1
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Falke S, Lieske J, Herrmann A, Loboda J, Karničar K, Günther S, Reinke PYA, Ewert W, Usenik A, Lindič N, Sekirnik A, Dretnik K, Tsuge H, Turk V, Chapman HN, Hinrichs W, Ebert G, Turk D, Meents A. Structural Elucidation and Antiviral Activity of Covalent Cathepsin L Inhibitors. J Med Chem 2024; 67:7048-7067. [PMID: 38630165 PMCID: PMC11089505 DOI: 10.1021/acs.jmedchem.3c02351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/22/2024] [Accepted: 03/28/2024] [Indexed: 05/15/2024]
Abstract
Emerging RNA viruses, including SARS-CoV-2, continue to be a major threat. Cell entry of SARS-CoV-2 particles via the endosomal pathway involves cysteine cathepsins. Due to ubiquitous expression, cathepsin L (CatL) is considered a promising drug target in the context of different viral and lysosome-related diseases. We characterized the anti-SARS-CoV-2 activity of a set of carbonyl- and succinyl epoxide-based inhibitors, which were previously identified as inhibitors of cathepsins or related cysteine proteases. Calpain inhibitor XII, MG-101, and CatL inhibitor IV possess antiviral activity in the very low nanomolar EC50 range in Vero E6 cells and inhibit CatL in the picomolar Ki range. We show a relevant off-target effect of CatL inhibition by the coronavirus main protease α-ketoamide inhibitor 13b. Crystal structures of CatL in complex with 14 compounds at resolutions better than 2 Å present a solid basis for structure-guided understanding and optimization of CatL inhibitors toward protease drug development.
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Affiliation(s)
- Sven Falke
- Center
for Free-Electron Laser Science CFEL, Deutsches
Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Julia Lieske
- Center
for Free-Electron Laser Science CFEL, Deutsches
Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Alexander Herrmann
- Institute
of Virology, Helmholtz Munich, Ingolstädter Landstraße 1, 85764 Neuherberg, Munich, Germany
| | - Jure Loboda
- Department
of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Katarina Karničar
- Department
of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Centre
of Excellence for Integrated Approaches in Chemistry and Biology of
Proteins, Jamova 39, 1000 Ljubljana, Slovenia
| | - Sebastian Günther
- Center
for Free-Electron Laser Science CFEL, Deutsches
Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Patrick Y. A. Reinke
- Center
for Free-Electron Laser Science CFEL, Deutsches
Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Wiebke Ewert
- Center
for Free-Electron Laser Science CFEL, Deutsches
Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Aleksandra Usenik
- Department
of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Centre
of Excellence for Integrated Approaches in Chemistry and Biology of
Proteins, Jamova 39, 1000 Ljubljana, Slovenia
| | - Nataša Lindič
- Department
of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Andreja Sekirnik
- Department
of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Klemen Dretnik
- Department
of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- The
Jožef Stefan International Postgraduate School, Jamova cesta 39, 1000 Ljubljana, Slovenia
| | - Hideaki Tsuge
- Faculty of
Life Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan
| | - Vito Turk
- Department
of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Henry N. Chapman
- Center
for Free-Electron Laser Science CFEL, Deutsches
Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
- Hamburg
Centre for Ultrafast Imaging, Universität
Hamburg, Luruper Chaussee
149, 22761 Hamburg, Germany
- Department
of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Winfried Hinrichs
- Institute
of Biochemistry, Universität Greifswald, Felix-Hausdorff-Str. 4, 17489 Greifswald, Germany
| | - Gregor Ebert
- Institute
of Virology, Helmholtz Munich, Ingolstädter Landstraße 1, 85764 Neuherberg, Munich, Germany
- Institute
of Virology, Technical University of Munich, Trogerstraße 30, 81675 Munich, Germany
| | - Dušan Turk
- Department
of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Centre
of Excellence for Integrated Approaches in Chemistry and Biology of
Proteins, Jamova 39, 1000 Ljubljana, Slovenia
| | - Alke Meents
- Center
for Free-Electron Laser Science CFEL, Deutsches
Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
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2
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Reinke PYA, Schubert R, Oberthür D, Galchenkova M, Rahmani Mashhour A, Günther S, Chretien A, Round A, Seychell BC, Norton-Baker B, Kim C, Schmidt C, Koua FHM, Tolstikova A, Ewert W, Peña Murillo GE, Mills G, Kirkwood H, Brognaro H, Han H, Koliyadu J, Schulz J, Bielecki J, Lieske J, Maracke J, Knoska J, Lorenzen K, Brings L, Sikorski M, Kloos M, Vakili M, Vagovic P, Middendorf P, de Wijn R, Bean R, Letrun R, Han S, Falke S, Geng T, Sato T, Srinivasan V, Kim Y, Yefanov OM, Gelisio L, Beck T, Doré AS, Mancuso AP, Betzel C, Bajt S, Redecke L, Chapman HN, Meents A, Turk D, Hinrichs W, Lane TJ. SARS-CoV-2 M pro responds to oxidation by forming disulfide and NOS/SONOS bonds. Nat Commun 2024; 15:3827. [PMID: 38714735 PMCID: PMC11076503 DOI: 10.1038/s41467-024-48109-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 04/19/2024] [Indexed: 05/10/2024] Open
Abstract
The main protease (Mpro) of SARS-CoV-2 is critical for viral function and a key drug target. Mpro is only active when reduced; turnover ceases upon oxidation but is restored by re-reduction. This suggests the system has evolved to survive periods in an oxidative environment, but the mechanism of this protection has not been confirmed. Here, we report a crystal structure of oxidized Mpro showing a disulfide bond between the active site cysteine, C145, and a distal cysteine, C117. Previous work proposed this disulfide provides the mechanism of protection from irreversible oxidation. Mpro forms an obligate homodimer, and the C117-C145 structure shows disruption of interactions bridging the dimer interface, implying a correlation between oxidation and dimerization. We confirm dimer stability is weakened in solution upon oxidation. Finally, we observe the protein's crystallization behavior is linked to its redox state. Oxidized Mpro spontaneously forms a distinct, more loosely packed lattice. Seeding with crystals of this lattice yields a structure with an oxidation pattern incorporating one cysteine-lysine-cysteine (SONOS) and two lysine-cysteine (NOS) bridges. These structures further our understanding of the oxidative regulation of Mpro and the crystallization conditions necessary to study this structurally.
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Affiliation(s)
- Patrick Y A Reinke
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Robin Schubert
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Dominik Oberthür
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Marina Galchenkova
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Aida Rahmani Mashhour
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Sebastian Günther
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Anaïs Chretien
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Adam Round
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Brandon Charles Seychell
- Institute of Physical Chemistry, Department of Chemistry, Universität Hamburg, Grindelallee 117, 20146, Hamburg, Germany
| | - Brenna Norton-Baker
- Max Plank Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
- Department of Chemistry, University of California at Irvine, Irvine, CA, 92697-2025, USA
| | - Chan Kim
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Faisal H M Koua
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Alexandra Tolstikova
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Wiebke Ewert
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Gisel Esperanza Peña Murillo
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Grant Mills
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Henry Kirkwood
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Hévila Brognaro
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Department of Chemistry, Universität Hamburg, Build. 22a, c/o DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Huijong Han
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Joachim Schulz
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Johan Bielecki
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Julia Lieske
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Julia Maracke
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Juraj Knoska
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | | | - Lea Brings
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Marcin Sikorski
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Marco Kloos
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Mohammad Vakili
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Patrik Vagovic
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Philipp Middendorf
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Raphael de Wijn
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Richard Bean
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Romain Letrun
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Seonghyun Han
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
- Gwangju Institute of Science and Technology, 123 Cheomdangwagi-ro, Buk-gu, Gwangju, 61005, Republic of Korea
| | - Sven Falke
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Tian Geng
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, CB21 6DG, Cambridge, UK
| | - Tokushi Sato
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Vasundara Srinivasan
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Department of Chemistry, Universität Hamburg, Build. 22a, c/o DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Yoonhee Kim
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Oleksandr M Yefanov
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Luca Gelisio
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Tobias Beck
- Institute of Physical Chemistry, Department of Chemistry, Universität Hamburg, Grindelallee 117, 20146, Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Andrew S Doré
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, CB21 6DG, Cambridge, UK
- CHARM Therapeutics Ltd., B900 Babraham Research Campus, CB22 3AT, Cambridge, UK
| | - Adrian P Mancuso
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
- La Trobe Institute for Molecular Science, Department of Chemistry and Physics, La Trobe University, Melbourne, VIC, 3086, Australia
- Diamond Light Source, Harwell Science and Innovation Campus, OX11 0DE, Didcot, UK
| | - Christian Betzel
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Department of Chemistry, Universität Hamburg, Build. 22a, c/o DESY, Notkestr. 85, 22607, Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Saša Bajt
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Lars Redecke
- Institute of Biochemistry, Universität zu Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Henry N Chapman
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Alke Meents
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Dušan Turk
- Jožef Stefan Institute, Jamova cesta 39, 1000, Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins Jamova 39, 1000, Ljubljana, Slovenia
| | - Winfried Hinrichs
- Universität Greifswald, Institute of Biochemistry, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Thomas J Lane
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany.
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany.
- CHARM Therapeutics Ltd., B900 Babraham Research Campus, CB22 3AT, Cambridge, UK.
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3
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Welker S, Chapman HN, Gerkmann T. DriftRec: Adapting Diffusion Models to Blind JPEG Restoration. IEEE Trans Image Process 2024; 33:2795-2807. [PMID: 38578859 DOI: 10.1109/tip.2024.3383776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/07/2024]
Abstract
In this work, we utilize the high-fidelity generation abilities of diffusion models to solve blind JPEG restoration at high compression levels. We propose an elegant modification of the forward stochastic differential equation of diffusion models to adapt them to this restoration task and name our method DriftRec. Comparing DriftRec against an L2 regression baseline with the same network architecture and state-of-the-art techniques for JPEG restoration, we show that our approach can escape the tendency of other methods to generate blurry images, and recovers the distribution of clean images significantly more faithfully. For this, only a dataset of clean/corrupted image pairs and no knowledge about the corruption operation is required, enabling wider applicability to other restoration tasks. In contrast to other conditional and unconditional diffusion models, we utilize the idea that the distributions of clean and corrupted images are much closer to each other than each is to the usual Gaussian prior of the reverse process in diffusion models. Our approach therefore requires only low levels of added noise and needs comparatively few sampling steps even without further optimizations. We show that DriftRec naturally generalizes to realistic and difficult scenarios such as unaligned double JPEG compression and blind restoration of JPEGs found online, without having encountered such examples during training.
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4
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Galchenkova M, Tolstikova A, Klopprogge B, Sprenger J, Oberthuer D, Brehm W, White TA, Barty A, Chapman HN, Yefanov O. Data reduction in protein serial crystallography. IUCrJ 2024; 11:190-201. [PMID: 38327201 PMCID: PMC10916297 DOI: 10.1107/s205225252400054x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 01/15/2024] [Indexed: 02/09/2024]
Abstract
Serial crystallography (SX) has become an established technique for protein structure determination, especially when dealing with small or radiation-sensitive crystals and investigating fast or irreversible protein dynamics. The advent of newly developed multi-megapixel X-ray area detectors, capable of capturing over 1000 images per second, has brought about substantial benefits. However, this advancement also entails a notable increase in the volume of collected data. Today, up to 2 PB of data per experiment could be easily obtained under efficient operating conditions. The combined costs associated with storing data from multiple experiments provide a compelling incentive to develop strategies that effectively reduce the amount of data stored on disk while maintaining the quality of scientific outcomes. Lossless data-compression methods are designed to preserve the information content of the data but often struggle to achieve a high compression ratio when applied to experimental data that contain noise. Conversely, lossy compression methods offer the potential to greatly reduce the data volume. Nonetheless, it is vital to thoroughly assess the impact of data quality and scientific outcomes when employing lossy compression, as it inherently involves discarding information. The evaluation of lossy compression effects on data requires proper data quality metrics. In our research, we assess various approaches for both lossless and lossy compression techniques applied to SX data, and equally importantly, we describe metrics suitable for evaluating SX data quality.
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Affiliation(s)
- Marina Galchenkova
- Center for Free-Electron Laser Science CFEL, Deutsche Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | | | - Bjarne Klopprogge
- Center for Free-Electron Laser Science CFEL, Deutsche Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Janina Sprenger
- Center for Free-Electron Laser Science CFEL, Deutsche Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Dominik Oberthuer
- Center for Free-Electron Laser Science CFEL, Deutsche Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Wolfgang Brehm
- Center for Free-Electron Laser Science CFEL, Deutsche Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Thomas A. White
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Anton Barty
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Henry N. Chapman
- Center for Free-Electron Laser Science CFEL, Deutsche Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science CFEL, Deutsche Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
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5
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Ekeberg T, Assalauova D, Bielecki J, Boll R, Daurer BJ, Eichacker LA, Franken LE, Galli DE, Gelisio L, Gumprecht L, Gunn LH, Hajdu J, Hartmann R, Hasse D, Ignatenko A, Koliyadu J, Kulyk O, Kurta R, Kuster M, Lugmayr W, Lübke J, Mancuso AP, Mazza T, Nettelblad C, Ovcharenko Y, Rivas DE, Rose M, Samanta AK, Schmidt P, Sobolev E, Timneanu N, Usenko S, Westphal D, Wollweber T, Worbs L, Xavier PL, Yousef H, Ayyer K, Chapman HN, Sellberg JA, Seuring C, Vartanyants IA, Küpper J, Meyer M, Maia FRNC. Observation of a single protein by ultrafast X-ray diffraction. Light Sci Appl 2024; 13:15. [PMID: 38216563 PMCID: PMC10786860 DOI: 10.1038/s41377-023-01352-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 01/14/2024]
Abstract
The idea of using ultrashort X-ray pulses to obtain images of single proteins frozen in time has fascinated and inspired many. It was one of the arguments for building X-ray free-electron lasers. According to theory, the extremely intense pulses provide sufficient signal to dispense with using crystals as an amplifier, and the ultrashort pulse duration permits capturing the diffraction data before the sample inevitably explodes. This was first demonstrated on biological samples a decade ago on the giant mimivirus. Since then, a large collaboration has been pushing the limit of the smallest sample that can be imaged. The ability to capture snapshots on the timescale of atomic vibrations, while keeping the sample at room temperature, may allow probing the entire conformational phase space of macromolecules. Here we show the first observation of an X-ray diffraction pattern from a single protein, that of Escherichia coli GroEL which at 14 nm in diameter is the smallest biological sample ever imaged by X-rays, and demonstrate that the concept of diffraction before destruction extends to single proteins. From the pattern, it is possible to determine the approximate orientation of the protein. Our experiment demonstrates the feasibility of ultrafast imaging of single proteins, opening the way to single-molecule time-resolved studies on the femtosecond timescale.
