalline binding phase prior to struvite-K crystallisation. Long-term corrosion trials using metallic uranium indicated that MKPC systems are capable of limiting uranium corrosion rates (reduced by half), when compared to a UK nuclear industry grout, which highlights their potential application radioactive waste immobilisation.
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May 2021
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I22-Small angle scattering & Diffraction
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Paolino
De Falco
,
Richard
Weinkamer
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Wolfgang
Wagermaier
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Chenghao
Li
,
Tim
Snow
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Nicholas J.
Terrill
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Himadri
Gupta
,
Pawan
Goyal
,
Martin
Stoll
,
Peter
Benner
,
Peter
Fratzl
Diamond Proposal Number(s):
[18524]
Open Access
Abstract: Small-angle X-ray scattering (SAXS) is an effective characterization technique for multi-phase nanocomposites. The structural complexity and heterogeneity of biological materials require the development of new techniques for the 3D characterization of their hierarchical structures. Emerging SAXS tomographic methods allow reconstruction of the 3D scattering pattern in each voxel but are costly in terms of synchrotron measurement time and computer time. To address this problem, an approach has been developed based on the reconstruction of SAXS invariants to allow for fast 3D characterization of nanostructured inhomogeneous materials. SAXS invariants are scalars replacing the 3D scattering patterns in each voxel, thus simplifying the 6D reconstruction problem to several 3D ones. Standard procedures for tomographic reconstruction can be directly adapted for this problem. The procedure is demonstrated by determining the distribution of the nanometric bone mineral particle thickness (T parameter) throughout a macroscopic 3D volume of bovine cortical bone. The T parameter maps display spatial patterns of particle thickness in fibrolamellar bone units. Spatial correlation between the mineral nanostructure and microscopic features reveals that the mineral particles are particularly thin in the vicinity of vascular channels.
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Apr 2021
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Zhou
Zhong
,
Jiying
Ning
,
Emerson A.
Boggs
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Sooin
Jang
,
Callen
Wallace
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Cheryl
Telmer
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Marcel P.
Bruchez
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Jinwoo
Ahn
,
Alan N.
Engelman
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Peijun
Zhang
,
Simon C.
Watkins
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Zandrea
Ambrose
Open Access
Abstract: Human immunodeficiency virus type 1 (HIV-1) capsid binds host proteins during infection, including cleavage and polyadenylation specificity factor 6 (CPSF6) and cyclophilin A (CypA). We observe that HIV-1 infection induces higher-order CPSF6 formation, and capsid-CPSF6 complexes cotraffic on microtubules. CPSF6-capsid complex trafficking is impacted by capsid alterations that reduce CPSF6 binding or by excess cytoplasmic CPSF6 expression, both of which are associated with decreased HIV-1 infection. Higher-order CPSF6 complexes bind and disrupt HIV-1 capsid assemblies in vitro. Disruption of HIV-1 capsid binding to CypA leads to increased CPSF6 binding and altered capsid trafficking, resulting in reduced infectivity. Our data reveal an interplay between CPSF6 and CypA that is important for cytoplasmic capsid trafficking and HIV-1 infection. We propose that CypA prevents HIV-1 capsid from prematurely engaging cytoplasmic CPSF6 and that differences in CypA cellular localization and innate immunity may explain variations in HIV-1 capsid trafficking and uncoating in CD4+ T cells and macrophages.
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Apr 2021
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I12-JEEP: Joint Engineering, Environmental and Processing
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Chi Ming
Yim
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Soumendra Nath
Panja
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Christopher
Trainer
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Craig
Topping
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Christoph
Heil
,
Alexandra S.
Gibbs
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Oxana
Magdysyuk
,
Vladimir
Tsurkan
,
Alois
Loidl
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Andreas W.
Rost
,
Peter
Wahl
Diamond Proposal Number(s):
[22974]
Open Access
Abstract: A key property of many quantum materials is that their ground state depends sensitively on small changes of an external tuning parameter, e.g., doping, magnetic field, or pressure, creating opportunities for potential technological applications. Here, we explore tuning of the ground state of the nonsuperconducting parent compound, Fe1+xTe, of the iron chalcogenides by uniaxial strain. Iron telluride exhibits a peculiar (π, 0) antiferromagnetic order unlike the (π, π) order observed in the Fe-pnictide superconductors. The (π, 0) order is accompanied by a significant monoclinic distortion. We explore tuning of the ground state by uniaxial strain combined with low-temperature scanning tunneling microscopy. We demonstrate that, indeed under strain, the surface of Fe1.1Te undergoes a transition to a (π, π)-charge-ordered state. Comparison with transport experiments on uniaxially strained samples shows that this is a surface phase, demonstrating the opportunities afforded by 2D correlated phases stabilized near surfaces and interfaces.
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Apr 2021
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Krios II-Titan Krios II at Diamond
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Yasunori
Watanabe
,
Luiza
Mendonca
,
Elizabeth R.
Allen
,
Andrew
Howe
,
Mercede
Lee
,
Joel D.
