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Instruments / Technical Area	Publication Details	Published
	Ultrasonic cavitation shock wave exfoliation dynamics of 2D materials revealed in situ by MHz XFEL imaging and multiphysics modeling 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 Science Advances 11 DOI: 10.1126/sciadv.ady9558 Open Access Show Abstract ▼ 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.	Nov 2025
	Pr and Pfr structures of plant phytochrome A Soshichiro Nagano , David Von Stetten , Kaoling Guan , Peng-Yuan Chen , Chen Song , Thomas Barends , Manfred S. Weiss , Christian G. Feiler , Katerina Dörner , Iñaki De Diego Martinez , Robin Schubert , Johan Bielecki , Lea Brings , Huijong Han , Konstantin Kharitonov , Chan Kim , Marco Kloos , Jayanath C. P. Koliyadu , Faisal H. M. Koua , Ekaterina Round , Abhisakh Sarma , Tokushi Sato , Christina Schmidt , Joana Valerio , Agnieszka Wrona , Joachim Schulz , Raphael De Wijn , Romain Letrun , Richard Bean , Adrian Mancuso , Karsten Heyne , Jon Hughes Nature Communications 16 DOI: 10.1038/s41467-025-60738-w Open Access Show Abstract ▼ Abstract: Phytochromes are biliprotein photoreceptors widespread amongst microorganisms and ubiquitous in plants where they control developmental processes as diverse as germination, stem elongation and floral induction through the photoconversion of inactive Pr to the Pfr signalling state. Here we report crystal structures of the chromophore-binding module of soybean phytochrome A, including ~2.2 Å XFEL structures of Pr and Pfr at ambient temperature and high resolution cryogenic structures of Pr. In the Pfr structure, the chromophore is exposed to the medium, the D-ring remaining α-facial following the likely clockwise photoflip. The chromophore shifts within its pocket, while its propionate side chains, their partners as well as three neighbouring tyrosines shift radically. Helices near the chromophore show substantial shifts that might represent components of the light signal. These changes reflect those in bacteriophytochromes despite their quite different signalling mechanisms, implying that fundamental aspects of phytochrome photoactivation have been repurposed for photoregulation in the eukaryotic plant.	Jun 2025
	Real-time analysis of liquid jet sample delivery stability for an X-ray free-electron laser using machine vision Jaydeep Patel , Adam Round , Raphael De Wijn , Mohammad Vakili , Gabriele Giovanetti , Diogo Filipe Monrroy Vilan E Melo , Juncheng E , Marcin Sikorski , Jayanth Koliyadu , Faisal H. M. Koua , Tokushi Sato , Adrian Mancuso , Andrew Peele , Brian Abbey Journal Of Applied Crystallography 57 DOI: 10.1107/S1600576724009853 Open Access Show Abstract ▼ Abstract: Automated evaluation of optical microscopy images of liquid jets, commonly used for sample delivery at X-ray free-electron lasers (XFELs), enables real-time tracking of the jet position and liquid jet hit rates, defined here as the proportion of XFEL pulses intersecting with the liquid jet. This method utilizes machine vision for preprocessing, feature extraction, segmentation and jet detection as well as tracking to extract key physical characteristics (such as the jet angle) from optical microscopy images captured during experiments. To determine the effectiveness of these tools in monitoring jet stability and enhancing sample delivery efficiency, we conducted XFEL experiments with various sample compositions (pure water, buffer and buffer with crystals), nozzle designs and jetting conditions. We integrated our real-time analysis algorithm into the Karabo control system at the European XFEL. The results indicate that the algorithm performs well in monitoring the jet angle and provides a quantitative characterization of liquid jet stability through optical image analysis conducted during experiments.	Dec 2024
B21-High Throughput SAXS	Microsecond time-resolved X-ray scattering by utilizing MHz repetition rate at second-generation XFELs Patrick E. Konold , Leonardo Monrroy , Alfredo Bellisario , Diogo Filipe , Patrick Adams , Roberto Alvarez , Richard Bean , Johan Bielecki , Szabolcs Bódizs , Gabriel Ducrocq , Helmut Grubmueller , Richard A. Kirian , Marco Kloos , Jayanath C. P. Koliyadu , Faisal H. M. Koua , Taru Larkiala , Romain Letrun , Fredrik Lindsten , Michael Maihöfer , Andrew Martin , Petra Mészáros , Jennifer Mutisya , Amke Nimmrich , Kenta Okamoto , Adam Round , Tokushi Sato , Joana Valerio , Daniel Westphal , August Wollter , Tej Varma Yenupuri , Tong You , Filipe Maia , Sebastian Westenhoff Nature Methods 17 DOI: 10.1038/s41592-024-02344-0 Open Access Show Abstract ▼ Abstract: Detecting microsecond structural perturbations in biomolecules has wide relevance in biology, chemistry and medicine. Here we show how MHz repetition rates at X-ray free-electron lasers can be used to produce microsecond time-series of protein scattering with exceptionally low noise levels of 0.001%. We demonstrate the approach by examining Jɑ helix unfolding of a light-oxygen-voltage photosensory domain. This time-resolved acquisition strategy is easy to implement and widely applicable for direct observation of structural dynamics of many biochemical processes.	Jul 2024