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Affiliation(s)
- Tomas Ekeberg
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124, Uppsala, Sweden
| | - Dameli Assalauova
- Deutsches Electronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | | | - Rebecca Boll
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Benedikt J Daurer
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, OX11 0DE, UK
| | - Lutz A Eichacker
- University of Stavanger, Centre Organelle Research, Richard-Johnsensgate 4, 4021, Stavanger, Norway
| | - Linda E Franken
- Leibniz Institute for Experimental Virology (HPI), Centre for Structural Systems Biology, Notkestraße 85, 22607, Hamburg, Germany
| | - Davide E Galli
- Dipartimento di Fisica "Aldo Pontremoli", Università degli Studi di Milano, via Celoria 16, 20133, Milano, Italy
| | - Luca Gelisio
- Deutsches Electronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Lars Gumprecht
- Center for Free-Electron Laser Science, DESY, 22607, Hamburg, Germany
| | - Laura H Gunn
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124, Uppsala, Sweden
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Janos Hajdu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124, Uppsala, Sweden
| | | | - Dirk Hasse
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124, Uppsala, Sweden
| | - Alexandr Ignatenko
- Deutsches Electronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Jayanath Koliyadu
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
- Biomedical and X-Ray Physics, Department of Applied Physics, AlbaNova University Center, KTH Royal Institute of Technology, SE-10691, Stockholm, Sweden
| | - Olena Kulyk
- ELI Beamlines/IoP Institute of Physics AS CR, v.v.i., Na Slovance 2, 182 21, Prague 8, Czech Republic
| | - Ruslan Kurta
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Markus Kuster
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Wolfgang Lugmayr
- Multi-User CryoEM Facility, Centre for Structural Systems Biology, Notkestr.85, 22607, Hamburg, Germany
- University Medical Center Hamburg-Eppendorf (UKE), Martinistrasse 52, 20246, Hamburg, Germany
| | - Jannik Lübke
- Center for Free-Electron Laser Science, DESY, 22607, Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Adrian P Mancuso
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Tommaso Mazza
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Carl Nettelblad
- Division of Scientific Computing, Science for Life Laboratory, Department of Information Technology, Uppsala University, Box 337, SE-75105, Uppsala, Sweden
| | | | | | - Max Rose
- Deutsches Electronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Amit K Samanta
- Center for Free-Electron Laser Science, DESY, 22607, Hamburg, Germany
| | | | - Egor Sobolev
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Nicusor Timneanu
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-75120, Uppsala, Sweden
| | - Sergey Usenko
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Daniel Westphal
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124, Uppsala, Sweden
| | - Tamme Wollweber
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
- Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Lena Worbs
- Center for Free-Electron Laser Science, DESY, 22607, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Paul Lourdu Xavier
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
- Center for Free-Electron Laser Science, DESY, 22607, Hamburg, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Hazem Yousef
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Kartik Ayyer
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
- Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Henry N Chapman
- Center for Free-Electron Laser Science, DESY, 22607, Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Jonas A Sellberg
- Biomedical and X-Ray Physics, Department of Applied Physics, AlbaNova University Center, KTH Royal Institute of Technology, SE-10691, Stockholm, Sweden
| | - Carolin Seuring
- Multi-User CryoEM Facility, Centre for Structural Systems Biology, Notkestr.85, 22607, Hamburg, Germany
- Department of Chemistry, Universität Hamburg, 20146, Hamburg, Germany
| | - Ivan A Vartanyants
- Deutsches Electronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Jochen Küpper
- Center for Free-Electron Laser Science, DESY, 22607, Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Michael Meyer
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Filipe R N C Maia
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124, Uppsala, Sweden.
- NERSC, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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6
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Williamson LJ, Galchenkova M, Best HL, Bean RJ, Munke A, Awel S, Pena G, Knoska J, Schubert R, Dörner K, Park HW, Bideshi DK, Henkel A, Kremling V, Klopprogge B, Lloyd-Evans E, Young MT, Valerio J, Kloos M, Sikorski M, Mills G, Bielecki J, Kirkwood H, Kim C, de Wijn R, Lorenzen K, Xavier PL, Rahmani Mashhour A, Gelisio L, Yefanov O, Mancuso AP, Federici BA, Chapman HN, Crickmore N, Rizkallah PJ, Berry C, Oberthür D. Structure of the Lysinibacillus sphaericus Tpp49Aa1 pesticidal protein elucidated from natural crystals using MHz-SFX. Proc Natl Acad Sci U S A 2023; 120:e2203241120. [PMID: 38015839 PMCID: PMC10710082 DOI: 10.1073/pnas.2203241120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 10/18/2023] [Indexed: 11/30/2023] Open
Abstract
The Lysinibacillus sphaericus proteins Tpp49Aa1 and Cry48Aa1 can together act as a toxin toward the mosquito Culex quinquefasciatus and have potential use in biocontrol. Given that proteins with sequence homology to the individual proteins can have activity alone against other insect species, the structure of Tpp49Aa1 was solved in order to understand this protein more fully and inform the design of improved biopesticides. Tpp49Aa1 is naturally expressed as a crystalline inclusion within the host bacterium, and MHz serial femtosecond crystallography using the novel nanofocus option at an X-ray free electron laser allowed rapid and high-quality data collection to determine the structure of Tpp49Aa1 at 1.62 Å resolution. This revealed the packing of Tpp49Aa1 within these natural nanocrystals as a homodimer with a large intermolecular interface. Complementary experiments conducted at varied pH also enabled investigation of the early structural events leading up to the dissolution of natural Tpp49Aa1 crystals-a crucial step in its mechanism of action. To better understand the cooperation between the two proteins, assays were performed on a range of different mosquito cell lines using both individual proteins and mixtures of the two. Finally, bioassays demonstrated Tpp49Aa1/Cry48Aa1 susceptibility of Anopheles stephensi, Aedes albopictus, and Culex tarsalis larvae-substantially increasing the potential use of this binary toxin in mosquito control.
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Affiliation(s)
| | - Marina Galchenkova
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, 22607Hamburg, Germany
| | - Hannah L. Best
- School of Biosciences, Cardiff University, CardiffCF10 3AX, United Kingdom
| | | | - Anna Munke
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, 22607Hamburg, Germany
| | - Salah Awel
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, 22607Hamburg, Germany
| | - Gisel Pena
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, 22607Hamburg, Germany
| | - Juraj Knoska
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, 22607Hamburg, Germany
| | | | | | - Hyun-Woo Park
- Department of Biological Sciences, California Baptist University, Riverside, CA92504
| | - Dennis K. Bideshi
- Department of Biological Sciences, California Baptist University, Riverside, CA92504
| | - Alessandra Henkel
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, 22607Hamburg, Germany
| | - Viviane Kremling
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, 22607Hamburg, Germany
| | - Bjarne Klopprogge
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, 22607Hamburg, Germany
| | - Emyr Lloyd-Evans
- School of Biosciences, Cardiff University, CardiffCF10 3AX, United Kingdom
| | - Mark T. Young
- School of Biosciences, Cardiff University, CardiffCF10 3AX, United Kingdom
| | | | - Marco Kloos
- European XFEL GmbH, 22869Schenefeld, Germany
| | | | - Grant Mills
- European XFEL GmbH, 22869Schenefeld, Germany
| | | | | | - Chan Kim
- European XFEL GmbH, 22869Schenefeld, Germany
| | | | | | - Paul Lourdu Xavier
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, 22607Hamburg, Germany
- Max-Planck Institute for the Structure and Dynamics of Matter, 22761Hamburg, Germany
| | - Aida Rahmani Mashhour
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, 22607Hamburg, Germany
| | - Luca Gelisio
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, 22607Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, 22607Hamburg, Germany
| | - Adrian P. Mancuso
- European XFEL GmbH, 22869Schenefeld, Germany
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC3086, Australia
| | - Brian A. Federici
- Department of Entomology and Institute for Integrative Genome Biology, University of California, Riverside, CA92521
| | - Henry N. Chapman
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, 22607Hamburg, Germany
- Centre for Ultrafast Imaging, Universität Hamburg, 22761Hamburg, Germany
- Department of Physics, Universität Hamburg, 22761Hamburg, Germany
| | - Neil Crickmore
- School of Life Sciences, University of Sussex, Falmer, BrightonBN1 9QG, United Kingdom
| | | | - Colin Berry
- School of Biosciences, Cardiff University, CardiffCF10 3AX, United Kingdom
| | - Dominik Oberthür
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, 22607Hamburg, Germany
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7
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Christou NE, Apostolopoulou V, Melo DVM, Ruppert M, Fadini A, Henkel A, Sprenger J, Oberthuer D, Günther S, Pateras A, Rahmani Mashhour A, Yefanov OM, Galchenkova M, Reinke PYA, Kremling V, Scheer TES, Lange ER, Middendorf P, Schubert R, De Zitter E, Lumbao-Conradson K, Herrmann J, Rahighi S, Kunavar A, Beale EV, Beale JH, Cirelli C, Johnson PJM, Dworkowski F, Ozerov D, Bertrand Q, Wranik M, Bacellar C, Bajt S, Wakatsuki S, Sellberg JA, Huse N, Turk D, Chapman HN, Lane TJ. Time-resolved crystallography captures light-driven DNA repair. Science 2023; 382:1015-1020. [PMID: 38033070 DOI: 10.1126/science.adj4270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/05/2023] [Indexed: 12/02/2023]
Abstract
Photolyase is an enzyme that uses light to catalyze DNA repair. To capture the reaction intermediates involved in the enzyme's catalytic cycle, we conducted a time-resolved crystallography experiment. We found that photolyase traps the excited state of the active cofactor, flavin adenine dinucleotide (FAD), in a highly bent geometry. This excited state performs electron transfer to damaged DNA, inducing repair. We show that the repair reaction, which involves the lysis of two covalent bonds, occurs through a single-bond intermediate. The transformation of the substrate into product crowds the active site and disrupts hydrogen bonds with the enzyme, resulting in stepwise product release, with the 3' thymine ejected first, followed by the 5' base.
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Affiliation(s)
- Nina-Eleni Christou
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Virginia Apostolopoulou
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Diogo V M Melo
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Matthias Ruppert
- Institute for Nanostructure and Solid-State Physics, CFEL Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Alisia Fadini
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK
| | - Alessandra Henkel
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Janina Sprenger
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Dominik Oberthuer
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Sebastian Günther
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Anastasios Pateras
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Aida Rahmani Mashhour
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Oleksandr M Yefanov
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Marina Galchenkova
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Patrick Y A Reinke
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Viviane Kremling
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - T Emilie S Scheer
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Esther R Lange
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Philipp Middendorf
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Robin Schubert
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Elke De Zitter
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, 38000 Grenoble, France
| | - Koya Lumbao-Conradson
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Rd, Menlo Park, CA 94025, USA
| | - Jonathan Herrmann
- Department of Structural Biology, Stanford University, 318 Campus Drive West, Stanford, CA 94305-5151, USA
| | - Simin Rahighi
- Department of Structural Biology, Stanford University, 318 Campus Drive West, Stanford, CA 94305-5151, USA
| | - Ajda Kunavar
- Laboratory for Fluid Dynamics and Thermodynamics, Faculty of Mechanical Engineering, University of Ljubljana, Aškerčeva 6, 1000 Ljubljana, Slovenia
| | - Emma V Beale
- Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland
| | - John H Beale
- Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland
| | | | | | | | - Dmitry Ozerov
- Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland
| | | | | | | | - Saša Bajt
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Soichi Wakatsuki
- Department of Structural Biology, Stanford University, 318 Campus Drive West, Stanford, CA 94305-5151, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Rd, Menlo Park, CA 94025, USA
| | - Jonas A Sellberg
- Biomedical and X-ray Physics, Department of Applied Physics, AlbaNova University Center, KTH Royal Institute of Technology, S-106 91 Stockholm, Sweden
| | - Nils Huse
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
- Institute for Nanostructure and Solid-State Physics, CFEL Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Dušan Turk
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000 Ljubljana, Slovenia
| | - Henry N Chapman
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Thomas J Lane
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
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8
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Birnsteinova S, Ferreira de Lima DE, Sobolev E, Kirkwood HJ, Bellucci V, Bean RJ, Kim C, Koliyadu JCP, Sato T, Dall’Antonia F, Asimakopoulou EM, Yao Z, Buakor K, Zhang Y, Meents A, Chapman HN, Mancuso AP, Villanueva-Perez P, Vagovič P. Online dynamic flat-field correction for MHz microscopy data at European XFEL. J Synchrotron Radiat 2023; 30:1030-1037. [PMID: 37729072 PMCID: PMC10624028 DOI: 10.1107/s1600577523007336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 08/21/2023] [Indexed: 09/22/2023]
Abstract
The high pulse intensity and repetition rate of the European X-ray Free-Electron Laser (EuXFEL) provide superior temporal resolution compared with other X-ray sources. In combination with MHz X-ray microscopy techniques, it offers a unique opportunity to achieve superior contrast and spatial resolution in applications demanding high temporal resolution. In both live visualization and offline data analysis for microscopy experiments, baseline normalization is essential for further processing steps such as phase retrieval and modal decomposition. In addition, access to normalized projections during data acquisition can play an important role in decision-making and improve the quality of the data. However, the stochastic nature of X-ray free-electron laser sources hinders the use of standard flat-field normalization methods during MHz X-ray microscopy experiments. Here, an online (i.e. near real-time) dynamic flat-field correction method based on principal component analysis of dynamically evolving flat-field images is presented. The method is used for the normalization of individual X-ray projections and has been implemented as a near real-time analysis tool at the Single Particles, Clusters, and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) instrument of EuXFEL.
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Affiliation(s)
| | | | | | | | | | | | - Chan Kim
- European XFEL GmbH, Schenefeld, Germany
| | | | | | | | | | - Zisheng Yao
- Synchrotron Radiation Research and NanoLund, Lund University, Lund, Sweden
| | - Khachiwan Buakor
- European XFEL GmbH, Schenefeld, Germany
- Synchrotron Radiation Research and NanoLund, Lund University, Lund, Sweden
| | - Yuhe Zhang
- Synchrotron Radiation Research and NanoLund, Lund University, Lund, Sweden
| | - Alke Meents
- Center for Free-Electron Laser Science (CFEL), DESY, Hamburg, Germany
| | - Henry N. Chapman
- Center for Free-Electron Laser Science (CFEL), DESY, Hamburg, Germany
- University of Hamburg, Hamburg, Germany
| | - Adrian P. Mancuso
- European XFEL GmbH, Schenefeld, Germany
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | | | - Patrik Vagovič
- European XFEL GmbH, Schenefeld, Germany
- Center for Free-Electron Laser Science (CFEL), DESY, Hamburg, Germany
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9
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Reinke PYA, de Souza EE, Günther S, Falke S, Lieske J, Ewert W, Loboda J, Herrmann A, Rahmani Mashhour A, Karničar K, Usenik A, Lindič N, Sekirnik A, Botosso VF, Santelli GMM, Kapronezai J, de Araújo MV, Silva-Pereira TT, Filho AFDS, Tavares MS, Flórez-Álvarez L, de Oliveira DBL, Durigon EL, Giaretta PR, Heinemann MB, Hauser M, Seychell B, Böhler H, Rut W, Drag M, Beck T, Cox R, Chapman HN, Betzel C, Brehm W, Hinrichs W, Ebert G, Latham SL, Guimarães AMDS, Turk D, Wrenger C, Meents A. Calpeptin is a potent cathepsin inhibitor and drug candidate for SARS-CoV-2 infections. Commun Biol 2023; 6:1058. [PMID: 37853179 PMCID: PMC10584882 DOI: 10.1038/s42003-023-05317-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 09/01/2023] [Indexed: 10/20/2023] Open
Abstract
Several drug screening campaigns identified Calpeptin as a drug candidate against SARS-CoV-2. Initially reported to target the viral main protease (Mpro), its moderate activity in Mpro inhibition assays hints at a second target. Indeed, we show that Calpeptin is an extremely potent cysteine cathepsin inhibitor, a finding additionally supported by X-ray crystallography. Cell infection assays proved Calpeptin's efficacy against SARS-CoV-2. Treatment of SARS-CoV-2-infected Golden Syrian hamsters with sulfonated Calpeptin at a dose of 1 mg/kg body weight reduces the viral load in the trachea. Despite a higher risk of side effects, an intrinsic advantage in targeting host proteins is their mutational stability in contrast to highly mutable viral targets. Here we show that the inhibition of cathepsins, a protein family of the host organism, by calpeptin is a promising approach for the treatment of SARS-CoV-2 and potentially other viral infections.
