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Kang
Xiang
,
Ling
Qin
,
Shi
Huang
,
Hongyuan
Song
,
Vasilii
Bazhenov
,
Sarlota
Birnšteinová
,
Raphael
De Wijn
,
Jayanath C. P.
Koliyadu
,
Faisal H. M.
Koua
,
Adam
Round
,
Ekaterina
Round
,
Abhisakh
Sarma
,
Tokushi
Sato
,
Marcin
Sikorski
,
Yuhe
Zhang
,
Eleni
Myrto Asimakopoulou
,
Pablo
Villanueva-Perez
,
Kyriakos
Porfyrakis
,
Iakovos
Tzanakis
,
Dmitry G.
Eskin
,
Nicole
Grobert
,
Adrian
Mancuso
,
Richard
Bean
,
Patrik
Vagovic
,
Jiawei
Mi
,
Valerio
Bellucci
Open Access
Abstract: Using megahertz x-ray free electron laser imaging with x-ray pulses of ~25 femtoseconds and a machine-learning strategy, we have conducted comprehensive in situ imaging studies on the dynamics of cavitation bubble clouds in ultrasound fields at the SPB/SFX beamline of the European XFEL. The research unambiguously revealed the quasi-simultaneous implosion of multiple bubbles and simultaneous collapse of bubble cloud in nanosecond scale and their dynamic impacts onto two-dimensional (2D) materials for layer exfoliation. We have also performed multiphysics modeling to simulate the shock wave emission, propagation, impact, and stresses produced. We elucidated the critical conditions for producing instant or fatigue exfoliation and the effects of bonding strengths and structural defects on the exfoliation rate. The discoveries have filled the long-standing missing knowledge gaps in the underlying physics of exfoliating 2D materials in ultrasound fields, providing a solid theoretical foundation for optimizing and scaling-up operation to produce 2D materials in a much more cost-effective and sustainable way.
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Nov 2025
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I04-Macromolecular Crystallography
|
Pyung-Gang
Lee
,
Linxiang
Yin
,
Xin
Wei
,
Jingyuan
Shi
,
Geoffrey
Masuyer
,
Travis G.
Wentz
,
Pengsheng
Chen
,
Ying
Xu
,
Junjie
Liang
,
Haonan
Zhang
,
Sara
Persson Kosenina
,
Briallen
Lobb
,
Michael
Mansfield
,
Sarjeet S.
Gill
,
Sabine
Pellett
,
Pal
Stenmark
,
Andrew C.
Doxey
,
Min
Dong
Open Access
Abstract: Insecticidal bacterial proteins play key roles in insect-bacteria interactions and have been used as biopesticides. Here, we identify two insecticidal proteins in Paeniclostridium ghonii, designated PG-toxin 1 (PG1) and PG-toxin 2 (PG2), which are homologs of botulinum neurotoxins (BoNTs). Unlike BoNTs, PG1 and PG2 contain two separate proteins: One is the protease light chain (LC), and the other is the heavy chain containing the translocation domain and the receptor binding domain. Crystal and cryo–electron microscopy structures show a conserved BoNT-like architecture but without an interchain disulfide bond. Functional characterizations establish that the LCs of PG1 and PG2 cleave insect synaptosomal–associated protein 25 (SNAP25), but not human or rat SNAP25, and microinjection of PG1 and PG2 caused paralysis and death in Drosophila and Aedes mosquitoes. These findings identified unique two-component BoNT-like insecticidal proteins, revealing insights into the evolution of the BoNT family of toxins, and broadening our understanding of bacteria that can be used for biopest controls.
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Nov 2025
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DIAD-Dual Imaging and Diffraction Beamline
|
Bruno
Becker-Kerber
,
Jochen J.
Brocks
,
Nathaly L.
Archilha
,
Cristiane B.
Rodella
,
Valeri
Petkov
,
Eduardo R.
Deazevedo
,
Tairine
Pimentel
,
Rodrigo
Garcia
,
Duane
Petts
,
Janina
Czas
,
Omid H.
Ardakani
,
Anthony
Chappaz
,
Ângela
Albuquerque
,
Javier
Ortega-Hernández
,
Rudy
Lerosey-Aubril
,
Michael A.