	Heterologous expression, purification and structural features of native Dictyostelium discoideum dye-decolorizing peroxidase bound to a natively incorporated heme Özlem Kalkan , Sravya Kantamneni , Lea Brings , Huijong Han , Richard Bean , Adrian P. Mancuso , Faisal H. M. Koua Frontiers In Chemistry 11 DOI: 10.3389/fchem.2023.1220543 Open Access Show Abstract ▼ Abstract: The Dictyostelium discoideum dye-decolorizing peroxidase (DdDyP) is a newly discovered peroxidase, which belongs to a unique class of heme peroxidase family that lacks homology to the known members of plant peroxidase superfamily. DdDyP catalyzes the H2O2-dependent oxidation of a wide-spectrum of substrates ranging from polycyclic dyes to lignin biomass, holding promise for potential industrial and biotechnological applications. To study the molecular mechanism of DdDyP, highly pure and functional protein with a natively incorporated heme is required, however, obtaining a functional DyP-type peroxidase with a natively bound heme is challenging and often requires addition of expensive biosynthesis precursors. Alternatively, a heme in vitro reconstitution approach followed by a chromatographic purification step to remove the excess heme is often used. Here, we show that expressing the DdDyP peroxidase in ×2 YT enriched medium at low temperature (20°C), without adding heme supplement or biosynthetic precursors, allows for a correct native incorporation of heme into the apo-protein, giving rise to a stable protein with a strong Soret peak at 402 nm. Further, we crystallized and determined the native structure of DdDyP at a resolution of 1.95 Å, which verifies the correct heme binding and its geometry. The structural analysis also reveals a binding of two water molecules at the distal site of heme plane bridging the catalytic residues (Arg239 and Asp149) of the GXXDG motif to the heme-Fe(III) via hydrogen bonds. Our results provide new insights into the geometry of native DdDyP active site and its implication on DyP catalysis.	Aug 2023
	Mix-and-extrude: high-viscosity sample injection towards time-resolved protein crystallography Mohammad Vakili , Huijong Han , Christina Schmidt , Agnieszka Wrona , Marco Kloos , Iñaki De Diego , Katerina Dörner , Tian Geng , Chan Kim , Faisal H. M. Koua , Diogo V. M. Melo , Mathieu Rappas , Adam Round , Ekaterina Round , Marcin Sikorski , Joana Valerio , Tiankun Zhou , Kristina Lorenzen , Joachim Schulz Journal Of Applied Crystallography 56 DOI: 10.1107/S1600576723004405 Open Access Show Abstract ▼ Abstract: Time-resolved crystallography enables the visualization of protein molecular motion during a reaction. Although light is often used to initiate reactions in time-resolved crystallography, only a small number of proteins can be activated by light. However, many biological reactions can be triggered by the interaction between proteins and ligands. The sample delivery method presented here uses a mix-and-extrude approach based on 3D-printed microchannels in conjunction with a micronozzle. The diffusive mixing enables the study of the dynamics of samples in viscous media. The device design allows mixing of the ligands and protein crystals in 2 to 20 s. The device characterization using a model system (fluorescence quenching of iq-mEmerald proteins by copper ions) demonstrated that ligand and protein crystals, each within lipidic cubic phase, can be mixed efficiently. The potential of this approach for time-resolved membrane protein crystallography to support the development of new drugs is discussed.	Aug 2023