Allen
,
Himanshi
Chawla
,
David
Pulido
,
Francesca
Donnellan
,
Hannah
Davies
,
Marta
Ulaszewska
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Sandra
Belij-Rammerstorfer
,
Susan
Morris
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Anna-Sophia
Krebs
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Wanwisa
Dejnirattisai
,
Juthathip
Mongkolsapaya
,
Piyada
Supasa
,
Gavin R.
Screaton
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Catherine M.
Green
,
Teresa
Lambe
,
Peijun
Zhang
,
Sarah C.
Gilbert
,
Max
Crispin
Diamond Proposal Number(s):
[18477, 21005, 21004]
Abstract: Vaccine development against the SARS-CoV-2 virus focuses on the principal target of the neutralizing immune response, the spike (S) glycoprotein. Adenovirus-vectored vaccines offer an effective platform for the delivery of viral antigen, but it is important for the generation of neutralizing antibodies that they produce appropriately processed and assembled viral antigen that mimics that observed on the SARS-CoV-2 virus. Here, we describe the structure, conformation, and glycosylation of the S protein derived from the adenovirus-vectored ChAdOx1 nCoV-19/AZD1222 vaccine. We demonstrate native-like post-translational processing and assembly, and reveal the expression of S proteins on the surface of cells adopting the trimeric prefusion conformation. The data presented here confirm the use of ChAdOx1 adenovirus vectors as a leading platform technology for SARS-CoV-2 vaccines.
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Apr 2021
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Abstract: Despite their ubiquitous usage and increasing societal dependence on Li-ion batteries, there remains a lack of detailed empirical evidence of Li intercalation/deintercalation into graphite even though this process dictates the performance, longevity, and safety of the system. Here, we report direct detection and dissociation of specific crystallographic phases in the lithiated graphite, which form through a stepwise staging process. Using operando measurements, LiC18, LiC12, and LiC6 phases are observed via distinct low-frequency Raman features, which are the result of displacement of the graphite lattice by induced local strain. Density functional theory calculations confirm the nature of the Raman-active vibrational modes, to the layer breathing modes (LBMs) of the lithiated graphite. The new findings indicate graphene-like characteristics in the lithiated graphite under the deep charged condition due to the imposed strain by the inserted Li. Moreover, our approach also provides a simple experimental tool to measure induced strain in the graphite structure under full intercalation conditions.
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Apr 2021
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Krios I-Titan Krios I at Diamond
Krios II-Titan Krios II at Diamond
Krios III-Titan Krios III at Diamond
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Luiza
Mendonca
,
Dapeng
Sun
,
Jiying
Ning
,
Jiwei
Liu
,
Abhay
Kotecha
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Mateusz
Olek
,
Thomas
Frosio
,
Xiaofeng
Fu
,
Benjamin A.
Himes
,
Alex B.
Kleinpeter
,
Eric O.
Freed
,
Jing
Zhou
,
Christopher
Aiken
,
Peijun
Zhang
Diamond Proposal Number(s):
[18477, 21005, 21004]
Open Access
Abstract: Gag is the HIV structural precursor protein which is cleaved by viral protease to produce mature infectious viruses. Gag is a polyprotein composed of MA (matrix), CA (capsid), SP1, NC (nucleocapsid), SP2 and p6 domains. SP1, together with the last eight residues of CA, have been hypothesized to form a six-helix bundle responsible for the higher-order multimerization of Gag necessary for HIV particle assembly. However, the structure of the complete six-helix bundle has been elusive. Here, we determined the structures of both Gag in vitro assemblies and Gag viral-like particles (VLPs) to 4.2 Å and 4.5 Å resolutions using cryo-electron tomography and subtomogram averaging by emClarity. A single amino acid mutation (T8I) in SP1 stabilizes the six-helix bundle, allowing to discern the entire CA-SP1 helix connecting to the NC domain. These structures provide a blueprint for future development of small molecule inhibitors that can lock SP1 in a stable helical conformation, interfere with virus maturation, and thus block HIV-1 infection.
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Apr 2021
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I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[18069]
Open Access
Abstract: Human prolyl‐hydroxylases (PHDs) are hypoxia‐sensing 2‐oxoglutarate (2OG) oxygenases, catalysis by which suppresses the transcription of hypoxia‐inducible factor target genes. PHD inhibition enables the treatment of anaemia/ischaemia‐related disease. The PHD inhibitor Molidustat is approved for the treatment of renal anaemia; it differs from other approved/late‐stage PHD inhibitors in lacking a glycinamide side chain. The first reported crystal structures of Molidustat and IOX4 (a brain‐penetrating derivative) complexed with PHD2 reveal how their contiguous triazole, pyrazolone and pyrimidine/pyridine rings bind at the active site. The inhibitors bind to the active‐site metal in a bidentate manner through their pyrazolone and pyrimidine nitrogens, with the triazole π‐π‐stacking with Tyr303 in the 2OG binding pocket. Comparison of the new structures with other PHD inhibitor complexes reveals differences in the conformations of Tyr303, Tyr310, and a mobile loop linking β2–β3, which are involved in dynamic substrate binding/product release.
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Apr 2021
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