I06-Nanoscience
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Filip
Krizek
,
Sonka
Reimers
,
Zdeněk
Kašpar
,
Alberto
Marmodoro
,
Jan
Michalička
,
Ondřej
Man
,
Alexander
Edström
,
Oliver J.
Amin
,
Kevin W.
Edmonds
,
Richard P.
Campion
,
Francesco
Maccherozzi
,
Sarnjeet S.
Dhesi
,
Jan
Zubáč
,
Domink
Kriegner
,
Dina
Carbone
,
Jakub
Železný
,
Karel
Výborný
,
Kamil
Olejník
,
Vít
Novák
,
Jan
Rusz
,
Juan-Carlos
Idrobo
,
Peter
Wadley
,
Tomas
Jungwirth
Diamond Proposal Number(s):
[22437]
Open Access
Abstract: The interest in understanding scaling limits of magnetic textures such as domain walls spans the entire field of magnetism from its physical fundamentals to applications in information technologies. Here, we explore antiferromagnetic CuMnAs in which imaging by x-ray photoemission reveals the presence of magnetic textures down to nanoscale, reaching the detection limit of this established microscopy in antiferromagnets. We achieve atomic resolution by using differential phase-contrast imaging within aberration-corrected scanning transmission electron microscopy. We identify abrupt domain walls in the antiferromagnetic film corresponding to the Néel order reversal between two neighboring atomic planes. Our work stimulates research of magnetic textures at the ultimate atomic scale and sheds light on electrical and ultrafast optical antiferromagnetic devices with magnetic field–insensitive neuromorphic functionalities.
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Apr 2022
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I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
I24-Microfocus Macromolecular Crystallography
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Nathan R.
Zaccai
,
Zuzana
Kadlecova
,
Veronica
Kane Dickson
,
Kseniya
Korobchevskaya
,
Jan
Kamenicky
,
Oleksiy
Kovtun
,
Perunthottathu K.
Umasankar
,
Antoni G.
Wrobel
,
Jonathan G. G.
Kaufman
,
Sally R.
Gray
,
Kun
Qu
,
Philip R.
Evans
,
Marco
Fritzsche
,
Filip
Sroubek
,
Stefan
Höning
,
John A. G.
Briggs
,
Bernard T.
Kelly
,
David J.
Owen
,
Linton M.
Traub
Abstract: Clathrin-mediated endocytosis (CME) is the main mechanism by which mammalian cells control their cell surface proteome. Proper operation of the pivotal CME cargo adaptor AP2 requires membrane-localized Fer/Cip4 homology domain-only proteins (FCHO). Here, live-cell enhanced total internal reflection fluorescence–structured illumination microscopy shows that FCHO marks sites of clathrin-coated pit (CCP) initiation, which mature into uniform-sized CCPs comprising a central patch of AP2 and clathrin corralled by an FCHO/Epidermal growth factor potential receptor substrate number 15 (Eps15) ring. We dissect the network of interactions between the FCHO interdomain linker and AP2, which concentrates, orients, tethers, and partially destabilizes closed AP2 at the plasma membrane. AP2’s subsequent membrane deposition drives its opening, which triggers FCHO displacement through steric competition with phosphatidylinositol 4,5-bisphosphate, clathrin, cargo, and CME accessory factors. FCHO can now relocate toward a CCP’s outer edge to engage and activate further AP2s to drive CCP growth/maturation.
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Apr 2022
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Krios I-Titan Krios I at Diamond
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Pu
Qian
,
Alastair T.
Gardiner
,
Ivana
Šímová
,
Katerina
Naydenova
,
Tristan I.
Croll
,
Philip J.
Jackson
,
Nupur
Nupur
,
Miroslav
Kloz
,
Petra
Čubáková
,
Marek
Kuzma
,
Yonghui
Zeng
,
Pablo
Castro-Hartmann
,
Bart
Van Knippenberg
,
Kenneth N.
Goldie
,
David
Kaftan
,
Pavel
Hrouzek
,
Jan
Hájek
,
Jon
Agirre
,
C. Alistair
Siebert
,
David
Bína
,
Kasim
Sader
,
Henning
Stahlberg
,
Roman
Sobotka
,
Christopher J.