Kipp
,
Benjamin
Johnson
,
Mathieu
Thoury
,
Cecilia M. A.
Oliveira
,
Hannah H. L. S. M.
Pimentel
,
Raul O.
Freitas
,
Flavio C.
Vicentin
,
Luiz G. F.
Borges
,
Jonathan
Almer
,
Jun-Sang
Park
,
Carla C.
Polo
,
Gilmar
Kerber
,
Lucas
Del Mouro
,
Milene
Figueiredo
,
Gustavo M. E. M.
Prado
,
Sharif
Ahmed
,
Miguel A. S.
Basei
Diamond Proposal Number(s):
[32319]
Open Access
Abstract: The origin of terrestrial life and ecosystems fundamentally changed the biosphere. Lichens, symbiotic fungi-algae partnerships, are crucial to nutrient cycling and carbon fixation today, yet their evolutionary history during the evolution of terrestrial ecosystems remains unclear due to a scarce fossil record. We demonstrate that the enigmatic Devonian fossil Spongiophyton from Brazil captures one of the earliest and most widespread records of lichens. The presence of internal hyphae networks, algal cells, possible reproductive structures, calcium oxalate pseudomorphs, abundant nitrogenous compounds, and fossil lipid composition confirms that it was among the first widespread representatives of lichenized fungi in Earth’s history. Spongiophyton abundance and wide paleogeographic distribution in Devonian successions reveal an ecologically prominent presence of lichens during the late stages of terrestrial colonization, just before the evolution of complex forest ecosystems.
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Oct 2025
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Krios I-Titan Krios I at Diamond
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Diamond Proposal Number(s):
[25452]
Open Access
Abstract: While archaeal viruses show a stunning diversity of morphologies, many bear a notable resemblance to tailed bacterial phages. This raises fundamental questions: Do all tailed viruses share a common origin and do they infect their hosts in similar ways? Answering these questions requires high-resolution structural insights, yet no complete atomic models of archaeal viruses have been available. Here, we present the near-atomic resolution structure of Haloferax tailed virus 1 (HFTV1), an archaeal virus thriving in extreme salinity. Using cryo–electron microscopy, we resolve the architecture and assembly of all structural proteins and capture conformational transitions associated with DNA ejection. Our data reveal genome spooling within the capsid and identify putative receptor-binding and catalytic sites for host recognition and infection. These findings uncover key mechanisms of archaeal virus assembly, principles of virus-host interactions, and evolutionary links connecting archaeal, bacterial, and eukaryotic viruses.
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Oct 2025
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Krios I-Titan Krios I at Diamond
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Rocio
Arranz
,
César
Santiago
,
Simonas
Masiulis
,
Esperanza
Rivera-De-Torre
,
Juan
Palacios-Ortega
,
Diego
Carlero
,
Diego
Heras-Márquez
,
José G.
Gavilanes
,
Ernesto
Arias-Palomo
,
Álvaro
Martínez-Del-Pozo
,
Sara
García-Linares
,
Jaime
Martin-Benito
Diamond Proposal Number(s):
[22006, 30374]
Open Access
Abstract: Pore-forming proteins exemplify the transformative potential of biological molecules. Produced as soluble monomers, they assemble into multimeric membrane-inserted complexes in response to specific membrane environments. Actinoporins, a class of pore-forming proteins from sea anemones, target membranes to kill cells. Here, we report cryogenic electron microscopy structures of two actinoporins, fragaceatoxin C and sticholysin II, reconstituted in lipid membranes. The structures reveal an ordered arrangement of dozens of lipid molecules that form an integral part of the pore architecture. We also captured distinct oligomeric intermediates, arc-shaped assemblies with monomers in transitional conformations, representing key snapshots along the pore formation pathway. These data provide direct structural evidence for a stepwise mechanism in which monomers sequentially bind the membrane and undergo conformational changes that drive pore assembly and membrane disruption. Our findings reveal how these proteins reshape membranes and offer mechanistic insights into their cytolytic activity. This work broadens our understanding of pore-forming proteins, which are gaining increasing relevance in diverse biotechnological applications.
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Sep 2025
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I04-Macromolecular Crystallography
I24-Microfocus Macromolecular Crystallography
|
Conchita Fraguas
Bringas
,
Mohd Syed
Ahanger
,
Joyceline
Cuenco
,
Hongling
Liu
,
Alex B.