	Antiviral activity of natural phenolic compounds in complex at an allosteric site of SARS-CoV-2 papain-like protease Vasundara Srinivasan , Hévila Brognaro , Prince R. Prabhu , Edmarcia Elisa De Souza , Sebastian Günther , Patrick Y. A. Reinke , Thomas J. Lane , Helen Ginn , Huijong Han , Wiebke Ewert , Janina Sprenger , Faisal H. M. Koua , Sven Falke , Nadine Werner , Hina Andaleeb , Najeeb Ullah , Bruno Alves Franca , Mengying Wang , Angélica Luana C. Barra , Markus Perbandt , Martin Schwinzer , Christina Schmidt , Lea Brings , Kristina Lorenzen , Robin Schubert , Rafael Rahal Guaragna Machado , Erika Donizette Candido , Danielle Bruna Leal Oliveira , Edison Luiz Durigon , Stephan Niebling , Angelica Struve Garcia , Oleksandr Yefanov , Julia Lieske , Luca Gelisio , Martin Domaracky , Philipp Middendorf , Michael Groessler , Fabian Trost , Marina Galchenkova , Aida Rahmani Mashhour , Sofiane Saouane , Johanna Hakanpää , Markus Wolf , Maria Garcia Alai , Dusan Turk , Arwen R. Pearson , Henry N. Chapman , Winfried Hinrichs , Carsten Wrenger , Alke Meents , Christian Betzel Communications Biology 5 DOI: 10.1038/s42003-022-03737-7 Open Access Show Abstract ▼ Abstract: SARS-CoV-2 papain-like protease (PLpro) covers multiple functions. Beside the cysteine-protease activity, facilitating cleavage of the viral polypeptide chain, PLpro has the additional and vital function of removing ubiquitin and ISG15 (Interferon-stimulated gene 15) from host-cell proteins to support coronaviruses in evading the host’s innate immune responses. We identified three phenolic compounds bound to PLpro, preventing essential molecular interactions to ISG15 by screening a natural compound library. The compounds identified by X-ray screening and complexed to PLpro demonstrate clear inhibition of PLpro in a deISGylation activity assay. Two compounds exhibit distinct antiviral activity in Vero cell line assays and one inhibited a cytopathic effect in non-cytotoxic concentration ranges. In the context of increasing PLpro mutations in the evolving new variants of SARS-CoV-2, the natural compounds we identified may also reinstate the antiviral immune response processes of the host that are down-regulated in COVID-19 infections.	Aug 2022
	X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease Sebastian Gunther , Patrick Y. A. Reinke , Yaiza Fernández-García , Julia Lieske , Thomas J. Lane , Helen M. Ginn , Faisal H. M. Koua , Christiane Ehrt , Wiebke Ewert , Dominik Oberthuer , Oleksandr Yefanov , Susanne Meier , Kristina Lorenzen , Boris Krichel , Janine-Denise Kopicki , Luca Gelisio , Wolfgang Brehm , Ilona Dunkel , Brandon Seychell , Henry Gieseler , Brenna Norton-Baker , Beatriz Escudero-Pérez , Martin Domaracky , Sofiane Saouane , Alexandra Tolstikova , Thomas A. White , Anna Hänle , Michael Groessler , Holger Fleckenstein , Fabian Trost , Marina Galchenkova , Yaroslav Gevorkov , Chufeng Li , Salah Awel , Ariana Peck , Miriam Barthelmess , Frank Schluenzen , Paulraj Lourdu Xavier , Nadine Werner , Hina Andaleeb , Najeeb Ullah , Sven Falke , Vasundara Srinivasan , Bruno Alves França , Martin Schwinzer , Hévila Brognaro , Cromarte Rogers , Diogo Melo , Joanna J. Zaitseva-Doyle , Juraj Knoska , Gisel E. Peña-Murillo , Aida Rahmani Mashhour , Vincent Hennicke , Pontus Fischer , Johanna Hakanpää , Jan Meyer , Philip Gribbon , Bernhard Ellinger , Maria Kuzikov , Markus Wolf , Andrea R. Beccari , Gleb Bourenkov , David Von Stetten , Guillaume Pompidor , Isabel Bento , Saravanan Panneerselvam , Ivars Karpics , Thomas R. Schneider , Maria Marta Garcia-Alai , Stephan Niebling , Christian Günther , Christina Schmidt , Robin Schubert , Huijong Han , Juliane Boger , Diana C. F. Monteiro , Linlin Zhang , Xinyuanyuan Sun , Jonathan Pletzer-Zelgert , Jan Wollenhaupt , Christian G. Feiler , Manfred S. Weiss , Eike-Christian Schulz , Pedram Mehrabi , Katarina Karničar , Aleksandra Usenik , Jure Loboda , Henning Tidow , Ashwin Chari , Rolf Hilgenfeld , Charlotte Uetrecht , Russell Cox , Andrea Zaliani , Tobias Beck , Matthias Rarey , Stephan Günther , Dusan Turk , Winfried Hinrichs , Henry N. Chapman , Arwen R. Pearson , Christian Betzel , Alke Meents Science DOI: 10.1126/science.abf7945 Open Access Show Abstract ▼ Abstract: The coronavirus disease (COVID-19) caused by SARS-CoV-2 is creating tremendous human suffering. To date, no effective drug is available to directly treat the disease. In a search for a drug against COVID-19, we have performed a high-throughput X-ray crystallographic screen of two repurposing drug libraries against the SARS-CoV-2 main protease (Mpro), which is essential for viral replication. In contrast to commonly applied X-ray fragment screening experiments with molecules of low complexity, our screen tested already approved drugs and drugs in clinical trials. From the three-dimensional protein structures, we identified 37 compounds that bind to Mpro. In subsequent cell-based viral reduction assays, one peptidomimetic and six non-peptidic compounds showed antiviral activity at non-toxic concentrations. We identified two allosteric binding sites representing attractive targets for drug development against SARS-CoV-2.	Apr 2021

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