I08-Scanning X-ray Microscopy beamline (SXM)
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James
Everett
,
Frederik
Lermyte
,
Jake
Brooks
,
Vindy
Tjendana-Tjhin
,
Germán
Plascencia-Villa
,
Ian
Hands-Portman
,
Jane M.
Donnelly
,
Kharmen
Billimoria
,
George
Perry
,
Xiongwei
Zhu
,
Peter J.
Sadler
,
Peter B.
O'Connor
,
Joanna F.
Collingwood
,
Neil D.
Telling
Diamond Proposal Number(s):
[15854]
Open Access
Abstract: The chemistry of copper and iron plays a critical role in normal brain function. A variety of enzymes and proteins containing positively charged Cu+, Cu2+, Fe2+, and Fe3+ control key processes, catalyzing oxidative metabolism and neurotransmitter and neuropeptide production. Here, we report the discovery of elemental (zero–oxidation state) metallic Cu0 accompanying ferromagnetic elemental Fe0 in the human brain. These nanoscale biometal deposits were identified within amyloid plaque cores isolated from Alzheimer’s disease subjects, using synchrotron x-ray spectromicroscopy. The surfaces of nanodeposits of metallic copper and iron are highly reactive, with distinctly different chemical and magnetic properties from their predominant oxide counterparts. The discovery of metals in their elemental form in the brain raises new questions regarding their generation and their role in neurochemistry, neurobiology, and the etiology of neurodegenerative disease.
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Jun 2021
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Krios I-Titan Krios I at Diamond
Krios II-Titan Krios II at Diamond
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Andreas
Schedlbauer
,
Idoia
Iturrioz
,
Borja
Ochoa-Lizarralde
,
Tammo
Diercks
,
Jorge Pedro
Lopez-Alonso
,
José Luis
Lavin
,
Tatsuya
Kaminishi
,
Retina
Çapuni
,
Neha
Dhimole
,
Elisa
De Astigarraga
,
David
Gil-Carton
,
Paola
Fucini
,
Sean R.
Connell
Diamond Proposal Number(s):
[17171, 15422]
Open Access
Abstract: While a structural description of the molecular mechanisms guiding ribosome assembly in eukaryotic systems is emerging, bacteria use an unrelated core set of assembly factors for which high-resolution structural information is still missing. To address this, we used single-particle cryo–electron microscopy to visualize the effects of bacterial ribosome assembly factors RimP, RbfA, RsmA, and RsgA on the conformational landscape of the 30S ribosomal subunit and obtained eight snapshots representing late steps in the folding of the decoding center. Analysis of these structures identifies a conserved secondary structure switch in the 16S ribosomal RNA central to decoding site maturation and suggests both a sequential order of action and molecular mechanisms for the assembly factors in coordinating and controlling this switch. Structural and mechanistic parallels between bacterial and eukaryotic systems indicate common folding features inherent to all ribosomes.
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Jun 2021
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I21-Resonant Inelastic X-ray Scattering (RIXS)
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Qisi
Wang
,
Karin
Von Arx
,
Masafumi
Horio
,
Deepak John
Mukkattukavil
,
Julia
Kuespert
,
Yasmine
Sassa
,
Thorsten
Schmitt
,
Abhishek
Nag
,
Sunseng
Pyon
,
Tomohiro
Takayama
,
Hidenori
Takagi
,
Mirian
Garcia-Fernandez
,
Ke-Jin
Zhou
,
Johan
Chang
Diamond Proposal Number(s):
[24481]
Open Access
Abstract: Charge order is universal to all hole-doped cuprates. Yet, the driving interactions remain an unsolved problem. Electron-electron interaction is widely believed to be essential, whereas the role of electron-phonon interaction is unclear. We report an ultrahigh-resolution resonant inelastic x-ray scattering (RIXS) study of the in-plane bond-stretching phonon mode in stripe-ordered cuprate La1.675Eu0.2Sr0.125CuO4. Phonon softening and lifetime shortening are found around the charge ordering wave vector. In addition to these self-energy effects, the electron-phonon coupling is probed by its proportionality to the RIXS cross section. We find an enhancement of the electron-phonon coupling around the charge-stripe ordering wave vector upon cooling into the low-temperature tetragonal structure phase. These results suggest that, in addition to electronic correlations, electron-phonon coupling contributes substantially to the emergence of long-range charge-stripe order in cuprates.
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Jun 2021
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I04-1-Macromolecular Crystallography (fixed wavelength)
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Marion
Schuller
,
Galen J.
Correy
,
Stefan
Gahbauer
,
Daren
Fearon
,
Taiasean
Wu
,
Roberto Efraín
Díaz
,
Iris D.
Young
,
Luan
Carvalho Martins
,
Dominique H.
Smith
,
Ursula
Schulze-Gahmen
,
Tristan W.
Owens
,
Ishan
Deshpande
,
Gregory E.
Merz
,
Aye C.
Thwin
,
Justin T.
Biel
,
Jessica K.