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Affiliation(s)
- Patrick Y A Reinke
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Edmarcia Elisa de Souza
- Department of Parasitology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo, Brazil
| | - Sebastian Günther
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Sven Falke
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Julia Lieske
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Wiebke Ewert
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Jure Loboda
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, Jamova 39, Ljubljana, Slovenia
| | | | - Aida Rahmani Mashhour
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Katarina Karničar
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000, Ljubljana, Slovenia
| | - Aleksandra Usenik
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000, Ljubljana, Slovenia
| | - Nataša Lindič
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia
| | - Andreja Sekirnik
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia
| | - Viviane Fongaro Botosso
- Virology Laboratory, Center of Development and Innovation, Butantan Institute, São Paulo, Brazil
| | - Gláucia Maria Machado Santelli
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Josana Kapronezai
- Virology Laboratory, Center of Development and Innovation, Butantan Institute, São Paulo, Brazil
| | - Marcelo Valdemir de Araújo
- Virology Laboratory, Center of Development and Innovation, Butantan Institute, São Paulo, Brazil
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Taiana Tainá Silva-Pereira
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, São Paulo, Brazil
| | | | - Mariana Silva Tavares
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Lizdany Flórez-Álvarez
- Department of Parasitology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo, Brazil
| | | | - Edison Luiz Durigon
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Paula Roberta Giaretta
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, 4474 TAMU, School Station, TX, USA
| | - Marcos Bryan Heinemann
- Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, São Paulo, Brazil
| | - Maurice Hauser
- Institute for Organic Chemistry and BMWZ, Leibniz University of Hannover, Schneiderberg 38, 30167, Hannover, Germany
| | - Brandon Seychell
- Department of Chemistry, Institute of Physical Chemistry, Universität Hamburg, Grindelallee 117, 20146, Hamburg, Germany
| | - Hendrik Böhler
- Department of Chemistry, Institute of Physical Chemistry, Universität Hamburg, Grindelallee 117, 20146, Hamburg, Germany
| | - Wioletta Rut
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
| | - Marcin Drag
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
| | - Tobias Beck
- Department of Chemistry, Institute of Physical Chemistry, Universität Hamburg, Grindelallee 117, 20146, Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Russell Cox
- Institute for Organic Chemistry and BMWZ, Leibniz University of Hannover, Schneiderberg 38, 30167, Hannover, Germany
| | - Henry N Chapman
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Christian Betzel
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, Universität Hamburg, 22607, Hamburg, Germany
| | - Wolfgang Brehm
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Winfried Hinrichs
- Universität Greifswald, Institute of Biochemistry, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Gregor Ebert
- Institute of Virology, Helmholtz Munich, Munich, Germany
- Institute of Virology, Technical University of Munich, Munich, Germany
| | - Sharissa L Latham
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, NSW, Australia
- St Vincent's Hospital Clinical School, UNSW, Sydney, NSW, Australia
| | - Ana Marcia de Sá Guimarães
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Dusan Turk
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia.
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000, Ljubljana, Slovenia.
| | - Carsten Wrenger
- Department of Parasitology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo, Brazil.
| | - Alke Meents
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany.
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10
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Blanchet CE, Round A, Mertens HDT, Ayyer K, Graewert M, Awel S, Franke D, Dörner K, Bajt S, Bean R, Custódio TF, de Wijn R, Juncheng E, Henkel A, Gruzinov A, Jeffries CM, Kim Y, Kirkwood H, Kloos M, Knoška J, Koliyadu J, Letrun R, Löw C, Makroczyova J, Mall A, Meijers R, Pena Murillo GE, Oberthür D, Round E, Seuring C, Sikorski M, Vagovic P, Valerio J, Wollweber T, Zhuang Y, Schulz J, Haas H, Chapman HN, Mancuso AP, Svergun D. Form factor determination of biological molecules with X-ray free electron laser small-angle scattering (XFEL-SAS). Commun Biol 2023; 6:1057. [PMID: 37853181 PMCID: PMC10585004 DOI: 10.1038/s42003-023-05416-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 10/04/2023] [Indexed: 10/20/2023] Open
Abstract
Free-electron lasers (FEL) are revolutionizing X-ray-based structural biology methods. While protein crystallography is already routinely performed at FELs, Small Angle X-ray Scattering (SAXS) studies of biological macromolecules are not as prevalent. SAXS allows the study of the shape and overall structure of proteins and nucleic acids in solution, in a quasi-native environment. In solution, chemical and biophysical parameters that have an influence on the structure and dynamics of molecules can be varied and their effect on conformational changes can be monitored in time-resolved XFEL and SAXS experiments. We report here the collection of scattering form factors of proteins in solution using FEL X-rays. The form factors correspond to the scattering signal of the protein ensemble alone; the scattering contributions from the solvent and the instrument are separately measured and accurately subtracted. The experiment was done using a liquid jet for sample delivery. These results pave the way for time-resolved studies and measurements from dilute samples, capitalizing on the intense and short FEL X-ray pulses.
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Affiliation(s)
- Clement E Blanchet
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany.
| | - Adam Round
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany.
| | - Haydyn D T Mertens
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany
| | - Kartik Ayyer
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Melissa Graewert
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany
| | - Salah Awel
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Daniel Franke
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany
- BIOSAXS GmbH, Notkestr. 85, 22607, Hamburg, Germany
| | - Katerina Dörner
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Saša Bajt
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Richard Bean
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Tânia F Custódio
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Notkestrasse 85, D-22607, Hamburg, Germany
| | - Raphael de Wijn
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - E Juncheng
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Alessandra Henkel
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Andrey Gruzinov
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany
| | - Cy M Jeffries
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany
| | - Yoonhee Kim
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Henry Kirkwood
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Marco Kloos
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Juraj Knoška
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | | | - Romain Letrun
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Christian Löw
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Notkestrasse 85, D-22607, Hamburg, Germany
| | | | - Abhishek Mall
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Rob Meijers
- Institute for Protein Innovation (IPI), 4 Blackfan Circle, Boston, MA, 02115, USA
| | - Gisel Esperanza Pena Murillo
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Dominik Oberthür
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Ekaterina Round
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Carolin Seuring
- Centre for Structural Systems Biology (CSSB), Notkestrasse 85, D-22607, Hamburg, Germany
- Department of Chemistry, University of Hamburg, Hamburg, Germany
- Leibniz Institute of Virology, Hamburg, Germany
| | - Marcin Sikorski
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Patrik Vagovic
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Joana Valerio
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Tamme Wollweber
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Yulong Zhuang
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Joachim Schulz
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Henry N Chapman
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Adrian P Mancuso
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia
| | - Dmitri Svergun
- European Molecular Biology Laboratory EMBL, Hamburg Site, c/o DESY Notkestrasse 85, 22603, Hamburg, Germany.
- BIOSAXS GmbH, Notkestr. 85, 22607, Hamburg, Germany.
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11
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Malla TN, Zielinski K, Aldama L, Bajt S, Feliz D, Hayes B, Hunter M, Kupitz C, Lisova S, Knoska J, Martin-Garcia JM, Mariani V, Pandey S, Poudyal I, Sierra RG, Tolstikova A, Yefanov O, Yoon CH, Ourmazd A, Fromme P, Schwander P, Barty A, Chapman HN, Stojkovic EA, Batyuk A, Boutet S, Phillips GN, Pollack L, Schmidt M. Heterogeneity in M. tuberculosis β-lactamase inhibition by Sulbactam. Nat Commun 2023; 14:5507. [PMID: 37679343 PMCID: PMC10485065 DOI: 10.1038/s41467-023-41246-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 08/27/2023] [Indexed: 09/09/2023] Open
Abstract
For decades, researchers have elucidated essential enzymatic functions on the atomic length scale by tracing atomic positions in real-time. Our work builds on possibilities unleashed by mix-and-inject serial crystallography (MISC) at X-ray free electron laser facilities. In this approach, enzymatic reactions are triggered by mixing substrate or ligand solutions with enzyme microcrystals. Here, we report in atomic detail (between 2.2 and 2.7 Å resolution) by room-temperature, time-resolved crystallography with millisecond time-resolution (with timepoints between 3 ms and 700 ms) how the Mycobacterium tuberculosis enzyme BlaC is inhibited by sulbactam (SUB). Our results reveal ligand binding heterogeneity, ligand gating, cooperativity, induced fit, and conformational selection all from the same set of MISC data, detailing how SUB approaches the catalytic clefts and binds to the enzyme noncovalently before reacting to a trans-enamine. This was made possible in part by the application of singular value decomposition to the MISC data using a program that remains functional even if unit cell parameters change up to 3 Å during the reaction.
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Affiliation(s)
- Tek Narsingh Malla
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Kara Zielinski
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA
| | - Luis Aldama
- Department of Biology, Northeastern Illinois University, Chicago, IL, USA
| | - Sasa Bajt
- The Hamburg Centre for Ultrafast Imaging, Hamburg, Germany
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen Synchrotron, Hamburg, Germany
| | - Denisse Feliz
- Department of Biology, Northeastern Illinois University, Chicago, IL, USA
| | - Brendon Hayes
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Mark Hunter
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Christopher Kupitz
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Stella Lisova
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Juraj Knoska
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen Synchrotron, Hamburg, Germany
| | - Jose Manuel Martin-Garcia
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Blas Cabrera, Spanish National Research Council (CSIC), Madrid, Spain
| | - Valerio Mariani
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Suraj Pandey
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Ishwor Poudyal
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Raymond G Sierra
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | | | - Oleksandr Yefanov
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen Synchrotron, Hamburg, Germany
| | - Chung Hong Yoon
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Abbas Ourmazd
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Petra Fromme
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, 20 Arizona State University, Tempe, AZ, USA
| | - Peter Schwander
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Anton Barty
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
- Center for Data and Computing in Natural Science CDCS, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Henry N Chapman
- The Hamburg Centre for Ultrafast Imaging, Hamburg, Germany
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen Synchrotron, Hamburg, Germany
- Department of Physics, Universität Hamburg, Hamburg, Germany
| | - Emina A Stojkovic
- Department of Biology, Northeastern Illinois University, Chicago, IL, USA
| | - Alexander Batyuk
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Sébastien Boutet
- Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - George N Phillips
- Department of BioSciences, Rice University, Houston, TX, USA
- Department of Chemistry, Rice University, Houston, TX, USA
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA
| | - Marius Schmidt
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA.
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12
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Peard N, Ayyer K, Chapman HN. Ab initio spatial phase retrieval via intensity triple correlations. Opt Express 2023; 31:25082-25092. [PMID: 37475321 DOI: 10.1364/oe.495920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/01/2023] [Indexed: 07/22/2023]
Abstract
Second-order intensity correlations from incoherent emitters can reveal the Fourier transform modulus of their spatial distribution, but retrieving the phase to enable completely general Fourier inversion to real space remains challenging. Phase retrieval via the third-order intensity correlations has relied on special emitter configurations which simplified an unaddressed sign problem in the computation. Without a complete treatment of this sign problem, the general case of retrieving the Fourier phase from a truly arbitrary configuration of emitters is not possible. In this paper, a general method for ab initio phase retrieval via the intensity triple correlations is described. Simulations demonstrate accurate phase retrieval for clusters of incoherent emitters which could be applied to imaging stars or fluorescent atoms and molecules. With this work, it is now finally tractable to perform Fourier inversion directly and reconstruct images of arbitrary arrays of independent emitters via far-field intensity correlations alone.
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13
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Li T, Dresselhaus JL, Ivanov N, Prasciolu M, Fleckenstein H, Yefanov O, Zhang W, Pennicard D, Dippel AC, Gutowski O, Villanueva-Perez P, Chapman HN, Bajt S. Dose-efficient scanning Compton X-ray microscopy. Light Sci Appl 2023; 12:130. [PMID: 37248250 DOI: 10.1038/s41377-023-01176-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/28/2023] [Accepted: 05/05/2023] [Indexed: 05/31/2023]
Abstract
The highest resolution of images of soft matter and biological materials is ultimately limited by modification of the structure, induced by the necessarily high energy of short-wavelength radiation. Imaging the inelastically scattered X-rays at a photon energy of 60 keV (0.02 nm wavelength) offers greater signal per energy transferred to the sample than coherent-scattering techniques such as phase-contrast microscopy and projection holography. We present images of dried, unstained, and unfixed biological objects obtained by scanning Compton X-ray microscopy, at a resolution of about 70 nm. This microscope was realised using novel wedged multilayer Laue lenses that were fabricated to sub-ångström precision, a new wavefront measurement scheme for hard X rays, and efficient pixel-array detectors. The doses required to form these images were as little as 0.02% of the tolerable dose and 0.05% of that needed for phase-contrast imaging at similar resolution using 17 keV photon energy. The images obtained provide a quantitative map of the projected mass density in the sample, as confirmed by imaging a silicon wedge. Based on these results, we find that it should be possible to obtain radiation damage-free images of biological samples at a resolution below 10 nm.
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Affiliation(s)
- Tang Li
- The Hamburg Centre for Ultrafast Imaging, 22761, Hamburg, Germany
| | | | - Nikolay Ivanov
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
| | - Mauro Prasciolu
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
| | - Holger Fleckenstein
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
| | - Wenhui Zhang
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
| | - David Pennicard
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
| | | | - Olof Gutowski
- Deutsches Elektronen Synchrotron DESY, 22607, Hamburg, Germany
| | | | - Henry N Chapman
- The Hamburg Centre for Ultrafast Imaging, 22761, Hamburg, Germany.
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany.
- Department of Physics, Universität Hamburg, 22761, Hamburg, Germany.
| | - Saša Bajt
- The Hamburg Centre for Ultrafast Imaging, 22761, Hamburg, Germany.
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany.
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14
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Bellucci V, Zdora MC, Mikeš L, Birnšteinová Š, Oberta P, Romagnoni M, Mazzolari A, Villanueva-Perez P, Mokso R, David C, Makita M, Cipiccia S, Uličný J, Meents A, Mancuso AP, Chapman HN, Vagovič P. Hard X-ray stereographic microscopy for single-shot differential phase imaging. Opt Express 2023; 31:18399-18406. [PMID: 37381551 DOI: 10.1364/oe.492137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/09/2023] [Indexed: 06/30/2023]
Abstract
The characterisation of fast phenomena at the microscopic scale is required for the understanding of catastrophic responses of materials to loads and shocks, the processing of materials by optical or mechanical means, the processes involved in many key technologies such as additive manufacturing and microfluidics, and the mixing of fuels in combustion. Such processes are usually stochastic in nature and occur within the opaque interior volumes of materials or samples, with complex dynamics that evolve in all three dimensions at speeds exceeding many meters per second. There is therefore a need for the ability to record three-dimensional X-ray movies of irreversible processes with resolutions of micrometers and frame rates of microseconds. Here we demonstrate a method to achieve this by recording a stereo phase-contrast image pair in a single exposure. The two images are combined computationally to reconstruct a 3D model of the object. The method is extendable to more than two simultaneous views. When combined with megahertz pulse trains of X-ray free-electron lasers (XFELs) it will be possible to create movies able to resolve 3D trajectories with velocities of kilometers per second.
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15
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Chapman HN. Fourth-generation light sources. IUCrJ 2023; 10:246-247. [PMID: 37144816 PMCID: PMC10161768 DOI: 10.1107/s2052252523003585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
New fourth-generation synchrotron radiation facilities bring large gains in X-ray source brightness, but also challenges in making full use of their potentials. Some of these challenges have been faced at X-ray free-electron laser facilities.
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Affiliation(s)
- Henry N Chapman
- Center for Free-Electron Laser Science CFEL, Deutsche Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
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16
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Henkel A, Galchenkova M, Maracke J, Yefanov O, Klopprogge B, Hakanpää J, Mesters JR, Chapman HN, Oberthuer D. JINXED: just in time crystallization for easy structure determination of biological macromolecules. IUCrJ 2023; 10:253-260. [PMID: 36892542 PMCID: PMC10161778 DOI: 10.1107/s2052252523001653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 02/23/2023] [Indexed: 05/06/2023]
Abstract
Macromolecular crystallography is a well established method in the field of structural biology and has led to the majority of known protein structures to date. After focusing on static structures, the method is now under development towards the investigation of protein dynamics through time-resolved methods. These experiments often require multiple handling steps of the sensitive protein crystals, e.g. for ligand-soaking and cryo-protection. These handling steps can cause significant crystal damage, and hence reduce data quality. Furthermore, in time-resolved experiments based on serial crystallography, which use micrometre-sized crystals for short diffusion times of ligands, certain crystal morphologies with small solvent channels can prevent sufficient ligand diffusion. Described here is a method that combines protein crystallization and data collection in a novel one-step process. Corresponding experiments were successfully performed as a proof-of-principle using hen egg-white lysozyme and crystallization times of only a few seconds. This method, called JINXED (Just IN time Crystallization for Easy structure Determination), promises high-quality data due to the avoidance of crystal handling and has the potential to enable time-resolved experiments with crystals containing small solvent channels by adding potential ligands to the crystallization buffer, simulating traditional co-crystallization approaches.
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Affiliation(s)
- Alessandra Henkel
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Marina Galchenkova
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Julia Maracke
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Bjarne Klopprogge
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Johanna Hakanpää
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Jeroen R Mesters
- Institut für Biochemie, Universität zu Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Henry N Chapman
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Dominik Oberthuer
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
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17
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Trost F, Ayyer K, Prasciolu M, Fleckenstein H, Barthelmess M, Yefanov O, Dresselhaus JL, Li C, Bajt S, Carnis J, Wollweber T, Mall A, Shen Z, Zhuang Y, Richter S, Karl S, Cardoch S, Patra KK, Möller J, Zozulya A, Shayduk R, Lu W, Brauße F, Friedrich B, Boesenberg U, Petrov I, Tomin S, Guetg M, Madsen A, Timneanu N, Caleman C, Röhlsberger R, von Zanthier J, Chapman HN. Imaging via Correlation of X-Ray Fluorescence Photons. Phys Rev Lett 2023; 130:173201. [PMID: 37172237 DOI: 10.1103/physrevlett.130.173201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 02/01/2023] [Accepted: 03/08/2023] [Indexed: 05/14/2023]
Abstract
We demonstrate that x-ray fluorescence emission, which cannot maintain a stationary interference pattern, can be used to obtain images of structures by recording photon-photon correlations in the manner of the stellar intensity interferometry of Hanbury Brown and Twiss. This is achieved utilizing femtosecond-duration pulses of a hard x-ray free-electron laser to generate the emission in exposures comparable to the coherence time of the fluorescence. Iterative phasing of the photon correlation map generated a model-free real-space image of the structure of the emitters. Since fluorescence can dominate coherent scattering, this may enable imaging uncrystallised macromolecules.
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Affiliation(s)
- Fabian Trost
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Kartik Ayyer
- Max Planck Institute for the Structure and Dynamics of Matter, 22607, Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Mauro Prasciolu
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Holger Fleckenstein
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Miriam Barthelmess
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - J Lukas Dresselhaus
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Chufeng Li
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Saša Bajt
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Jerome Carnis
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Tamme Wollweber
- Max Planck Institute for the Structure and Dynamics of Matter, 22607, Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Abhishek Mall
- Max Planck Institute for the Structure and Dynamics of Matter, 22607, Hamburg, Germany
| | - Zhou Shen
- Max Planck Institute for the Structure and Dynamics of Matter, 22607, Hamburg, Germany
| | - Yulong Zhuang
- Max Planck Institute for the Structure and Dynamics of Matter, 22607, Hamburg, Germany
| | - Stefan Richter
- Department of Physics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstrasse 1, 91058 Erlangen, Germany
- Erlangen Graduate School in Advanced Optical Technologies (SAOT), Friedrich-Alexander Universität Erlangen-Nürnberg, Paul-Gordan-Str. 6, 91052, Erlangen, Germany
| | - Sebastian Karl
- Department of Physics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstrasse 1, 91058 Erlangen, Germany
| | - Sebastian Cardoch
- Department of Physics and Astronomy, Uppsala University, Box 516, Uppsala SE-75120, Sweden
| | - Kajwal Kumar Patra
- Department of Physics and Astronomy, Uppsala University, Box 516, Uppsala SE-75120, Sweden
| | - Johannes Möller
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Alexey Zozulya
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Roman Shayduk
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Wei Lu
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Felix Brauße
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Bertram Friedrich
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Ulrike Boesenberg
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Ilia Petrov
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Sergey Tomin
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Marc Guetg
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Anders Madsen
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Nicusor Timneanu
- Department of Physics and Astronomy, Uppsala University, Box 516, Uppsala SE-75120, Sweden
| | - Carl Caleman
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- Department of Physics and Astronomy, Uppsala University, Box 516, Uppsala SE-75120, Sweden
| | - Ralf Röhlsberger
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- Helmholtz-Institut Jena, Fröbelstieg 3, 07743 Jena, Germany
- GSI Helmholtzzentrum für Schwerionenforschung, Planckstrasse 1, 62491 Jena, Germany
- Institut für Optik und Quantenelektronik, Friedrich-Schiller-Universität Jena, Max-Wien-Platz 1, 07743 Jena, Germany
| | - Joachim von Zanthier
- Department of Physics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstrasse 1, 91058 Erlangen, Germany
- Erlangen Graduate School in Advanced Optical Technologies (SAOT), Friedrich-Alexander Universität Erlangen-Nürnberg, Paul-Gordan-Str. 6, 91052, Erlangen, Germany
| | - Henry N Chapman
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Physics and Astronomy, Uppsala University, Box 516, Uppsala SE-75120, Sweden
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
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18
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Brehm W, White T, Chapman HN. Crystal diffraction prediction and partiality estimation using Gaussian basis functions. Acta Crystallogr A Found Adv 2023; 79:145-162. [PMID: 36862040 PMCID: PMC9979942 DOI: 10.1107/s2053273323000682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 01/25/2023] [Indexed: 02/19/2023] Open
Abstract
The recent diversification of macromolecular crystallographic experiments including the use of pink beams, convergent electron diffraction and serial snapshot crystallography has shown the limitations of using the Laue equations for diffraction prediction. This article gives a computationally efficient way of calculating approximate crystal diffraction patterns given varying distributions of the incoming beam, crystal shapes and other potentially hidden parameters. This approach models each pixel of a diffraction pattern and improves data processing of integrated peak intensities by enabling the correction of partially recorded reflections. The fundamental idea is to express the distributions as weighted sums of Gaussian functions. The approach is demonstrated on serial femtosecond crystallography data sets, showing a significant decrease in the required number of patterns to refine a structure to a given error.
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Affiliation(s)
- Wolfgang Brehm
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany,Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany,Correspondence e-mail: ,
| | - Thomas White
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Henry N. Chapman
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany,Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany,The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany,Correspondence e-mail: ,
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19
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Zupan B, Peña-Murillo GE, Zahoor R, Gregorc J, Šarler B, Knoška J, Gañán-Calvo AM, Chapman HN, Bajt S. An experimental study of liquid micro-jets produced with a gas dynamic virtual nozzle under the influence of an electric field. Front Mol Biosci 2023; 10:1006733. [PMID: 36743214 PMCID: PMC9892056 DOI: 10.3389/fmolb.2023.1006733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 01/06/2023] [Indexed: 01/21/2023] Open
Abstract
The results of an experimental study of micro-jets produced with a gas dynamic virtual nozzle (GDVN) under the influence of an electric field are provided and discussed for the first time. The experimental study is performed with a 50% volume mixture of water and ethanol, and nitrogen focusing gas. The liquid sample and gas Reynolds numbers range from 0.09-5.4 and 0-190, respectively. The external electrode was positioned 400-500 μm downstream of the nozzle tip and an effect of electric potential between the electrode and the sample liquid from 0-7 kV was investigated. The jetting parametric space is examined as a function of operating gas and liquid flow rates, outlet chamber pressure, and an external electric field. The experimentally observed jet diameter, length and velocity ranged from 1-25 μm, 50-500 μm and 0.5-10 m/s, respectively. The jetting shape snapshots were processed automatically using purposely developed computer vision software. The velocity of the jet was calculated from the measured jet diameter and the sample flow rate. It is found that micro-jets accelerate in the direction of the applied electric field in the downstream direction at a constant acceleration as opposed to the standard GDVNs. New jetting modes were observed, where either the focusing gas or the electric forces dominate, encouraging further theoretical and numerical studies towards optimized system design. The study shows the potential to unlock a new generation of low background sample delivery for serial diffraction measurements of weakly scattering objects.
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Affiliation(s)
- Bor Zupan
- Laboratory for Fluid Dynamics and Thermodynamics, Faculty of Mechanical Engineering, University of Ljubljana, Ljubljana, Slovenia
| | | | - Rizwan Zahoor
- Laboratory for Fluid Dynamics and Thermodynamics, Faculty of Mechanical Engineering, University of Ljubljana, Ljubljana, Slovenia
| | - Jurij Gregorc
- Laboratory for Fluid Dynamics and Thermodynamics, Faculty of Mechanical Engineering, University of Ljubljana, Ljubljana, Slovenia
| | - Božidar Šarler
- Laboratory for Fluid Dynamics and Thermodynamics, Faculty of Mechanical Engineering, University of Ljubljana, Ljubljana, Slovenia,Laboratory for Simulation of Materials and Processes, Institute of Metals and Technology, Ljubljana, Slovenia
| | - Juraj Knoška
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Alfonso M. Gañán-Calvo
- Departamento de Ingeniería Aeroespacial y Mecánica de Fluidos, Universidad de Sevilla, Sevilla, Spain,Laboratory of Engineering for Energy and Environmental Sustainability, Universidad de Sevilla, Sevilla, Spain
| | - Henry N. Chapman
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany,The Hamburg Centre for Ultrafast Imaging, Hamburg, Germany,Department of Physics, Universität Hamburg, Hamburg, Germany
| | - Saša Bajt
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany,The Hamburg Centre for Ultrafast Imaging, Hamburg, Germany,*Correspondence: Saša Bajt,
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20
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Trost F, Ayyer K, Oberthuer D, Yefanov O, Bajt S, Caleman C, Weimer A, Feld A, Weller H, Boutet S, Koglin J, Timneanu N, von Zanthier J, Röhlsberger R, Chapman HN. Speckle contrast of interfering fluorescence X-rays. J Synchrotron Radiat 2023; 30:11-23. [PMID: 36601922 PMCID: PMC9814059 DOI: 10.1107/s1600577522009997] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 10/12/2022] [Indexed: 05/27/2023]
Abstract
With the development of X-ray free-electron lasers (XFELs), producing pulses of femtosecond durations comparable with the coherence times of X-ray fluorescence, it has become possible to observe intensity-intensity correlations due to the interference of emission from independent atoms. This has been used to compare durations of X-ray pulses and to measure the size of a focusedX-ray beam, for example. Here it is shown that it is also possible to observe the interference of fluorescence photons through the measurement of the speckle contrast of angle-resolved fluorescence patterns. Speckle contrast is often used as a measure of the degree of coherence of the incident beam or the fluctuations of the illuminated sample as determined from X-ray diffraction patterns formed by elastic scattering, rather than from fluorescence patterns as addressed here. Commonly used approaches to estimate speckle contrast were found to suffer when applied to XFEL-generated fluorescence patterns due to low photon counts and a significant variation of the excitation pulse energy from shot to shot. A new method to reliably estimate speckle contrast under such conditions, using a weighting scheme, is introduced. The method is demonstrated by comparing the speckle contrast of fluorescence observed with pulses of 3 fs to 15 fs duration.
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Affiliation(s)
- Fabian Trost
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, D-22761 Hamburg, Germany
| | - Kartik Ayyer
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, D-22761 Hamburg, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany
| | - Dominik Oberthuer
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Saša Bajt
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, D-22761 Hamburg, Germany
| | - Carl Caleman
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Department of Physics and Astronomy, Uppsala University, SE-75120 Uppsala, Sweden
| | - Agnes Weimer
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, D-22761 Hamburg, Germany
- Institute of Physical Chemistry, Universität Hamburg, Grindelallee 117, D-20146 Hamburg, Germany
| | - Artur Feld
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, D-22761 Hamburg, Germany
- Institute of Physical Chemistry, Universität Hamburg, Grindelallee 117, D-20146 Hamburg, Germany
| | - Horst Weller
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, D-22761 Hamburg, Germany
- Institute of Physical Chemistry, Universität Hamburg, Grindelallee 117, D-20146 Hamburg, Germany
- Department of Chemistry, Fraunhofer-CAN, Grindelallee 117, D-20146 Hamburg, Germany
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Jason Koglin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Nicusor Timneanu
- Department of Physics and Astronomy, Uppsala University, SE-75120 Uppsala, Sweden
| | - Joachim von Zanthier
- AG Quantum Optics and Quantum Information, University of Erlangen-Nürnberg, Staudtstrasse 1, D-91058 Erlangen, Germany
| | - Ralf Röhlsberger
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, Hamburg, Germany
| | - Henry N. Chapman
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, D-22761 Hamburg, Germany
- Department of Physics and Astronomy, Uppsala University, SE-75120 Uppsala, Sweden
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, Hamburg, Germany
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21
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Cardoch S, Trost F, Scott HA, Chapman HN, Caleman C, Timneanu N. Decreasing ultrafast x-ray pulse durations with saturable absorption and resonant transitions. Phys Rev E 2023; 107:015205. [PMID: 36797944 DOI: 10.1103/physreve.107.015205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 12/09/2022] [Indexed: 01/19/2023]
Abstract
Saturable absorption is a nonlinear effect where a material's ability to absorb light is frustrated due to a high influx of photons and the creation of electron vacancies. Experimentally induced saturable absorption in copper revealed a reduction in the temporal duration of transmitted x-ray laser pulses, but a detailed account of changes in opacity and emergence of resonances is still missing. In this computational work, we employ nonlocal thermodynamic equilibrium plasma simulations to study the interaction of femtosecond x rays and copper. Following the onset of frustrated absorption, we find that a K-M resonant transition occurring at highly charged states turns copper opaque again. The changes in absorption generate a transient transparent window responsible for the shortened transmission signal. We also propose using fluorescence induced by the incident beam as an alternative source to achieve shorter x-ray pulses. Intense femtosecond x rays are valuable to probe the structure and dynamics of biological samples or to reach extreme states of matter. Shortened pulses could be relevant for emerging imaging techniques.
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Affiliation(s)
- Sebastian Cardoch
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Fabian Trost
- Center for Free-Electron Laser Science CFEL, Deutsches-Elektronen Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Howard A Scott
- Lawrence Livermore National Laboratory, L-18, P.O. Box 808, Livermore, California 94550, USA
| | - Henry N Chapman
- Center for Free-Electron Laser Science CFEL, Deutsches-Elektronen Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany.,The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany.,Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Carl Caleman
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden.,Center for Free-Electron Laser Science CFEL, Deutsches-Elektronen Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Nicusor Timneanu
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
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22
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Stagno JR, Knoska J, Chapman HN, Wang YX. Mix-and-Inject Serial Femtosecond Crystallography to Capture RNA Riboswitch Intermediates. Methods Mol Biol 2023; 2568:243-249. [PMID: 36227573 DOI: 10.1007/978-1-0716-2687-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Time-resolved structure determination of macromolecular conformations and ligand-bound intermediates is extremely challenging, particularly for RNA. With rapid technological advances in both microfluidic liquid injection and X-ray free electron lasers (XFEL), a new frontier has emerged in time-resolved crystallography whereby crystals can be mixed with ligand and then probed with X-rays (mix-and-inject) in real time and at room temperature. This chapter outlines the basic setup and procedures for mix-and-inject experiments for recording time-resolved crystallographic data of riboswitch RNA reaction states using serial femtosecond crystallography (SFX) and an XFEL.
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Affiliation(s)
- Jason R Stagno
- Protein-Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Juraj Knoska
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
- Department of Physics, Universität Hamburg, Hamburg, Germany
| | - Henry N Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
- Department of Physics, Universität Hamburg, Hamburg, Germany
- Centre for Ultrafast Imaging, Universität Hamburg, Hamburg, Germany
| | - Yun-Xing Wang
- Protein-Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.
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23
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Sadri A, Hadian-Jazi M, Yefanov O, Galchenkova M, Kirkwood H, Mills G, Sikorski M, Letrun R, de Wijn R, Vakili M, Oberthuer D, Komadina D, Brehm W, Mancuso AP, Carnis J, Gelisio L, Chapman HN. Automatic bad-pixel mask maker for X-ray pixel detectors with application to serial crystallography. J Appl Crystallogr 2022; 55:1549-1561. [PMID: 36570663 PMCID: PMC9721322 DOI: 10.1107/s1600576722009815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 10/06/2022] [Indexed: 11/22/2022] Open
Abstract
X-ray crystallography has witnessed a massive development over the past decade, driven by large increases in the intensity and brightness of X-ray sources and enabled by employing high-frame-rate X-ray detectors. The analysis of large data sets is done via automatic algorithms that are vulnerable to imperfections in the detector and noise inherent with the detection process. By improving the model of the behaviour of the detector, data can be analysed more reliably and data storage costs can be significantly reduced. One major requirement is a software mask that identifies defective pixels in diffraction frames. This paper introduces a methodology and program based upon concepts of machine learning, called robust mask maker (RMM), for the generation of bad-pixel masks for large-area X-ray pixel detectors based on modern robust statistics. It is proposed to discriminate normally behaving pixels from abnormal pixels by analysing routine measurements made with and without X-ray illumination. Analysis software typically uses a Bragg peak finder to detect Bragg peaks and an indexing method to detect crystal lattices among those peaks. Without proper masking of the bad pixels, peak finding methods often confuse the abnormal values of bad pixels in a pattern with true Bragg peaks and flag such patterns as useful regardless, leading to storage of enormous uninformative data sets. Also, it is computationally very expensive for indexing methods to search for crystal lattices among false peaks and the solution may be biased. This paper shows how RMM vastly improves peak finders and prevents them from labelling bad pixels as Bragg peaks, by demonstrating its effectiveness on several serial crystallography data sets.
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Affiliation(s)
- Alireza Sadri
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany,Correspondence e-mail:
| | - Marjan Hadian-Jazi
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany,ARC Centre of Excellence in Advanced Molecular Imaging, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Australia,Australian Nuclear Science and Technology Organisation (ANSTO), Australia
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Marina Galchenkova
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Henry Kirkwood
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Grant Mills
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Marcin Sikorski
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Romain Letrun
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Raphael de Wijn
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Mohammad Vakili
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Dominik Oberthuer
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Dana Komadina
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Wolfgang Brehm
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Adrian P. Mancuso
- European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany,Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Jerome Carnis
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Luca Gelisio
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Henry N. Chapman
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany,Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany,The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
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24
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Zielinski KA, Prester A, Andaleeb H, Bui S, Yefanov O, Catapano L, Henkel A, Wiedorn MO, Lorbeer O, Crosas E, Meyer J, Mariani V, Domaracky M, White TA, Fleckenstein H, Sarrou I, Werner N, Betzel C, Rohde H, Aepfelbacher M, Chapman HN, Perbandt M, Steiner RA, Oberthuer D. Rapid and efficient room-temperature serial synchrotron crystallography using the CFEL TapeDrive. IUCrJ 2022; 9:778-791. [PMID: 36381150 PMCID: PMC9634612 DOI: 10.1107/s2052252522010193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 10/21/2022] [Indexed: 05/22/2023]
Abstract
Serial crystallography at conventional synchrotron light sources (SSX) offers the possibility to routinely collect data at room temperature using micrometre-sized crystals of biological macromolecules. However, SSX data collection is not yet as routine and currently takes significantly longer than the standard rotation series cryo-crystallography. Thus, its use for high-throughput approaches, such as fragment-based drug screening, where the possibility to measure at physio-logical temperatures would be a great benefit, is impaired. On the way to high-throughput SSX using a conveyor belt based sample delivery system - the CFEL TapeDrive - with three different proteins of biological relevance (Klebsiella pneumoniae CTX-M-14 β-lactamase, Nectria haematococca xylanase GH11 and Aspergillus flavus urate oxidase), it is shown here that complete datasets can be collected in less than a minute and only minimal amounts of sample are required.
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Affiliation(s)
- Kara A Zielinski
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Andreas Prester
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
| | - Hina Andaleeb
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Building 22a, Notkestr. 85, 22603 Hamburg, Germany
| | - Soi Bui
- Randall Centre of Cell and Molecular Biophysics, King’s College London, United Kingdom
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Lucrezia Catapano
- Randall Centre of Cell and Molecular Biophysics, King’s College London, United Kingdom
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Alessandra Henkel
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Max O. Wiedorn
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Olga Lorbeer
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Eva Crosas
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Jan Meyer
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Valerio Mariani
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Martin Domaracky
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Thomas A. White
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Holger Fleckenstein
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Iosifina Sarrou
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Nadine Werner
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Building 22a, Notkestr. 85, 22603 Hamburg, Germany
| | - Christian Betzel
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Building 22a, Notkestr. 85, 22603 Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Holger Rohde
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
| | - Martin Aepfelbacher
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
| | - Henry N. Chapman
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Markus Perbandt
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Building 22a, Notkestr. 85, 22603 Hamburg, Germany
| | - Roberto A. Steiner
- Randall Centre of Cell and Molecular Biophysics, King’s College London, United Kingdom
- Department of Biomedical Sciences, University of Padova, via Ugo Bassi 58/B, Padova 35131, Italy
| | - Dominik Oberthuer
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
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25
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Holmes S, Kirkwood HJ, Bean R, Giewekemeyer K, Martin AV, Hadian-Jazi M, Wiedorn MO, Oberthür D, Marman H, Adriano L, Al-Qudami N, Bajt S, Barák I, Bari S, Bielecki J, Brockhauser S, Coleman MA, Cruz-Mazo F, Danilevski C, Dörner K, Gañán-Calvo AM, Graceffa R, Fanghor H, Heymann M, Frank M, Kaukher A, Kim Y, Kobe B, Knoška J, Laurus T, Letrun R, Maia L, Messerschmidt M, Metz M, Michelat T, Mills G, Molodtsov S, Monteiro DCF, Morgan AJ, Münnich A, Peña Murillo GE, Previtali G, Round A, Sato T, Schubert R, Schulz J, Shelby M, Seuring C, Sellberg JA, Sikorski M, Silenzi A, Stern S, Sztuk-Dambietz J, Szuba J, Trebbin M, Vagovic P, Ve T, Weinhausen B, Wrona K, Xavier PL, Xu C, Yefanov O, Nugent KA, Chapman HN, Mancuso AP, Barty A, Abbey B, Darmanin C. Megahertz pulse trains enable multi-hit serial femtosecond crystallography experiments at X-ray free electron lasers. Nat Commun 2022; 13:4708. [PMID: 35953469 PMCID: PMC9372077 DOI: 10.1038/s41467-022-32434-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 07/28/2022] [Indexed: 11/12/2022] Open
Abstract
The European X-ray Free Electron Laser (XFEL) and Linac Coherent Light Source (LCLS) II are extremely intense sources of X-rays capable of generating Serial Femtosecond Crystallography (SFX) data at megahertz (MHz) repetition rates. Previous work has shown that it is possible to use consecutive X-ray pulses to collect diffraction patterns from individual crystals. Here, we exploit the MHz pulse structure of the European XFEL to obtain two complete datasets from the same lysozyme crystal, first hit and the second hit, before it exits the beam. The two datasets, separated by <1 µs, yield up to 2.1 Å resolution structures. Comparisons between the two structures reveal no indications of radiation damage or significant changes within the active site, consistent with the calculated dose estimates. This demonstrates MHz SFX can be used as a tool for tracking sub-microsecond structural changes in individual single crystals, a technique we refer to as multi-hit SFX. Free-electron lasers are capable of high repetition rates and it is assumed that protein crystals often do not survive the first X-ray pulse. Here the authors address these issues with a demonstration of multi-hit serial crystallography in which multiple FEL pulses interact with the sample without destroying it.
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Affiliation(s)
- Susannah Holmes
- Department of Mathematical and Physical Sciences, School of Engineering, Computing and Mathematical Sciences, La Trobe University, Melbourne, VIC, 3086, Australia.,La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | | | - Richard Bean
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Andrew V Martin
- School of Science, RMIT University, Melbourne, VIC, 3000, Australia
| | - Marjan Hadian-Jazi
- Department of Mathematical and Physical Sciences, School of Engineering, Computing and Mathematical Sciences, La Trobe University, Melbourne, VIC, 3086, Australia.,European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany.,Australian Nuclear Science and Technology Organisation (ANSTO), Sydney, NSW, 2234, Australia
| | - Max O Wiedorn
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany
| | - Dominik Oberthür
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany
| | - Hugh Marman
- Department of Mathematical and Physical Sciences, School of Engineering, Computing and Mathematical Sciences, La Trobe University, Melbourne, VIC, 3086, Australia.,La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Luigi Adriano
- Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany
| | | | - Saša Bajt
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, Hamburg, 22761, Germany
| | - Imrich Barák
- Institute of Molecular Biology, SAS, Dubravska cesta 21, 845 51, Bratislava, Slovakia
| | - Sadia Bari
- Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany
| | | | | | - Mathew A Coleman
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA, 94550, USA
| | - Francisco Cruz-Mazo
- Dept. de Ingeniería Aeroespacial y Mecánica de Fluidos, ETSI, Universidad de Sevilla, 41092, Sevilla, Spain.,Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ, 08544, USA
| | | | | | - Alfonso M Gañán-Calvo
- Dept. de Ingeniería Aeroespacial y Mecánica de Fluidos, ETSI, Universidad de Sevilla, 41092, Sevilla, Spain
| | - Rita Graceffa
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Hans Fanghor
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany.,Max-Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 175, 22761, Hamburg, Germany.,University of Southampton, Southampton, SO17 1BJ, UK
| | - Michael Heymann
- Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Am Pfaffenwaldring 57, 70569, Stuttgart, Germany
| | - Matthias Frank
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA, 94550, USA
| | | | - Yoonhee Kim
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Juraj Knoška
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany.,Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Torsten Laurus
- Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany
| | - Romain Letrun
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Luis Maia
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Marc Messerschmidt
- School of Molecular Science, Arizona State University, Tempe, AZ, 85281, USA
| | - Markus Metz
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany
| | | | - Grant Mills
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Serguei Molodtsov
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany.,Institute of Experimental Physics, TU Bergakademie Freiberg, Leipziger, Str. 23, 09599, Freiberg, Germany.,ITMO University, Kronverksky pr. 49, St. Petersburg, 197101, Russia
| | - Diana C F Monteiro
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, Hamburg, 22761, Germany.,Hauptman-Woodward Medical Research Institute, 700 Ellicott St., Buffalo, NY, 14203, USA
| | - Andrew J Morgan
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany.,Department of Physics, University of Melbourne, Parkville, VIC, 3010, Australia
| | | | - Gisel E Peña Murillo
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany
| | | | - Adam Round
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Tokushi Sato
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany.,Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany
| | | | | | - Megan Shelby
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA, 94550, USA
| | - Carolin Seuring
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, Hamburg, 22761, Germany
| | - Jonas A Sellberg
- Biomedical and X-ray Physics, Department of Applied Physics, AlbaNova University Center, KTH Royal Institute of Technology, SE-106 91, Stockholm, Sweden
| | | | | | - Stephan Stern
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Janusz Szuba
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Martin Trebbin
- Institute of Experimental Physics, TU Bergakademie Freiberg, Leipziger, Str. 23, 09599, Freiberg, Germany.,Department of Chemistry, State University of New York at Buffalo, 760 Natural Sciences Complex, Buffalo, NY, 14260, USA
| | | | - Thomas Ve
- Institute for Glycomics, Griffith University, Southport, QLD, 4222, Australia
| | | | | | - Paul Lourdu Xavier
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany.,Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany.,Max-Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 175, 22761, Hamburg, Germany
| | - Chen Xu
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany
| | - Keith A Nugent
- Department of Quantum Science and Technology, Research School of Physics, Australian National University, Canberra, ACT, 2601, Australia
| | - Henry N Chapman
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, Hamburg, 22761, Germany.,Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Adrian P Mancuso
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany.,La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Anton Barty
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr 85, 22607, Hamburg, Germany
| | - Brian Abbey
- Department of Mathematical and Physical Sciences, School of Engineering, Computing and Mathematical Sciences, La Trobe University, Melbourne, VIC, 3086, Australia. .,La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia.
| | - Connie Darmanin
- Department of Mathematical and Physical Sciences, School of Engineering, Computing and Mathematical Sciences, La Trobe University, Melbourne, VIC, 3086, Australia. .,La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia.
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26
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Srinivasan V, Brognaro H, Prabhu PR, de Souza EE, Günther S, Reinke PYA, Lane TJ, Ginn H, Han H, Ewert W, Sprenger J, Koua FHM, Falke S, Werner N, Andaleeb H, Ullah N, Franca BA, Wang M, Barra ALC, Perbandt M, Schwinzer M, Schmidt C, Brings L, Lorenzen K, Schubert R, Machado RRG, Candido ED, Oliveira DBL, Durigon EL, Niebling S, Garcia AS, Yefanov O, Lieske J, Gelisio L, Domaracky M, Middendorf P, Groessler M, Trost F, Galchenkova M, Mashhour AR, Saouane S, Hakanpää J, Wolf M, Alai MG, Turk D, Pearson AR, Chapman HN, Hinrichs W, Wrenger C, Meents A, Betzel C. Antiviral activity of natural phenolic compounds in complex at an allosteric site of SARS-CoV-2 papain-like protease. Commun Biol 2022; 5:805. [PMID: 35953531 PMCID: PMC9366811 DOI: 10.1038/s42003-022-03737-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 07/18/2022] [Indexed: 11/09/2022] Open
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.
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Affiliation(s)
- Vasundara Srinivasan
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany.
| | - Hévila Brognaro
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany
| | - Prince R Prabhu
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany.,Hamburg Centre for Ultrafast Imaging (CUI), Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Edmarcia Elisa de Souza
- Department of Parasitology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo, Brazil
| | - Sebastian Günther
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Patrick Y A Reinke
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Thomas J Lane
- Hamburg Centre for Ultrafast Imaging (CUI), Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.,Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Helen Ginn
- Diamond Light Source Ltd. Diamond House, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Huijong Han
- European XFEL GmbH. Holzkoppel 4, 22869, Schenefeld, Germany
| | - Wiebke Ewert
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Janina Sprenger
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Faisal H M Koua
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Sven Falke
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany.,Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Nadine Werner
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany
| | - Hina Andaleeb
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany.,Department of Biochemistry, Bahauddin Zakariya University Multan-, 60800, Punjab, Pakistan
| | - Najeeb Ullah
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany.,Department of Biochemistry, Bahauddin Zakariya University Multan-, 60800, Punjab, Pakistan
| | - Bruno Alves Franca
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany
| | - Mengying Wang
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany
| | - Angélica Luana C Barra
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany.,Pólo TerRa, São Carlos Institute of Physics, University of São Paulo, São Carlos, Brazil
| | - Markus Perbandt
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany
| | - Martin Schwinzer
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany
| | | | - Lea Brings
- European XFEL GmbH. Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Robin Schubert
- European XFEL GmbH. Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Erika Donizette Candido
- Department of Microbiology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo, Brazil
| | - Danielle Bruna Leal Oliveira
- Department of Microbiology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo, Brazil.,Clinical Laboratory, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Edison Luiz Durigon
- Department of Microbiology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo, Brazil.,Scientific Platform Pasteur USP, São Paulo, Brazil
| | - Stephan Niebling
- European Molecular Biology Laboratory Hamburg, c/o DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Angelica Struve Garcia
- European Molecular Biology Laboratory Hamburg, c/o DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Julia Lieske
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Luca Gelisio
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Martin Domaracky
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Philipp Middendorf
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Michael Groessler
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Fabian Trost
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Marina Galchenkova
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Aida Rahmani Mashhour
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Sofiane Saouane
- Photon Science, Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607, Hamburg, Germany
| | - Johanna Hakanpää
- Photon Science, Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607, Hamburg, Germany
| | - Markus Wolf
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee114, 22525, Hamburg, Germany
| | - Maria Garcia Alai
- European Molecular Biology Laboratory Hamburg, c/o DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Dusan Turk
- Department of Biochemistry & Molecular & Structural Biology, Jozef Stefan Institute, Jamova 39, 1 000, Ljubljana, Slovenia.,Centre of excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKEBIP), Jamova 39, 1 000, Ljubljana, Slovenia
| | - Arwen R Pearson
- Hamburg Centre for Ultrafast Imaging (CUI), Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.,Institut für Nanostruktur- und Festkörperphysik, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Henry N Chapman
- Hamburg Centre for Ultrafast Imaging (CUI), Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.,Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.,Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Winfried Hinrichs
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Carsten Wrenger
- Department of Parasitology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo, Brazil
| | - Alke Meents
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Christian Betzel
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany. .,Hamburg Centre for Ultrafast Imaging (CUI), Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.
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27
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Ivanov N, Lukas Dresselhaus J, Carnis J, Domaracky M, Fleckenstein H, Li C, Li T, Prasciolu M, Yefanov O, Zhang W, Bajt S, Chapman HN. Robust ptychographic X-ray speckle tracking with multilayer Laue lenses. Opt Express 2022; 30:25450-25473. [PMID: 36237075 DOI: 10.1364/oe.460903] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 05/30/2022] [Indexed: 06/16/2023]
Abstract
In recent years, X-ray speckle tracking techniques have emerged as viable tools for wavefront metrology and sample imaging applications, and have been actively developed for use at synchrotron light sources. Speckle techniques can recover an image free of aberrations and can be used to measure wavefronts with a high angular sensitivity. Since they are compatible with low-coherence sources they can be also used with laboratory X-ray sources. A new implementation of the ptychographic X-ray speckle tracking method, suitable for the metrology of highly divergent wavefields, such as those created by multilayer Laue lenses, is presented here. This new program incorporates machine learning techniques such as Huber and non-parametric regression and enables robust and quick wavefield measurements and data evaluation even for low brilliance X-ray beams, and the imaging of low-contrast samples. To realize this, a software suite was written in Python 3, with a C back-end capable of concurrent calculations for high performance. It is accessible as a Python module and is available as source code under Version 3 or later of the GNU General Public License.
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28
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Dresselhaus JL, Fleckenstein H, Domaracký M, Prasciolu M, Ivanov N, Carnis J, Murray KT, Morgan AJ, Chapman HN, Bajt S. Precise wavefront characterization of x-ray optical elements using a laboratory source. Rev Sci Instrum 2022; 93:073704. [PMID: 35922318 DOI: 10.1063/5.0092269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 06/12/2022] [Indexed: 06/15/2023]
Abstract
Improvements in x-ray optics critically depend on the measurement of their optical performance. The knowledge of wavefront aberrations, for example, can be used to improve the fabrication of optical elements or to design phase correctors to compensate for these errors. At present, the characterization of such optics is made using intense x-ray sources, such as synchrotrons. However, the limited access to these facilities can substantially slow down the development process. Improvements in the brightness of lab-based x-ray micro-sources in combination with the development of new metrology methods, particularly ptychographic x-ray speckle tracking, enable characterization of x-ray optics in the lab with a precision and sensitivity not possible before. Here, we present a laboratory setup that utilizes a commercially available x-ray source and can be used to characterize different types of x-ray optics. The setup is used in our laboratory on a routine basis to characterize multilayer Laue lenses of high numerical aperture and other optical elements. This typically includes measurements of the wavefront distortions, optimum operating photon energy, and focal length of the lens. To check the sensitivity and accuracy of this laboratory setup, we compared the results to those obtained at the synchrotron and saw no significant difference. To illustrate the feedback of measurements on performance, we demonstrated the correction of the phase errors of a particular multilayer Laue lens using a 3D printed compound refractive phase plate.
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Affiliation(s)
- J Lukas Dresselhaus
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Holger Fleckenstein
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Martin Domaracký
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Mauro Prasciolu
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Nikolay Ivanov
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Jerome Carnis
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Kevin T Murray
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Andrew J Morgan
- School of Physics, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Henry N Chapman
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Saša Bajt
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
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29
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Zhuang Y, Awel S, Barty A, Bean R, Bielecki J, Bergemann M, Daurer BJ, Ekeberg T, Estillore AD, Fangohr H, Giewekemeyer K, Hunter MS, Karnevskiy M, Kirian RA, Kirkwood H, Kim Y, Koliyadu J, Lange H, Letrun R, Lübke J, Mall A, Michelat T, Morgan AJ, Roth N, Samanta AK, Sato T, Shen Z, Sikorski M, Schulz F, Spence JCH, Vagovic P, Wollweber T, Worbs L, Xavier PL, Yefanov O, Maia FRNC, Horke DA, Küpper J, Loh ND, Mancuso AP, Chapman HN, Ayyer K. Unsupervised learning approaches to characterizing heterogeneous samples using X-ray single-particle imaging. IUCrJ 2022; 9:204-214. [PMID: 35371510 PMCID: PMC8895023 DOI: 10.1107/s2052252521012707] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 11/30/2021] [Indexed: 06/12/2023]
Abstract
One of the outstanding analytical problems in X-ray single-particle imaging (SPI) is the classification of structural heterogeneity, which is especially difficult given the low signal-to-noise ratios of individual patterns and the fact that even identical objects can yield patterns that vary greatly when orientation is taken into consideration. Proposed here are two methods which explicitly account for this orientation-induced variation and can robustly determine the structural landscape of a sample ensemble. The first, termed common-line principal component analysis (PCA), provides a rough classification which is essentially parameter free and can be run automatically on any SPI dataset. The second method, utilizing variation auto-encoders (VAEs), can generate 3D structures of the objects at any point in the structural landscape. Both these methods are implemented in combination with the noise-tolerant expand-maximize-compress (EMC) algorithm and its utility is demonstrated by applying it to an experimental dataset from gold nanoparticles with only a few thousand photons per pattern. Both discrete structural classes and continuous deformations are recovered. These developments diverge from previous approaches of extracting reproducible subsets of patterns from a dataset and open up the possibility of moving beyond the study of homogeneous sample sets to addressing open questions on topics such as nanocrystal growth and dynamics, as well as phase transitions which have not been externally triggered.
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Affiliation(s)
- Yulong Zhuang
- Max Planck Institute for the Structure and Dynamics of Matter, 22761 Hamburg, Germany
- Center for Free-Electron Laser Science, 22761 Hamburg, Germany
| | - Salah Awel
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Anton Barty
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | | | | | | | - Benedikt J. Daurer
- Center for Bio-Imaging Sciences, National University of Singapore, 117557, Singapore
| | - Tomas Ekeberg
- Department of Cell and Molecular Biology, Uppsala University, 75124 Uppsala, Sweden
| | - Armando D. Estillore
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Hans Fangohr
- Max Planck Institute for the Structure and Dynamics of Matter, 22761 Hamburg, Germany
- Center for Free-Electron Laser Science, 22761 Hamburg, Germany
- European XFEL, 22869 Schenefeld, Germany
- University of Southampton, Southampton SO17 1BJ, United Kingdom
| | | | - Mark S. Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | | | - Richard A. Kirian
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | | | | | | | - Holger Lange
- Hamburg Center for Ultrafast Imaging, Universität Hamburg, 22761 Hamburg, Germany
- Institute of Physical Chemistry, Universität Hamburg, 20146 Hamburg, Germany
| | | | - Jannik Lübke
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
- Hamburg Center for Ultrafast Imaging, Universität Hamburg, 22761 Hamburg, Germany
- Department of Physics, Universität Hamburg, 22761 Hamburg, Germany
| | - Abhishek Mall
- Max Planck Institute for the Structure and Dynamics of Matter, 22761 Hamburg, Germany
- Center for Free-Electron Laser Science, 22761 Hamburg, Germany
| | | | - Andrew J. Morgan
- Department of Physics, University of Melbourne, Victoria 3010, Australia
| | - Nils Roth
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
- Department of Physics, Universität Hamburg, 22761 Hamburg, Germany
| | - Amit K. Samanta
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | | | - Zhou Shen
- Center for Bio-Imaging Sciences, National University of Singapore, 117557, Singapore
| | - Marcin Sikorski
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Florian Schulz
- Hamburg Center for Ultrafast Imaging, Universität Hamburg, 22761 Hamburg, Germany
- Institute of Nanostructure and Solid State Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - John C. H. Spence
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Patrik Vagovic
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
- European XFEL, 22869 Schenefeld, Germany
| | - Tamme Wollweber
- Max Planck Institute for the Structure and Dynamics of Matter, 22761 Hamburg, Germany
- Center for Free-Electron Laser Science, 22761 Hamburg, Germany
- Hamburg Center for Ultrafast Imaging, Universität Hamburg, 22761 Hamburg, Germany
| | - Lena Worbs
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
- Department of Physics, Universität Hamburg, 22761 Hamburg, Germany
| | - P. Lourdu Xavier
- Max Planck Institute for the Structure and Dynamics of Matter, 22761 Hamburg, Germany
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
- Hamburg Center for Ultrafast Imaging, Universität Hamburg, 22761 Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Filipe R. N. C. Maia
- Department of Cell and Molecular Biology, Uppsala University, 75124 Uppsala, Sweden
- NERSC, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Daniel A. Horke
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
- Hamburg Center for Ultrafast Imaging, Universität Hamburg, 22761 Hamburg, Germany
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, Netherlands
| | - Jochen Küpper
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
- Hamburg Center for Ultrafast Imaging, Universität Hamburg, 22761 Hamburg, Germany
- Department of Physics, Universität Hamburg, 22761 Hamburg, Germany
- Department of Chemistry, Universität Hamburg, 20146 Hamburg, Germany
| | - N. Duane Loh
- Center for Bio-Imaging Sciences, National University of Singapore, 117557, Singapore
- Department of Physics, National University of Singapore, 117551, Singapore
| | - Adrian P. Mancuso
- European XFEL, 22869 Schenefeld, Germany
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Henry N. Chapman
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
- Hamburg Center for Ultrafast Imaging, Universität Hamburg, 22761 Hamburg, Germany
- Department of Physics, Universität Hamburg, 22761 Hamburg, Germany
| | - Kartik Ayyer
- Max Planck Institute for the Structure and Dynamics of Matter, 22761 Hamburg, Germany
- Center for Free-Electron Laser Science, 22761 Hamburg, Germany
- Hamburg Center for Ultrafast Imaging, Universität Hamburg, 22761 Hamburg, Germany
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30
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Doppler D, Rabbani MT, Letrun R, Cruz Villarreal J, Kim DH, Gandhi S, Egatz-Gomez A, Sonker M, Chen J, Koua FHM, Yang J, Youssef M, Mazalova V, Bajt S, Shelby ML, Coleman MA, Wiedorn MO, Knoska J, Schön S, Sato T, Hunter MS, Hosseinizadeh A, Kuptiz C, Nazari R, Alvarez RC, Karpos K, Zaare S, Dobson Z, Discianno E, Zhang S, Zook JD, Bielecki J, de Wijn R, Round AR, Vagovic P, Kloos M, Vakili M, Ketawala GK, Stander NE, Olson TL, Morin K, Mondal J, Nguyen J, Meza-Aguilar JD, Kodis G, Vaiana S, Martin-Garcia JM, Mariani V, Schwander P, Schmidt M, Messerschmidt M, Ourmazd A, Zatsepin N, Weierstall U, Bruce BD, Mancuso AP, Grant T, Barty A, Chapman HN, Frank M, Fromme R, Spence JCH, Botha S, Fromme P, Kirian RA, Ros A. Co-flow injection for serial crystallography at X-ray free-electron lasers. J Appl Crystallogr 2022; 55:1-13. [PMID: 35153640 PMCID: PMC8805165 DOI: 10.1107/s1600576721011079] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 10/22/2021] [Indexed: 02/03/2023] Open
Abstract
Serial femtosecond crystallography (SFX) is a powerful technique that exploits X-ray free-electron lasers to determine the structure of macro-molecules at room temperature. Despite the impressive exposition of structural details with this novel crystallographic approach, the methods currently available to introduce crystals into the path of the X-ray beam sometimes exhibit serious drawbacks. Samples requiring liquid injection of crystal slurries consume large quantities of crystals (at times up to a gram of protein per data set), may not be compatible with vacuum configurations on beamlines or provide a high background due to additional sheathing liquids present during the injection. Proposed and characterized here is the use of an immiscible inert oil phase to supplement the flow of sample in a hybrid microfluidic 3D-printed co-flow device. Co-flow generation is reported with sample and oil phases flowing in parallel, resulting in stable injection conditions for two different resin materials experimentally. A numerical model is presented that adequately predicts these flow-rate conditions. The co-flow generating devices reduce crystal clogging effects, have the potential to conserve protein crystal samples up to 95% and will allow degradation-free light-induced time-resolved SFX.
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Affiliation(s)
- Diandra Doppler
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Mohammad T. Rabbani
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | | | - Jorvani Cruz Villarreal
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Dai Hyun Kim
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Sahir Gandhi
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Ana Egatz-Gomez
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Mukul Sonker
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Joe Chen
- Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Faisal H. M. Koua
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Jayhow Yang
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Mohamed Youssef
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Victoria Mazalova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Saša Bajt
- Hamburg Center for Ultrafast Imaging, Hamburg, Germany,Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Megan L. Shelby
- Lawrence Livermore National Laboratory (LLNL), Livermore, California, USA
| | - Matt A. Coleman
- Lawrence Livermore National Laboratory (LLNL), Livermore, California, USA
| | - Max O. Wiedorn
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany,Hamburg Center for Ultrafast Imaging, Hamburg, Germany,Department of Physics, Universität Hamburg, Hamburg, Germany
| | - Juraj Knoska
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Silvan Schön
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | | | - Mark S. Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Ahmad Hosseinizadeh
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Christopher Kuptiz
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Reza Nazari
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Roberto C. Alvarez
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Konstantinos Karpos
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Sahba Zaare
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Zachary Dobson
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Erin Discianno
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Shangji Zhang
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - James D. Zook
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | | | | | - Adam R. Round
- European XFEL, Schenefeld, Germany,School of Chemical and Physical Sciences, Keele University, Staffordshire, UK
| | - Patrik Vagovic
- European XFEL, Schenefeld, Germany,Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | | | | | - Gihan K. Ketawala
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Natasha E. Stander
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Tien L. Olson
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Katherine Morin
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Jyotirmory Mondal
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, USA
| | - Jonathan Nguyen
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - José Domingo Meza-Aguilar
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,European XFEL, Schenefeld, Germany
| | - Gerdenis Kodis
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Sara Vaiana
- Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Jose M. Martin-Garcia
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Crystallography and Structural Biology, Institute of Physical Chemistry ‘Rocasolano’, CSIC, Madrid, Spain
| | - Valerio Mariani
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Peter Schwander
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Marius Schmidt
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Marc Messerschmidt
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Abbas Ourmazd
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Nadia Zatsepin
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA,Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Uwe Weierstall
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Barry D. Bruce
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, USA
| | - Adrian P. Mancuso
- European XFEL, Schenefeld, Germany,Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Thomas Grant
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, New York, USA
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany,Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany,Center for Data and Computing in Natural Science CDCS, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Henry N. Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany,Hamburg Center for Ultrafast Imaging, Hamburg, Germany,Department of Physics, Universität Hamburg, Hamburg, Germany
| | - Matthias Frank
- Lawrence Livermore National Laboratory (LLNL), Livermore, California, USA
| | - Raimund Fromme
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - John C. H. Spence
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Sabine Botha
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Petra Fromme
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Richard A. Kirian
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Alexandra Ros
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA,Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA,Correspondence e-mail:
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31
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Pandey S, Calvey G, Katz AM, Malla TN, Koua FHM, Martin-Garcia JM, Poudyal I, Yang JH, Vakili M, Yefanov O, Zielinski KA, Bajt S, Awel S, Doerner K, Frank M, Gelisio L, Jernigan R, Kirkwood H, Kloos M, Koliyadu J, Mariani V, Miller MD, Mills G, Nelson G, Olmos JL, Sadri A, Sato T, Tolstikova A, Xu W, Ourmazd A, Spence JCH, Schwander P, Barty A, Chapman HN, Fromme P, Mancuso AP, Phillips GN, Bean R, Pollack L, Schmidt M. Observation of substrate diffusion and ligand binding in enzyme crystals using high-repetition-rate mix-and-inject serial crystallography. IUCrJ 2021; 8:878-895. [PMID: 34804542 PMCID: PMC8562667 DOI: 10.1107/s2052252521008125] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/06/2021] [Indexed: 05/22/2023]
Abstract
Here, we illustrate what happens inside the catalytic cleft of an enzyme when substrate or ligand binds on single-millisecond timescales. The initial phase of the enzymatic cycle is observed with near-atomic resolution using the most advanced X-ray source currently available: the European XFEL (EuXFEL). The high repetition rate of the EuXFEL combined with our mix-and-inject technology enables the initial phase of ceftriaxone binding to the Mycobacterium tuberculosis β-lactamase to be followed using time-resolved crystallography in real time. It is shown how a diffusion coefficient in enzyme crystals can be derived directly from the X-ray data, enabling the determination of ligand and enzyme-ligand concentrations at any position in the crystal volume as a function of time. In addition, the structure of the irreversible inhibitor sulbactam bound to the enzyme at a 66 ms time delay after mixing is described. This demonstrates that the EuXFEL can be used as an important tool for biomedically relevant research.
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Affiliation(s)
- Suraj Pandey
- Physics Department, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, WI 53211, USA
| | - George Calvey
- School of Applied and Engineering Physics, Cornell University, 254 Clark Hall, Ithaca, NY 14853, USA
| | - Andrea M. Katz
- School of Applied and Engineering Physics, Cornell University, 254 Clark Hall, Ithaca, NY 14853, USA
| | - Tek Narsingh Malla
- Physics Department, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, WI 53211, USA
| | - Faisal H. M. Koua
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Jose M. Martin-Garcia
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-1604, USA
- Institute of Physical Chemistry Rocasolano, Spanish National Research Council, Calle de Serrano 119, 28006 Madrid, Spain
| | - Ishwor Poudyal
- Physics Department, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, WI 53211, USA
| | - Jay-How Yang
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-1604, USA
| | | | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Kara A. Zielinski
- School of Applied and Engineering Physics, Cornell University, 254 Clark Hall, Ithaca, NY 14853, USA
| | - Sasa Bajt
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Salah Awel
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | | | - Matthias Frank
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - Luca Gelisio
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Rebecca Jernigan
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-1604, USA
| | | | - Marco Kloos
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | - Valerio Mariani
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- SLAC National Accelerator Laboratory, 2575 Sand Hill Rd, Menlo Park, California 94025, USA
| | - Mitchell D. Miller
- Department of BioSciences, Rice University, 6100 Main Street, Houston, TX 77005, USA
| | - Grant Mills
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Garrett Nelson
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Jose L. Olmos
- Department of BioSciences, Rice University, 6100 Main Street, Houston, TX 77005, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Alireza Sadri
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Tokushi Sato
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Alexandra Tolstikova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Weijun Xu
- Department of BioSciences, Rice University, 6100 Main Street, Houston, TX 77005, USA
| | - Abbas Ourmazd
- Physics Department, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, WI 53211, USA
| | - John C. H. Spence
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Peter Schwander
- Physics Department, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, WI 53211, USA
| | - Anton Barty
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Henry N. Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Petra Fromme
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Adrian P. Mancuso
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - George N. Phillips
- Department of BioSciences, Rice University, 6100 Main Street, Houston, TX 77005, USA
- Department of Chemistry, Rice University, 6100 Main Street, Houston, TX 77005, USA
| | - Richard Bean
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, 254 Clark Hall, Ithaca, NY 14853, USA
| | - Marius Schmidt
- Physics Department, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, WI 53211, USA
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32
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Awel S, Bohne S, Ebrahimifard R, Trieu HK, Bajt S, Chapman HN. Optical bunching of particles in a liquid flow. Opt Express 2021; 29:34394-34410. [PMID: 34809231 DOI: 10.1364/oe.440173] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 09/29/2021] [Indexed: 06/13/2023]
Abstract
High-speed liquid micro-jets are used to rapidly and repeatedly deliver protein microcrystals to focused and pulsed X-ray beams in the method of serial femtosecond crystallography. However, the current continuous flow of crystals is mismatched to the arrival of X-ray pulses, wasting vast amounts of an often rare and precious sample. Here, we introduce a method to address this problem by periodically trapping and releasing crystals in the liquid flow, creating locally concentrated crystal bunches, using an optical trap integrated in the microfluidic supply line. We experimentally demonstrate a 30-fold increase of particle concentration into 10 Hz bunches of 6.4 μm diameter polystyrene particles. Furthermore, using particle trajectory simulations, a comprehensive description of the optical bunching process and parameter space is presented. Adding this compact optofluidics device to existing injection systems would thereby dramatically reduce sample consumption and extend the application of serial crystallography to a greater range of protein crystal systems that cannot be produced in high abundance. Our approach is suitable for other microfluidic systems that require synchronous measurements of flowing objects.
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33
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Hadian-Jazi M, Sadri A, Barty A, Yefanov O, Galchenkova M, Oberthuer D, Komadina D, Brehm W, Kirkwood H, Mills G, de Wijn R, Letrun R, Kloos M, Vakili M, Gelisio L, Darmanin C, Mancuso AP, Chapman HN, Abbey B. Data reduction for serial crystallography using a robust peak finder. J Appl Crystallogr 2021; 54:1360-1378. [PMID: 34667447 PMCID: PMC8493619 DOI: 10.1107/s1600576721007317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 07/14/2021] [Indexed: 11/23/2022] Open
Abstract
This article focuses on the challenges of hit finding and data reduction in serial crystallography (SX). An effective and reliable Bragg-peak-finding method, called robust peak finder (RPF), has been developed. RPF is based on the principle of robust statistics and can be used for SX data analysis. A peak-finding algorithm for serial crystallography (SX) data analysis based on the principle of ‘robust statistics’ has been developed. Methods which are statistically robust are generally more insensitive to any departures from model assumptions and are particularly effective when analysing mixtures of probability distributions. For example, these methods enable the discretization of data into a group comprising inliers (i.e. the background noise) and another group comprising outliers (i.e. Bragg peaks). Our robust statistics algorithm has two key advantages, which are demonstrated through testing using multiple SX data sets. First, it is relatively insensitive to the exact value of the input parameters and hence requires minimal optimization. This is critical for the algorithm to be able to run unsupervised, allowing for automated selection or ‘vetoing’ of SX diffraction data. Secondly, the processing of individual diffraction patterns can be easily parallelized. This means that it can analyse data from multiple detector modules simultaneously, making it ideally suited to real-time data processing. These characteristics mean that the robust peak finder (RPF) algorithm will be particularly beneficial for the new class of MHz X-ray free-electron laser sources, which generate large amounts of data in a short period of time.
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Affiliation(s)
- Marjan Hadian-Jazi
- ARC Centre of Excellence in Advanced Molecular Imaging, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Australia.,Australian Nuclear Science and Technology Organisation (ANSTO), Australia.,European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Alireza Sadri
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Marina Galchenkova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Dominik Oberthuer
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Dana Komadina
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Wolfgang Brehm
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | | | - Grant Mills
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | - Romain Letrun
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Marco Kloos
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | - Luca Gelisio
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Connie Darmanin
- ARC Centre of Excellence in Advanced Molecular Imaging, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Australia
| | - Adrian P Mancuso
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany.,Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Henry N Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany.,Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Brian Abbey
- ARC Centre of Excellence in Advanced Molecular Imaging, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Australia
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34
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Chapman HN, Bajt S. High-resolution achromatic X-ray optical systems for broad-band imaging and for focusing attosecond pulses. Proc Math Phys Eng Sci 2021; 477:20210334. [PMID: 34276244 PMCID: PMC8277474 DOI: 10.1098/rspa.2021.0334] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 06/15/2021] [Indexed: 11/12/2022] Open
Abstract
Achromatic focusing systems for hard X-rays are examined which consist of a refractive lens paired with a diffractive lens. Compared with previous analyses, we take into account the behaviour of thick refractive lenses, such as compound refractive lenses and waveguide gradient index refractive lenses, in which both the focal length and the position of the principal planes vary with wavelength. Achromatic systems formed by the combination of such a thick refractive lens with a multilayer Laue lens are found that can operate at a focusing resolution of about 3 nm, over a relative bandwidth of about 1%. With the appropriate distance between the refractive and diffractive lenses, apochromatic systems can also be found, which operate over relative bandwidth greater than 10%. These systems can be used to focus short pulses without distorting them in time by more than several attoseconds. Such systems are suitable for high-flux scanning microscopy and for creating high intensities from attosecond X-ray pulses.
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Affiliation(s)
- H N Chapman
- Center for Free-Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany.,Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany.,Molecular and Condensed Matter Physics, Department of Physics and Astronomy, Uppsala University, Box 516, 751 20 Uppsala, Sweden
| | - S Bajt
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
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35
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Günther S, Reinke PYA, Fernández-García Y, Lieske J, Lane TJ, Ginn HM, Koua FHM, Ehrt C, Ewert W, Oberthuer D, Yefanov O, Meier S, Lorenzen K, Krichel B, Kopicki JD, Gelisio L, Brehm W, Dunkel I, Seychell B, Gieseler H, Norton-Baker B, Escudero-Pérez B, Domaracky M, Saouane S, Tolstikova A, White TA, Hänle A, Groessler M, Fleckenstein H, Trost F, Galchenkova M, Gevorkov Y, Li C, Awel S, Peck A, Barthelmess M, Schlünzen F, Lourdu Xavier P, Werner N, Andaleeb H, Ullah N, Falke S, Srinivasan V, França BA, Schwinzer M, Brognaro H, Rogers C, Melo D, Zaitseva-Doyle JJ, Knoska J, Peña-Murillo GE, Mashhour AR, Hennicke V, Fischer P, Hakanpää J, Meyer J, Gribbon P, Ellinger B, Kuzikov M, Wolf M, Beccari AR, Bourenkov G, von Stetten D, Pompidor G, Bento I, Panneerselvam S, Karpics I, Schneider TR, Garcia-Alai MM, Niebling S, Günther C, Schmidt C, Schubert R, Han H, Boger J, Monteiro DCF, Zhang L, Sun X, Pletzer-Zelgert J, Wollenhaupt J, Feiler CG, Weiss MS, Schulz EC, Mehrabi P, Karničar K, Usenik A, Loboda J, Tidow H, Chari A, Hilgenfeld R, Uetrecht C, Cox R, Zaliani A, Beck T, Rarey M, Günther S, Turk D, Hinrichs W, Chapman HN, Pearson AR, Betzel C, Meents A. X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease. Science 2021; 372:642-646. [PMID: 33811162 PMCID: PMC8224385 DOI: 10.1126/science.abf7945] [Citation(s) in RCA: 203] [Impact Index Per Article: 67.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 03/29/2021] [Indexed: 12/17/2022]
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 nonpeptidic compounds showed antiviral activity at nontoxic concentrations. We identified two allosteric binding sites representing attractive targets for drug development against SARS-CoV-2.
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Affiliation(s)
- Sebastian Günther
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany.
| | - Patrick Y A Reinke
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Yaiza Fernández-García
- Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Str. 74, 20359 Hamburg, Germany
| | - Julia Lieske
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Thomas J Lane
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Helen M Ginn
- Diamond Light Source Ltd., Diamond House, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Faisal H M Koua
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Christiane Ehrt
- Universität Hamburg, Center for Bioinformatics, Bundesstr. 43, 20146 Hamburg, Germany
| | - Wiebke Ewert
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Dominik Oberthuer
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Susanne Meier
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Institut für Nanostruktur- und Festkörperphysik, Luruper Chaussee 149, 22761 Hamburg, Germany
| | | | - Boris Krichel
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistr. 52, 20251 Hamburg, Germany
| | - Janine-Denise Kopicki
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistr. 52, 20251 Hamburg, Germany
| | - Luca Gelisio
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Wolfgang Brehm
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Ilona Dunkel
- Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Brandon Seychell
- Universität Hamburg, Department of Chemistry, Institute of Physical Chemistry, Grindelallee 117, 20146 Hamburg, Germany
| | - Henry Gieseler
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Institut für Nanostruktur- und Festkörperphysik, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Brenna Norton-Baker
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Chemistry, UC Irvine, Irvine, CA 92697-2025, USA
| | - Beatriz Escudero-Pérez
- Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Str. 74, 20359 Hamburg, Germany
| | - Martin Domaracky
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Sofiane Saouane
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Alexandra Tolstikova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Thomas A White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Anna Hänle
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Michael Groessler
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Holger Fleckenstein
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Fabian Trost
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Marina Galchenkova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Yaroslav Gevorkov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- Vision Systems, Hamburg University of Technology, 21071 Hamburg, Germany
| | - Chufeng Li
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Salah Awel
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Ariana Peck
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Miriam Barthelmess
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Frank Schlünzen
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - P Lourdu Xavier
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Nadine Werner
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
| | - Hina Andaleeb
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
| | - Najeeb Ullah
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
| | - Sven Falke
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
| | - Vasundara Srinivasan
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
| | - Bruno Alves França
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
| | - Martin Schwinzer
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
| | - Hévila Brognaro
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
| | - Cromarte Rogers
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Institut für Nanostruktur- und Festkörperphysik, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Diogo Melo
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Institut für Nanostruktur- und Festkörperphysik, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Joanna J Zaitseva-Doyle
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Institut für Nanostruktur- und Festkörperphysik, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Juraj Knoska
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Gisel E Peña-Murillo
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Aida Rahmani Mashhour
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Vincent Hennicke
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Pontus Fischer
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Johanna Hakanpää
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Jan Meyer
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Philip Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology and Fraunhofer Cluster of Excellence for Immune Mediated Diseases, Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Bernhard Ellinger
- Fraunhofer Institute for Translational Medicine and Pharmacology and Fraunhofer Cluster of Excellence for Immune Mediated Diseases, Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Maria Kuzikov
- Fraunhofer Institute for Translational Medicine and Pharmacology and Fraunhofer Cluster of Excellence for Immune Mediated Diseases, Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Markus Wolf
- Fraunhofer Institute for Translational Medicine and Pharmacology and Fraunhofer Cluster of Excellence for Immune Mediated Diseases, Schnackenburgallee 114, 22525 Hamburg, Germany
| | | | - Gleb Bourenkov
- EMBL Outstation Hamburg, c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - David von Stetten
- EMBL Outstation Hamburg, c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | | | - Isabel Bento
- EMBL Outstation Hamburg, c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | | | - Ivars Karpics
- EMBL Outstation Hamburg, c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | | | | | - Stephan Niebling
- EMBL Outstation Hamburg, c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Christian Günther
- EMBL Outstation Hamburg, c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | | | - Robin Schubert
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Huijong Han
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Juliane Boger
- Institute of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany
| | - Diana C F Monteiro
- Hauptmann Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Linlin Zhang
- Institute of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany
- German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems Site, University of Lübeck, 23562 Lübeck, Germany
| | - Xinyuanyuan Sun
- Institute of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany
- German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems Site, University of Lübeck, 23562 Lübeck, Germany
| | | | - Jan Wollenhaupt
- Helmholtz Zentrum Berlin, Macromolecular Crystallography, Albert-Einstein-Str. 15, 12489 Berlin, Germany
| | - Christian G Feiler
- Helmholtz Zentrum Berlin, Macromolecular Crystallography, Albert-Einstein-Str. 15, 12489 Berlin, Germany
| | - Manfred S Weiss
- Helmholtz Zentrum Berlin, Macromolecular Crystallography, Albert-Einstein-Str. 15, 12489 Berlin, Germany
| | - Eike-Christian Schulz
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Pedram Mehrabi
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Katarina Karničar
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000 Ljubljana, Slovenia
| | - Aleksandra Usenik
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000 Ljubljana, Slovenia
| | - Jure Loboda
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Henning Tidow
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Ashwin Chari
- Research Group for Structural Biochemistry and Mechanisms, Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Rolf Hilgenfeld
- Institute of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany
- German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems Site, University of Lübeck, 23562 Lübeck, Germany
| | - Charlotte Uetrecht
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistr. 52, 20251 Hamburg, Germany
| | - Russell Cox
- Institute for Organic Chemistry and BMWZ, Leibniz University of Hannover, Schneiderberg 38, 30167 Hannover, Germany
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology and Fraunhofer Cluster of Excellence for Immune Mediated Diseases, Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Tobias Beck
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Department of Chemistry, Institute of Physical Chemistry, Grindelallee 117, 20146 Hamburg, Germany
| | - Matthias Rarey
- Universität Hamburg, Center for Bioinformatics, Bundesstr. 43, 20146 Hamburg, Germany
| | - Stephan Günther
- Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Str. 74, 20359 Hamburg, Germany
| | - Dusan Turk
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000 Ljubljana, Slovenia
| | - Winfried Hinrichs
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
- Universität Greifswald, Institute of Biochemistry, Felix-Hausdorff-Str. 4, 17489 Greifswald, Germany
| | - Henry N Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Department of Physics, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Arwen R Pearson
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Institut für Nanostruktur- und Festkörperphysik, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Christian Betzel
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
| | - Alke Meents
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany.