Addinsall
,
Maria
Lindahl
,
Ashley J.
Ovens
,
Mark A.
Febbraio
,
Marc
Foretz
,
Olga
Göransson
,
John W.
Scott
,
Elton
Zeqiraj
,
Kei
Sakamoto
Diamond Proposal Number(s):
[29074, 35120]
Open Access
Abstract: Inhibition of adenosine 5′-monophosphate (AMP)–activated protein kinase (AMPK) is under increasing investigation for its therapeutic potential in many diseases. Existing AMPK inhibitors are however limited, with poor selectivity and substantial off-target effects. Here, we provide mechanistic insights and describe the cellular selectivity of the recently identified AMPK inhibitor BAY-3827. A 2.5-Å cocrystal structure of the AMPK kinase domain with BAY-3827 revealed distinct features including a disulfide bridge between the αD helix Cys106 and the activation loop residue Cys174. This bridge appears to stabilize the activation loop such that Asn162 repositions the Asp-Phe-Gly (DFG) motif Phe158 toward the C-terminal lobe, displacing His137 and disrupting the regulatory spine, promoting an inactive kinase state. In hepatocytes, BAY-3827 blocked AMPK activator (MK-8722)–mediated phosphorylation of ACC1 and corresponding inhibition of lipogenesis. Transcriptome analysis revealed that BAY-3827 down-regulated ~30% of MK-8722–stimulated AMPK-dependent genes. We establish the molecular and cellular basis of BAY-3827’s selectivity and utility for delineating AMPK functions while highlighting its limitations.
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Aug 2025
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I14-Hard X-ray Nanoprobe
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Alexander
Triccas
,
Daniel M.
Chevrier
,
Mariana
Verezhak
,
Johannes
Ihli
,
Manuel
Guizar-Sicairos
,
Mirko
Holler
,
André
Scheffel
,
Noriaki
Ozaki
,
Virginie
Chamard
,
Rachel
Wood
,
Tilman A.
Grünewald
,
Fabio
Nudelman
Diamond Proposal Number(s):
[23602, 28868]
Open Access
Abstract: Coccolithophores are abundant marine phytoplankton that produce biomineralized calcite scales, called coccoliths, which sequester substantial amounts of carbon and play a substantial role in biogeochemical cycles. However, mechanisms underlying the storage and transport of ions essential for calcification remain unresolved. We used ptychographic x-ray computed tomography under cryogenic conditions to visualize intracellular calcium-rich structures involved in the storage of calcium ions in the coccolithophore species Chrysotila carterae. During calcification, we observed a range of structures, from small electron-dense bodies within larger compartments to denser and distributed globular compartments, before returning to small bodies once scale formation is complete. Nanobeam-scanning x-ray fluorescence measurements further revealed that these electron-dense bodies are rich in phosphorus and calcium (molar ratio of ~4:1). The dynamic nature of structures suggests that these bodies are part of the required cellular calcium ion transport pathways, a fundamental process critical for understanding the response of coccolithophores to climate change.
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Jul 2025
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I18-Microfocus Spectroscopy
|
R.
Kinet
,
M.
Bourdenx
,
S.
Dovero
,
M.
Darricau
,
M.-L.
Arotcarena
,
S.
Camus
,
G.
Porras
,
M.-L.
Thiolat
,
I.
Trigo-Damas
,
S.
Bohic
,
M.
Morari
,
E.
Doudnikoff
,
M.
Goikoetxea
,
S.
Claverol
,
C.
Tokarski
,
N.
Kruse
,
B.
Mollenhauer
,
C.
Estrada
,
N.
Garcia-Carrillo
,
M. T.
Herrero
,
M.
Vila
,
J. A.
Obeso
,
E.
Bezard
,
B.
Dehay
Diamond Proposal Number(s):
[13009]
Open Access
Abstract: The presence of α-synuclein (α-syn) aggregates, such as Lewy bodies in patients with Parkinson’s disease (PD), contributes to dopaminergic cell death. Injection of PD patient–derived α-syn in nonhuman primates has illustrated the exquisite vulnerability of primate dopaminergic neurons. Here, we aimed to elucidate the temporal and spatial pathological changes induced by two distinct α-syn pathogenic structures, having large or small sizes. To unravel the underlying molecular pathways, we conducted a proteomic analysis of the putamen and the entorhinal cortex, two brain regions carrying notable α-syn pathology. We demonstrate that distinct assemblies of α-syn aggregates drive unique pathogenic changes that ultimately result in a comparable extent of nigrostriatal degeneration at the level of nigral dopaminergic neuron cell bodies and striatal dopaminergic terminals. More broadly, our findings identify pathogenic trajectories associated with large or small α-syn aggregates, suggesting the existence of several possible concomitant pathogenic routes in PD.
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Jun 2025
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Krios III-Titan Krios III at Diamond
|
Diamond Proposal Number(s):
[29812]
Open Access
Abstract: During HIV-1 maturation, the matrix (MA) lattice underlying the viral membrane undergoes a structural rearrangement, and the newly released capsid (CA) protein forms a mature CA. While it is well established that CA formation is essential for particle infectivity, the functional role of MA structural maturation remains unclear. Here, we examine maturation of an MA triple mutant, L20K/E73K/A82T, which, despite replicating similarly to wild-type (WT) in some cell lines, exhibits distinct biochemical behaviors that suggest altered MA-MA interactions. Cryo–electron tomography with subtomogram averaging reveals that, although the MA lattice in immature L20K/E73K/A82T virions closely resembles that of the WT, mature L20K/E73K/A82T virions lack a detectable MA lattice. All-atom molecular dynamics simulations suggest that this absence results from destabilized inter-trimer MA interactions in mature L20K/E73K/A82T mutant virions. These findings suggest that an ordered, membrane-associated mature MA lattice is not essential for HIV-1 infectivity, providing insights into the structural requirements for HIV-1 particle maturation and generation of infectious particles.
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May 2025
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Luisa
Sauthof
,
Michal
Szczepek
,
Andrea
Schmidt
,
Asmit
Bhowmick
,
Medhanjali
Dasgupta
,
Megan J.
Mackintosh
,
Sheraz
Gul
,
Franklin D.
Fuller
,
Ruchira
Chatterjee
,
Iris D.
Young
,
Norbert
Michael
,
Nicolas Andreas
Heyder
,
Brian
Bauer
,
Anja
Koch
,
Isabel
Bogacz
,
In-Sik
Kim
,
Philipp S.
Simon
,
Agata
Butryn
,
Pierre
Aller
,
Volha U.
Chukhutsina
,
James M.
Baxter
,
Christopher D. M.
Hutchison
,
Dorothee
Liebschner
,
Billy
Poon
,
Nicholas K.
Sauter
,
Mitchell D.
Miller
,
George N.
Phillips
,
Roberto
Alonso-Mori
,
Mark S.
Hunter
,
Alexander
Batyuk
,
Shigeki
Owada
,
Kensuke
Tono
,
Rie
Tanaka
,
Jasper J.
Van Thor
,
Norbert
Krauß
,
Tilman
Lamparter
,
Aaron S.
Brewster
,
Igor
Schapiro
,
Allen M.
Orville
,
Vittal K.
Yachandra
,
Junko
Yano
,
Peter
Hildebrandt
,
Jan F.
Kern
,
Patrick
Scheerer
Open Access
Abstract: The photoreaction and commensurate structural changes of a chromophore within biological photoreceptors elicit conformational transitions of the protein promoting the switch between deactivated and activated states. We investigated how this coupling is achieved in a bacterial phytochrome variant, Agp2-PAiRFP2. Contrary to classical protein crystallography, which only allows probing (cryo-trapped) stable states, we have used time-resolved serial femtosecond x-ray crystallography (tr-SFX) and pump-probe techniques with various illumination and delay times with respect to photoexcitation of the parent Pfr state. Thus, structural data for seven time frames were sorted into groups of molecular events along the reaction coordinate. They range from chromophore isomerization to the formation of Meta-F, the intermediate that precedes the functional relevant secondary structure transition of the tongue. Structural data for the early events were used to calculate the photoisomerization pathway to complement the experimental data. Late events allow identifying the molecular switch that is linked to the intramolecular proton transfer as a prerequisite for the following structural transitions.
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May 2025
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