Peters
,
Michelle
Moritz
,
Nadia
Herrera
,
Huong T.
Kratochvil
,
Anthony
Aimon
,
James
Bennett
,
Jose
Brandao Neto
,
Aina E.
Cohen
,
Alexandre
Dias
,
Alice
Douangamath
,
Louise
Dunnett
,
Oleg
Fedorov
,
Matteo P.
Ferla
,
Martin R.
Fuchs
,
Tyler J.
Gorrie-Stone
,
James M.
Holton
,
Michael G.
Johnson
,
Tobias
Krojer
,
George
Meigs
,
Alisa J.
Powell
,
Johannes Gregor Matthias
Rack
,
Victor
Rangel
,
Silvia
Russi
,
Rachael E.
Skyner
,
Clyde A.
Smith
,
Alexei S.
Soares
,
Jennifer L.
Wierman
,
Kang
Zhu
,
Peter
O’brien
,
Natalia
Jura
,
Alan
Ashworth
,
John J.
Irwin
,
Michael C.
Thompson
,
Jason E.
Gestwicki
,
Frank
Von Delft
,
Brian K.
Shoichet
,
James S.
Fraser
,
Ivan
Ahel
Diamond Proposal Number(s):
[27001]
Open Access
Abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) macrodomain within the nonstructural protein 3 counteracts host-mediated antiviral adenosine diphosphate–ribosylation signaling. This enzyme is a promising antiviral target because catalytic mutations render viruses nonpathogenic. Here, we report a massive crystallographic screening and computational docking effort, identifying new chemical matter primarily targeting the active site of the macrodomain. Crystallographic screening of 2533 diverse fragments resulted in 214 unique macrodomain-binders. An additional 60 molecules were selected from docking more than 20 million fragments, of which 20 were crystallographically confirmed. X-ray data collection to ultra-high resolution and at physiological temperature enabled assessment of the conformational heterogeneity around the active site. Several fragment hits were confirmed by solution binding using three biophysical techniques (differential scanning fluorimetry, homogeneous time-resolved fluorescence, and isothermal titration calorimetry). The 234 fragment structures explore a wide range of chemotypes and provide starting points for development of potent SARS-CoV-2 macrodomain inhibitors.
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Apr 2021
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I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[19880]
Open Access
Abstract: ADAMTS13 is a plasma metalloprotease that is essential for the regulation of von Willebrand factor (VWF) function, mediator of platelet recruitment to sites of blood vessel damage. ADAMTS13 function is dynamically regulated by structural changes induced by VWF binding that convert it from a latent to active conformation. ADAMTS13 global latency is manifest by the interaction of its C-terminal CUB1-2 domains with its central Spacer domain. We resolved the crystal structure of the ADAMTS13 CUB1-2 domains revealing a previously unreported configuration for the tandem CUB domains. Docking simulations between the CUB1-2 domains with the Spacer domain in combination with enzyme kinetic functional characterization of ADAMTS13 CUB domain mutants enabled the mapping of the CUB1-2 domain site that binds the Spacer domain. Together, these data reveal the molecular basis of the ADAMTS13 Spacer-CUB interaction and the control of ADAMTS13 global latency.
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Apr 2021
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P.
Mehrabi
,
R.
Bücker
,
G.
Bourenkov
,
H. M.
Ginn
,
D.
Von Stetten
,
H. M.
Müller-Werkmeister
,
A.
Kuo
,
T.
Morizumi
,
B.t.
Eger
,
W.-L.
Ou
,
S.
Oghbaey
,
A.
Sarracini
,
J. E.
Besaw
,
O.
Pare´-Labrosse
,
S.
Meier
,
H.
Schikora
,
F.
Tellkamp
,
A.
Marx
,
D. A.
Sherrell
,
D.
Axford
,
R. I.
Owen
,
O. P.
Ernst
,
E. F.
Pai
,
E. C.
Schulz
,
R. J. D.
Miller
Open Access
Abstract: For the two proteins myoglobin and fluoroacetate dehalogenase, we present a systematic comparison of crystallographic diffraction data collected by serial femtosecond (SFX) and serial synchrotron crystallography (SSX). To maximize comparability, we used the same batch of micron-sized crystals, the same sample delivery device, and the same data analysis software. Overall figures of merit indicate that the data of both radiation sources are of equivalent quality. For both proteins, reasonable data statistics can be obtained with approximately 5000 room-temperature diffraction images irrespective of the radiation source. The direct comparability of SSX and SFX data indicates that the quality of diffraction data obtained from these samples is linked to the properties of the crystals rather than to the radiation source. Therefore, for other systems with similar properties, time-resolved experiments can be conducted at the radiation source that best matches the desired time resolution.
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Mar 2021
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I03-Macromolecular Crystallography
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Samuel L.
Rose
,
Svetlana V.
Antonyuk
,
Daisuke
Sasaki
,
Keitaro
Yamashita
,
Kunio
Hirata
,
Go
Ueno
,
Hideo
Ago
,
Robert R.
Eady
,
Takehiko
Tosha
,
Masaki
Yamamoto
,
S. Samar
Hasnain
Diamond Proposal Number(s):
[15991]
Open Access
Abstract: Copper-containing nitrite reductases (CuNiRs), encoded by nirK gene, are found in all kingdoms of life with only 5% of CuNiR denitrifiers having two or more copies of nirK. Recently, we have identified two copies of nirK genes in several α-proteobacteria of the order Rhizobiales including Bradyrhizobium sp. ORS 375, encoding a four-domain heme-CuNiR and the usual two-domain CuNiR (Br2DNiR). Compared with two of the best-studied two-domain CuNiRs represented by the blue (AxNiR) and green (AcNiR) subclasses, Br2DNiR, a blue CuNiR, shows a substantially lower catalytic efficiency despite a sequence identity of ~70%. Advanced synchrotron radiation and x-ray free-electron laser are used to obtain the most accurate (atomic resolution with unrestrained SHELX refinement) and damage-free (free from radiation-induced chemistry) structures, in as-isolated, substrate-bound, and product-bound states. This combination has shed light on the protonation states of essential catalytic residues, additional reaction intermediates, and how catalytic efficiency is modulated.
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Jan 2021
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Krios II-Titan Krios II at Diamond
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David J. K.
Swainsbury
,
Pu
Qian
,
Philip J.
Jackson
,
Kaitlyn M.
Faries
,
Dariusz M.
Niedzwiedzki
,
Elizabeth C.
Martin
,
David A.
Farmer
,
Lorna A.
Malone
,
Rebecca F.
Thompson
,
Neil A.
Ranson
,
Daniel P.
Canniffe
,
Mark J.
Dickman
,
Dewey
Holten
,
Christine
Kirmaier
,
Andrew
Hitchcock
,
C. Neil
Hunter
Diamond Proposal Number(s):
[19832]
Open Access
Abstract: The reaction-center light-harvesting complex 1 (RC-LH1) is the core photosynthetic component in purple phototrophic bacteria. We present two cryo–electron microscopy structures of RC-LH1 complexes from Rhodopseudomonas palustris. A 2.65-Å resolution structure of the RC-LH114-W complex consists of an open 14-subunit LH1 ring surrounding the RC interrupted by protein-W, whereas the complex without protein-W at 2.80-Å resolution comprises an RC completely encircled by a closed, 16-subunit LH1 ring. Comparison of these structures provides insights into quinone dynamics within RC-LH1 complexes, including a previously unidentified conformational change upon quinone binding at the RC QB site, and the locations of accessory quinone binding sites that aid their delivery to the RC. The structurally unique protein-W prevents LH1 ring closure, creating a channel for accelerated quinone/quinol exchange.
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Jan 2021
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Open Access
Abstract: The use of metals of nanometer dimensions to enhance and manipulate light-matter interactions for emerging plasmonics-enabled nanophotonic and optoelectronic applications is an interesting yet not highly explored area of research beyond plasmonics. Even more importantly, the concept of an active metal that can undergo an optical nonvolatile transition has not been explored. Here, we demonstrate that antimony (Sb), a pure metal, is optically distinguishable between two programmable states as nanoscale thin films. We show that these states, corresponding to the crystalline and amorphous phases of the metal, are stable at room temperature. Crucially from an application standpoint, we demonstrate both its optoelectronic modulation capabilities and switching speed using single subpicosecond pulses. The simplicity of depositing a single metal portends its potential for use in any optoelectronic application where metallic conductors with an actively tunable state are important.
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Jan 2021
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I05-ARPES
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Niels B. M.
Schroeter
,
Iñigo
Robredo
,
Sebastian
Klemenz
,
Robert J.
Kirby
,
Jonas A.
Krieger
,
Ding
Pei
,
Tianlun
Yu
,
Samuel
Stolz
,
Thorsten
Schmitt
,
Pavel
Dudin
,
Timur K.
Kim
,
Cephise
Cacho
,
Andreas
Schnyder
,
Aitor
Bergara
,
Vladimir N.
Strocov
,
Fernando
De Juan
,
Maia G.
Vergniory
,
Leslie M.
Schoop
Diamond Proposal Number(s):
[26098, 20617]
Open Access
Abstract: Magnetic Weyl semimetals are a newly discovered class of topological materials that may serve as a platform for exotic phenomena, such as axion insulators or the quantum anomalous Hall effect. Here, we use angle-resolved photoelectron spectroscopy and ab initio calculations to discover Weyl cones in CoS2, a ferromagnet with pyrite structure that has been long studied as a candidate for half-metallicity, which makes it an attractive material for spintronic devices. We directly observe the topological Fermi arc surface states that link the Weyl nodes, which will influence the performance of CoS2 as a spin injector by modifying its spin polarization at interfaces. In addition, we directly observe a minority-spin bulk electron pocket in the corner of the Brillouin zone, which proves that CoS2 cannot be a true half-metal.
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Dec 2020
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