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36
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Villanueva-Perez P, Fleckenstein H, Prasciolu M, Murray KT, Domaracký M, Gregorič K, Mariani V, Gelisio L, Kuhn M, Hannappel J, Yefanov O, Ivanov N, Sarrou I, Pennicard D, Becker J, von Zimmermann M, Gutowski O, Dippel AC, Chapman HN, Bajt S. Scanning Compton X-ray microscopy. Opt Lett 2021; 46:1920-1923. [PMID: 33857104 DOI: 10.1364/ol.421232] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/18/2021] [Indexed: 06/12/2023]
Abstract
X-ray microscopy offers the opportunity to image biological and radiosensitive materials without special sample preparations, bridging optical and electron microscopy capabilities. However, the performance of such microscopes, when imaging radiosensitive samples, is not limited by their intrinsic resolution, but by the radiation damage induced on such samples. Here, we demonstrate a novel, to the best of our knowledge, radio-efficient microscope, scanning Compton X-ray microscopy (SCXM), which uses coherently and incoherently (Compton) scattered photons to minimize the deposited energy per unit of mass for a given imaging signal. We implemented SCXM, using lenses capable of efficiently focusing 60 keV X-ray photons into the sub-micrometer scale, and probe its radio-efficient capabilities. SCXM, when implemented in high-energy diffraction-limited storage rings, e.g., European Synchrotron Radiation Facility Extremely Brilliant Source and PETRA IV, will open the opportunity to explore the nanoscale of unstained, unsectioned, and undamaged radiosensitive materials.
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37
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Sanchez-Cano C, Alvarez-Puebla RA, Abendroth JM, Beck T, Blick R, Cao Y, Caruso F, Chakraborty I, Chapman HN, Chen C, Cohen BE, Conceição ALC, Cormode DP, Cui D, Dawson KA, Falkenberg G, Fan C, Feliu N, Gao M, Gargioni E, Glüer CC, Grüner F, Hassan M, Hu Y, Huang Y, Huber S, Huse N, Kang Y, Khademhosseini A, Keller TF, Körnig C, Kotov NA, Koziej D, Liang XJ, Liu B, Liu S, Liu Y, Liu Z, Liz-Marzán LM, Ma X, Machicote A, Maison W, Mancuso AP, Megahed S, Nickel B, Otto F, Palencia C, Pascarelli S, Pearson A, Peñate-Medina O, Qi B, Rädler J, Richardson JJ, Rosenhahn A, Rothkamm K, Rübhausen M, Sanyal MK, Schaak RE, Schlemmer HP, Schmidt M, Schmutzler O, Schotten T, Schulz F, Sood AK, Spiers KM, Staufer T, Stemer DM, Stierle A, Sun X, Tsakanova G, Weiss PS, Weller H, Westermeier F, Xu M, Yan H, Zeng Y, Zhao Y, Zhao Y, Zhu D, Zhu Y, Parak WJ. X-ray-Based Techniques to Study the Nano-Bio Interface. ACS Nano 2021; 15:3754-3807. [PMID: 33650433 PMCID: PMC7992135 DOI: 10.1021/acsnano.0c09563] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/25/2021] [Indexed: 05/03/2023]
Abstract
X-ray-based analytics are routinely applied in many fields, including physics, chemistry, materials science, and engineering. The full potential of such techniques in the life sciences and medicine, however, has not yet been fully exploited. We highlight current and upcoming advances in this direction. We describe different X-ray-based methodologies (including those performed at synchrotron light sources and X-ray free-electron lasers) and their potentials for application to investigate the nano-bio interface. The discussion is predominantly guided by asking how such methods could better help to understand and to improve nanoparticle-based drug delivery, though the concepts also apply to nano-bio interactions in general. We discuss current limitations and how they might be overcome, particularly for future use in vivo.
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Affiliation(s)
- Carlos Sanchez-Cano
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 182, 20014 Donostia San Sebastián, Spain
| | - Ramon A. Alvarez-Puebla
- Universitat
Rovira i Virgili, 43007 Tarragona, Spain
- ICREA, Passeig Lluís
Companys 23, 08010 Barcelona, Spain
| | - John M. Abendroth
- Department
of Materials Science and Engineering, Stanford
University, Stanford, California 94305, United States
| | - Tobias Beck
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Robert Blick
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Yuan Cao
- Department
of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
- Biointerfaces
Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Frank Caruso
- ARC
Centre of Excellence in Convergent Bio-Nano Science and Technology
and the Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Indranath Chakraborty
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Henry N. Chapman
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
- Centre
for Ultrafast Imaging, Universität
Hamburg, 22761 Hamburg, Germany
- Deutsches
Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Chunying Chen
- National
Center for Nanoscience and Technology (NCNST), 100190 Beijing China
| | - Bruce E. Cohen
- The
Molecular Foundry and Division of Molecular Biophysics and Integrated
Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | | | - David P. Cormode
- Radiology
Department, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Daxiang Cui
- School
of Chemistry and Chemical Engineering, Frontiers Science Center for
Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | | | - Gerald Falkenberg
- Deutsches
Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Chunhai Fan
- School
of Chemistry and Chemical Engineering, Frontiers Science Center for
Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Neus Feliu
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
- CAN, Fraunhofer Institut, 20146 Hamburg, Germany
| | - Mingyuan Gao
- Department
of Radiotherapy and Radiation Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Elisabetta Gargioni
- Department
of Radiotherapy and Radiation Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Claus-C. Glüer
- Section
Biomedical Imaging, Department of Radiology and Neuroradiology, University Medical Clinic Schleswig-Holstein and Christian-Albrechts-University
Kiel, 24105 Kiel, Germany
| | - Florian Grüner
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
- Universität
Hamburg and Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Moustapha Hassan
- Karolinska University Hospital, Huddinge, and Karolinska
Institutet, 17177 Stockholm, Sweden
| | - Yong Hu
- College of Engineering and Applied Sciences, Nanjing University, Nanjing 210093, China
| | - Yalan Huang
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Samuel Huber
- Department
of Radiotherapy and Radiation Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Nils Huse
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Yanan Kang
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Ali Khademhosseini
- Terasaki Institute for Biomedical Innovation, Los Angeles, California 90049, United States
| | - Thomas F. Keller
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
- Deutsches
Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Christian Körnig
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
- Universität
Hamburg and Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Nicholas A. Kotov
- Department
of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
- Biointerfaces
Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Materials Science and Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
- Michigan
Institute for Translational Nanotechnology (MITRAN), Ypsilanti, Michigan 48198, United States
| | - Dorota Koziej
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Xing-Jie Liang
- National
Center for Nanoscience and Technology (NCNST), 100190 Beijing China
| | - Beibei Liu
- Department
of Radiotherapy and Radiation Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Sijin Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology,
Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085 China
| | - Yang Liu
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Ziyao Liu
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Luis M. Liz-Marzán
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 182, 20014 Donostia San Sebastián, Spain
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
- Centro de Investigación Biomédica
en Red de Bioingeniería,
Biomateriales y Nanomedicina (CIBER-BBN), Paseo de Miramon 182, 20014 Donostia-San Sebastián, Spain
| | - Xiaowei Ma
- National
Center for Nanoscience and Technology (NCNST), 100190 Beijing China
| | - Andres Machicote
- Department
of Radiotherapy and Radiation Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Wolfgang Maison
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Adrian P. Mancuso
- European XFEL, 22869 Schenefeld, Germany
- Department of Chemistry and Physics, La
Trobe Institute for Molecular
Science, La Trobe University, Melbourne 3086, Victoria, Australia
| | - Saad Megahed
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Bert Nickel
- Sektion Physik, Ludwig Maximilians Universität
München, 80539 München, Germany
| | - Ferdinand Otto
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Cristina Palencia
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | | | - Arwen Pearson
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Oula Peñate-Medina
- Section
Biomedical Imaging, Department of Radiology and Neuroradiology, University Medical Clinic Schleswig-Holstein and Christian-Albrechts-University
Kiel, 24105 Kiel, Germany
| | - Bing Qi
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Joachim Rädler
- Sektion Physik, Ludwig Maximilians Universität
München, 80539 München, Germany
| | - Joseph J. Richardson
- ARC
Centre of Excellence in Convergent Bio-Nano Science and Technology
and the Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Axel Rosenhahn
- Department
of Radiotherapy and Radiation Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Kai Rothkamm
- Department
of Radiotherapy and Radiation Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Michael Rübhausen
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | | | - Raymond E. Schaak
- Department of Chemistry, Department of Chemical Engineering,
and
Materials Research Institute, The Pennsylvania
State University, University Park, Pensylvania 16802, United States
| | - Heinz-Peter Schlemmer
- Department of Radiology, German Cancer
Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Marius Schmidt
- Department of Physics, University
of Wisconsin-Milwaukee, 3135 N. Maryland Avenue, Milwaukee, Wisconsin 53211, United States
| | - Oliver Schmutzler
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
- Universität
Hamburg and Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany
| | | | - Florian Schulz
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - A. K. Sood
- Department of Physics, Indian Institute
of Science, Bangalore 560012, India
| | - Kathryn M. Spiers
- Deutsches
Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Theresa Staufer
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
- Universität
Hamburg and Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Dominik M. Stemer
- California NanoSystems Institute, University
of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Materials Science and Engineering, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Andreas Stierle
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
- Deutsches
Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Xing Sun
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
- Molecular Science and Biomedicine Laboratory (MBL) State
Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry
and Chemical Engineering, Hunan University, Changsha 410082, P.R. China
| | - Gohar Tsakanova
- Institute of Molecular Biology of National
Academy of Sciences of
Republic of Armenia, 7 Hasratyan str., 0014 Yerevan, Armenia
- CANDLE Synchrotron Research Institute, 31 Acharyan str., 0040 Yerevan, Armenia
| | - Paul S. Weiss
- California NanoSystems Institute, University
of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Materials Science and Engineering, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Bioengineering, University
of California, Los Angeles, Los Angeles, California 90095, United States
| | - Horst Weller
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
- CAN, Fraunhofer Institut, 20146 Hamburg, Germany
| | - Fabian Westermeier
- Deutsches
Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Ming Xu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology,
Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085 China
| | - Huijie Yan
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Yuan Zeng
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Ying Zhao
- Karolinska University Hospital, Huddinge, and Karolinska
Institutet, 17177 Stockholm, Sweden
| | - Yuliang Zhao
- National
Center for Nanoscience and Technology (NCNST), 100190 Beijing China
| | - Dingcheng Zhu
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
| | - Ying Zhu
- Bioimaging Center, Shanghai Synchrotron Radiation Facility,
Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
- Division of Physical Biology, CAS Key Laboratory
of Interfacial
Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Wolfgang J. Parak
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 182, 20014 Donostia San Sebastián, Spain
- Mathematics,
Informatics, and Natural Sciences (MIN) Faculty, University of Hamburg, 20354 Hamburg, Germany
- School
of Chemistry and Chemical Engineering, Frontiers Science Center for
Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
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38
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Ramakrishnan S, Stagno JR, Conrad CE, Ding J, Yu P, Bhandari YR, Lee YT, Pauly G, Yefanov O, Wiedorn MO, Knoska J, Oberthür D, White TA, Barty A, Mariani V, Li C, Brehm W, Heinz WF, Magidson V, Lockett S, Hunter MS, Boutet S, Zatsepin NA, Zuo X, Grant TD, Pandey S, Schmidt M, Spence JCH, Chapman HN, Wang YX. Synchronous RNA conformational changes trigger ordered phase transitions in crystals. Nat Commun 2021; 12:1762. [PMID: 33741910 PMCID: PMC7979858 DOI: 10.1038/s41467-021-21838-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 12/02/2020] [Indexed: 11/20/2022] Open
Abstract
Time-resolved studies of biomacromolecular crystals have been limited to systems involving only minute conformational changes within the same lattice. Ligand-induced changes greater than several angstroms, however, are likely to result in solid-solid phase transitions, which require a detailed understanding of the mechanistic interplay between conformational and lattice transitions. Here we report the synchronous behavior of the adenine riboswitch aptamer RNA in crystal during ligand-triggered isothermal phase transitions. Direct visualization using polarized video microscopy and atomic force microscopy shows that the RNA molecules undergo cooperative rearrangements that maintain lattice order, whose cell parameters change distinctly as a function of time. The bulk lattice order throughout the transition is further supported by time-resolved diffraction data from crystals using an X-ray free electron laser. The synchronous molecular rearrangements in crystal provide the physical basis for studying large conformational changes using time-resolved crystallography and micro/nanocrystals. Time-resolved crystallography (TRX) is used for monitoring only small conformational changes of biomacromolecules within the same lattice. Here, the authors report the interplay between synchronous molecular rearrangements and lattice phase transitions in RNA crystals, providing the basis for the investigation of large conformational changes using TRX.
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Affiliation(s)
| | - Jason R Stagno
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Chelsie E Conrad
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, USA.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Jienyu Ding
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Ping Yu
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Yuba R Bhandari
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Yun-Tzai Lee
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Gary Pauly
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Max O Wiedorn
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Juraj Knoska
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.,Department of Physics, Universität Hamburg, Hamburg, Germany
| | - Dominik Oberthür
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Thomas A White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Valerio Mariani
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Chufeng Li
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.,Department of Physics, Arizona State University, Tempe, AZ, USA
| | - Wolfgang Brehm
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - William F Heinz
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Valentin Magidson
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Stephen Lockett
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Nadia A Zatsepin
- Department of Physics, Arizona State University, Tempe, AZ, USA.,Department of Chemistry and Physics, ARC Centre of Excellence in Advanced Molecular Imaging, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, 3086, Victoria, Australia
| | - Xiaobing Zuo
- X-ray Science Division, Argonne National Laboratory, Lemont, IL, USA
| | - Thomas D Grant
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, NY, USA
| | - Suraj Pandey
- Kenwood Interdisciplinary Research Complex Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Marius Schmidt
- Kenwood Interdisciplinary Research Complex Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - John C H Spence
- Department of Physics, Arizona State University, Tempe, AZ, USA
| | - Henry N Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.,Department of Physics, Universität Hamburg, Hamburg, Germany.,Centre for Ultrafast Imaging, Universität Hamburg, Hamburg, Germany
| | - Yun-Xing Wang
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, USA.
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39
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Chapman HN, Prasciolu M, Murray KT, Lukas Dresselhaus J, Bajt S. Analysis of X-ray multilayer Laue lenses made by masked deposition. Opt Express 2021; 29:3097-3113. [PMID: 33770916 DOI: 10.1364/oe.413916] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 01/07/2021] [Indexed: 06/12/2023]
Abstract
Multilayer Laue lenses are diffractive optics for hard X-rays. To achieve high numerical aperture and resolution, diffracting structures of nanometer periods are required in such lenses, and a thickness (in the direction of propagation) of several micrometers is needed for high diffracting efficiency. Such structures must be oriented to satisfy Bragg's law, which can only be achieved consistently over the entire lens if the layers vary in their tilt relative to the incident beam. The correct tilt, for a particular wavelength, can be achieved with a very simple technique of using a straight-edge mask to give the necessary gradient of the layers. An analysis of the properties of lenses cut from such a shaded profile is presented and it is shown how to design, prepare, and characterize matched pairs of lenses that operate at a particular wavelength and focal length. It is also shown how to manufacture lenses with ideal curved layers for optimal efficiency.
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40
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Xavier PL, Ayyer K, Yefanov O, Gelisio L, Bielecki J, Samanta AK, Bajt S, Sha R, Bushnell DA, Kornberg RD, Ovcharenko Y, Kuepper J, Meyer M, Seeman NC, Chapman HN. Femtosecond Single-Particle Diffractive Imaging of 3D DNA-Origami Molecular Scaffolds with XFEL Pulses. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.1697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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41
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Metz M, Arnal RD, