I04-Macromolecular Crystallography
|
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.
|
Apr 2021
|
|
I04-1-Macromolecular Crystallography (fixed wavelength)
|
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.
|
Apr 2021
|
|
|
|
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.
|
Mar 2021
|
|
I03-Macromolecular Crystallography
|
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.
|
Jan 2021
|
|
|
|
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.
|
Jan 2021
|
|
Krios II-Titan Krios II at Diamond
|
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.
|
Jan 2021
|
|
I05-ARPES
|
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.
|
Dec 2020
|
|
I24-Microfocus Macromolecular Crystallography
|
Angeliki
Ditsiou
,
Chiara
Cilibrasi
,
Nikiana
Simigdala
,
Athanasios
Papakyriakou
,
Leanne
Milton-harris
,
Viviana
Vella
,
Joanne E.
Nettleship
,
Jae Ho
Lo
,
Shivani
Soni
,
Goar
Smbatyan
,
Panagiota
Ntavelou
,
Teresa
Gagliano
,
Maria Chiara
Iachini
,
Sahir
Khurshid
,
Thomas
Simon
,
Lihong
Zhou
,
Storm
Hassell-hart
,
Philip
Carter
,
Laurence H.
Pearl
,
Robin L.
Owen
,
Raymond J.
Owens
,
S. Mark
Roe
,
Naomi E.
Chayen
,
Heinz-josef
Lenz
,
John
Spencer
,
Chrisostomos
Prodromou
,
Apostolos
Klinakis
,
Justin
Stebbing
,
Georgios
Giamas
Diamond Proposal Number(s):
[14493]
Open Access
Abstract: Elucidating signaling driven by lemur tyrosine kinase 3 (LMTK3) could help drug development. Here, we solve the crystal structure of LMTK3 kinase domain to 2.1Å resolution, determine its consensus motif and phosphoproteome, unveiling in vitro and in vivo LMTK3 substrates. Via high-throughput homogeneous time-resolved fluorescence screen coupled with biochemical, cellular, and biophysical assays, we identify a potent LMTK3 small-molecule inhibitor (C28). Functional and mechanistic studies reveal LMTK3 is a heat shock protein 90 (HSP90) client protein, requiring HSP90 for folding and stability, while C28 promotes proteasome-mediated degradation of LMTK3. Pharmacologic inhibition of LMTK3 decreases proliferation of cancer cell lines in the NCI-60 panel, with a concomitant increase in apoptosis in breast cancer cells, recapitulating effects of LMTK3 gene silencing. Furthermore, LMTK3 inhibition reduces growth of xenograft and transgenic breast cancer mouse models without displaying systemic toxicity at effective doses. Our data reinforce LMTK3 as a druggable target for cancer therapy.
|
Nov 2020
|
|
I19-Small Molecule Single Crystal Diffraction
|
Weihua
Ning
,
Jinke
Bao
,
Yuttapoom
Puttisong
,
Fabrizo
Moro
,
Libor
Kobera
,
Seiya
Shimono
,
Linqin
Wang
,
Fuxiang
Ji
,
Maria
Cuartero
,
Shogo
Kawaguchi
,
Sabina
Abbrent
,
Hiroki
Ishibashi
,
Roland
De Marco
,
Irina A.
Bouianova
,
Gaston A.
Crespo
,
Yoshiki
Kubota
,
Jiri
Brus
,
Duck Young
Chung
,
Licheng
Sun
,
Weimin M.
Chen
,
Mercouri G.
Kanatzidis
,
Feng
Gao
Diamond Proposal Number(s):
[20805]
Open Access
Abstract: Spintronics holds great potential for next-generation high-speed and low–power consumption information technology. Recently, lead halide perovskites (LHPs), which have gained great success in optoelectronics, also show interesting magnetic properties. However, the spin-related properties in LHPs originate from the spin-orbit coupling of Pb, limiting further development of these materials in spintronics. Here, we demonstrate a new generation of halide perovskites, by alloying magnetic elements into optoelectronic double perovskites, which provide rich chemical and structural diversities to host different magnetic elements. In our iron-alloyed double perovskite, Cs2Ag(Bi:Fe)Br6, Fe3+ replaces Bi3+ and forms FeBr6 clusters that homogenously distribute throughout the double perovskite crystals. We observe a strong temperature-dependent magnetic response at temperatures below 30 K, which is tentatively attributed to a weak ferromagnetic or antiferromagnetic response from localized regions. We anticipate that this work will stimulate future efforts in exploring this simple yet efficient approach to develop new spintronic materials based on lead-free double perovskites.
|
Nov 2020
|
|
I03-Macromolecular Crystallography
|
Sarah V.
Faull
,
Emma L. K.
Elliston
,
Bibek
Gooptu
,
Alistair M.
Jagger
,
Ibrahim
Aldobiyan
,
Adam
Redzej
,
Magd
Badaoui
,
Nina
Heyer-chauhan
,
S. Tamir
Rashid
,
Gary M.
Reynolds
,
David H.
Adams
,
Elena
Miranda
,
Elena V.
Orlova
,
James A.
Irving
,
David A.
Lomas
Diamond Proposal Number(s):
[17201]
Open Access
Abstract: The serpinopathies are among a diverse set of conformational diseases that involve the aberrant self-association of proteins into ordered aggregates. α1-Antitrypsin deficiency is the archetypal serpinopathy and results from the formation and deposition of mutant forms of α1-antitrypsin as “polymer” chains in liver tissue. No detailed structural analysis has been performed of this material. Moreover, there is little information on the relevance of well-studied artificially induced polymers to these disease-associated molecules. We have isolated polymers from the liver tissue of Z α1-antitrypsin homozygotes (E342K) who have undergone transplantation, labeled them using a Fab fragment, and performed single-particle analysis of negative-stain electron micrographs. The data show structural equivalence between heat-induced and ex vivo polymers and that the intersubunit linkage is best explained by a carboxyl-terminal domain swap between molecules of α1-antitrypsin.
|
Oct 2020
|
|