Russo
,
Tomáš
Polívka
,
C. Neil
Hunter
,
Michal
Koblížek
Diamond Proposal Number(s):
[29785]
Open Access
Abstract: Phototrophic Gemmatimonadetes evolved the ability to use solar energy following horizontal transfer of photosynthesis-related genes from an ancient phototrophic proteobacterium. The electron cryo-microscopy structure of the Gemmatimonas phototrophica photosystem at 2.4 Å reveals a unique, double-ring complex. Two unique membrane-extrinsic polypeptides, RC-S and RC-U, hold the central type 2 reaction center (RC) within an inner 16-subunit light-harvesting 1 (LH1) ring, which is encircled by an outer 24-subunit antenna ring (LHh) that adds light-gathering capacity. Femtosecond kinetics reveal the flow of energy within the RC-dLH complex, from the outer LHh ring to LH1 and then to the RC. This structural and functional study shows that G. phototrophica has independently evolved its own compact, robust, and highly effective architecture for harvesting and trapping solar energy.
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Feb 2022
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I03-Macromolecular Crystallography
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Theresa
Kissel
,
Lise
Hafkenscheid
,
Joanneke C.
Kwekkeboom
,
Changrong
Ge
,
Linda M.
Slot
,
Marco
Cavallari
,
Yibo
He
,
Karin A.
Van Schie
,
Rochelle D.
Vergroesen
,
Arieke S. B.
Kampstra
,
Sanne
Reijm
,
Gerrie
Stoeken-Rijsbergen
,
Carolien
Koeleman
,
Lennard M.
Voortman
,
Laura H.
Heitman
,
Bingze
Xu
,
Ger J. M.
Pruijn
,
Manfred
Wuhrer
,
Theo
Rispens
,
Tom W. J.
Huizinga
,
Hans Ulrich
Scherer
,
Michael
Reth
,
Rikard
Holmdahl
,
Rene E. M.
Toes
Diamond Proposal Number(s):
[15806]
Open Access
Abstract: The hallmark autoantibodies in rheumatoid arthritis are characterized by variable domain glycans (VDGs). Their abundant occurrence results from the selective introduction of N-linked glycosylation sites during somatic hypermutation, and their presence is predictive for disease development. However, the functional consequences of VDGs on autoreactive B cells remain elusive. Combining crystallography, glycobiology, and functional B cell assays allowed us to dissect key characteristics of VDGs on human B cell biology. Crystal structures showed that VDGs are positioned in the vicinity of the antigen-binding pocket, and dynamic modeling combined with binding assays elucidated their impact on binding. We found that VDG-expressing B cell receptors stay longer on the B cell surface and that VDGs enhance B cell activation. These results provide a rationale on how the acquisition of VDGs might contribute to the breach of tolerance of autoreactive B cells in a major human autoimmune disease.
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Feb 2022
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Piush
Behera
,
Molly A.
May
,
Fernando
Gómez-Ortiz
,
Sandhya
Susarla
,
Sujit
Das
,
Christopher T.
Nelson
,
Lucas
Caretta
,
Shang-Lin
Hsu
,
Margaret R.
Mccarter
,
Benjamin H.
Savitzky
,
Edward S.
Barnard
,
Archana
Raja
,
Zijian
Hong
,
Pablo
García-Fernandez
,
Stephen W.
Lovesey
,
Gerrit
Van Der Laan
,
Peter
Ercius
,
Colin
Ophus
,
Lane W.
Martin
,
Javier
Junquera
,
Markus B.
Raschke
,
Ramamoorthy
Ramesh
Open Access
Abstract: Polar textures have attracted substantial attention in recent years as a promising analog to spin-based textures in ferromagnets. Here, using optical second-harmonic generation–based circular dichroism, we demonstrate deterministic and reversible control of chirality over mesoscale regions in ferroelectric vortices using an applied electric field. The microscopic origins of the chirality, the pathway during the switching, and the mechanism for electric field control are described theoretically via phase-field modeling and second-principles simulations, and experimentally by examination of the microscopic response of the vortices under an applied field. The emergence of chirality from the combination of nonchiral materials and subsequent control of the handedness with an electric field has far-reaching implications for new electronics based on chirality as a field-controllable order parameter.
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Jan 2022
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Krios I-Titan Krios I at Diamond
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Jennifer
Ross
,
Zak
Mciver
,
Thomas
Lambert
,
Cecilia
Piergentili
,
Jasmine Emma
Bird
,
Kelly J.
Gallagher
,
Faye L.
Cruickshank
,
Patrick
James
,
Efrain
Zarazúa-Arvizu
,
Louise E.
Horsfall
,
Kevin J.
Waldron
,
Marcus D.
Wilson
,
C. Logan
Mackay
,
Arnaud
Basle
,
David J.
Clarke
,
Jon
Marles-Wright
Diamond Proposal Number(s):
[16637]
Open Access
Abstract: Encapsulins are protein nanocompartments that house various cargo enzymes, including a family of decameric ferritin-like proteins. Here, we study a recombinant Haliangium ochraceum encapsulin:encapsulated ferritin complex using cryo–electron microscopy and hydrogen/deuterium exchange mass spectrometry to gain insight into the structural relationship between the encapsulin shell and its protein cargo. An asymmetric single-particle reconstruction reveals four encapsulated ferritin decamers in a tetrahedral arrangement within the encapsulin nanocompartment. This leads to a symmetry mismatch between the protein cargo and the icosahedral encapsulin shell. The encapsulated ferritin decamers are offset from the interior face of the encapsulin shell. Using hydrogen/deuterium exchange mass spectrometry, we observed the dynamic behavior of the major fivefold pore in the encapsulin shell and show the pore opening via the movement of the encapsulin A-domain. These data will accelerate efforts to engineer the encapsulation of heterologous cargo proteins and to alter the permeability of the encapsulin shell via pore modifications.
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Jan 2022
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I03-Macromolecular Crystallography
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Alexander T.
Baker
,
Ryan J.
Boyd
,
Daipayan
Sarkar
,
Alicia
Teijeira-Crespo
,
Chun Kit
Chan
,
Emily
Bates
,
Kasim
Waraich
,
John
Vant
,
Eric
Wilson
,
Chloe D.
Truong
,
Magdalena
Lipka-Lloyd
,
Petra
Fromme
,
Josh
Vermaas
,
Dewight
Williams
,
Leeann
Machiesky
,
Meike
Heurich
,
Bolni M.
Nagalo
,
Lynda
Coughlan
,
Scott
Umlauf
,
Po-Lin
Chiu
,
Pierre J.
Rizkallah
,
Taylor S.
Cohen
,
Alan L.
Parker
,
Abhishek
Singharoy
,
Mitesh J.
Borad
Diamond Proposal Number(s):
[20147]
Open Access
Abstract: Vaccines derived from chimpanzee adenovirus Y25 (ChAdOx1), human adenovirus type 26 (HAdV-D26), and human adenovirus type 5 (HAdV-C5) are critical in combatting the severe acute respiratory coronavirus 2 (SARS-CoV-2) pandemic. As part of the largest vaccination campaign in history, ultrarare side effects not seen in phase 3 trials, including thrombosis with thrombocytopenia syndrome (TTS), a rare condition resembling heparin-induced thrombocytopenia (HIT), have been observed. This study demonstrates that all three adenoviruses deployed as vaccination vectors versus SARS-CoV-2 bind to platelet factor 4 (PF4), a protein implicated in the pathogenesis of HIT. We have determined the structure of the ChAdOx1 viral vector and used it in state-of-the-art computational simulations to demonstrate an electrostatic interaction mechanism with PF4, which was confirmed experimentally by surface plasmon resonance. These data confirm that PF4 is capable of forming stable complexes with clinically relevant adenoviruses, an important step in unraveling the mechanisms underlying TTS.
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Dec 2021
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I12-JEEP: Joint Engineering, Environmental and Processing
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Yongqiang
Chen
,
Holger
Steeb
,
Hamidreza
Erfani
,
Nikolaos K.
Karadimitriou
,
Monika
Walczak
,
Matthias
Ruf
,
Dongwon
Lee
,
Senyou
An
,
Sharul
Hasan
,
Thomas
Connolley
,
Nghia T.
Vo
,
Vahid
Niasar
Diamond Proposal Number(s):
[20072]
Open Access
Abstract: Experimental and field studies reported a significant discrepancy between the cleanup and contamination time scales, while its cause is not yet addressed. Using high-resolution fast synchrotron x-ray computed tomography, we characterized the solute transport in a fully saturated sand packing for both contamination and cleanup processes at similar hydrodynamic conditions. The discrepancy in the time scales has been demonstrated by the nonuniqueness of hydrodynamic dispersion coefficient versus injection rate (Péclet number). Observations show that in the mixed advection-diffusion regime, the hydrodynamic dispersion coefficient of cleanup is significantly larger than that of the contamination process. This nonuniqueness has been attributed to the concentration-dependent diffusion coefficient during the cocurrent and countercurrent advection and diffusion, present in contamination and cleanup processes. The new findings enhance our fundamental understanding of transport processes and improve our capability to estimate the transport time scales of chemicals or pollution in geological and engineering systems.
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Dec 2021
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Krios I-Titan Krios I at Diamond
Krios II-Titan Krios II at Diamond
Krios IV-Titan Krios IV at Diamond
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Tao
Ni
,
Yanan
Zhu
,
Zhengyi
Yang
,
Chaoyi
Xu
,
Yuriy
Chaban
,
Tanya
Nesterova
,
Jiying
Ning
,
Till
Böcking
,
Michael W.
Parker
,
Christina
Monnie
,
Jinwoo
Ahn
,
Juan R.
Perilla
,
Peijun
Zhang
Diamond Proposal Number(s):
[21004, 20223]
Open Access
Abstract: The viral capsid plays essential roles in HIV replication and is a major platform engaging host factors. To overcome challenges in study native capsid structure, we used the perfringolysin O to perforate the membrane of HIV-1 particles, thus allowing host proteins and small molecules to access the native capsid while improving cryo–electron microscopy image quality. Using cryo–electron tomography and subtomogram averaging, we determined the structures of native capsomers in the presence and absence of inositol hexakisphosphate (IP6) and cyclophilin A and constructed an all-atom model of a complete HIV-1 capsid. Our structures reveal two IP6 binding sites and modes of cyclophilin A interactions. Free energy calculations substantiate the two binding sites at R18 and K25 and further show a prohibitive energy barrier for IP6 to pass through the pentamer. Our results demonstrate that perfringolysin O perforation is a valuable tool for structural analyses of enveloped virus capsids and interactions with host cell factors.
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Nov 2021
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I03-Macromolecular Crystallography
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Itxaso
Anso
,
Luis G. M.
Basso
,
Lei
Wang
,
Alberto
Marina
,
Edgar D.
Páez-Pérez
,
Christian
Jäger
,
Floriane
Gavotto
,
Montse
Tersa
,
Sebastian
Perrone
,
F.-Xabier
Contreras
,
Jacques
Prandi
,
Martine
Gilleron
,
Carole L.
Linster
,
Francisco
Corzana
,
Todd L.
Lowary
,
Beatriz
Trastoy
,
Marcelo E.
Guerin
Diamond Proposal Number(s):
[20113]
Open Access
Abstract: Glycolipids are prominent components of bacterial membranes that play critical roles not only in maintaining the structural integrity of the cell but also in modulating host-pathogen interactions. PatA is an essential acyltransferase involved in the biosynthesis of phosphatidyl-myo-inositol mannosides (PIMs), key structural elements and virulence factors of Mycobacterium tuberculosis. We demonstrate by electron spin resonance spectroscopy and surface plasmon resonance that PatA is an integral membrane acyltransferase tightly anchored to anionic lipid bilayers, using a two-helix structural motif and electrostatic interactions. PatA dictates the acyl chain composition of the glycolipid by using an acyl chain selectivity “ruler.” We established this by a combination of structural biology, enzymatic activity, and binding measurements on chemically synthesized nonhydrolyzable acyl–coenzyme A (CoA) derivatives. We propose an interfacial catalytic mechanism that allows PatA to acylate hydrophobic PIMs anchored in the inner membrane of mycobacteria, through the use of water-soluble acyl-CoA donors.
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Oct 2021
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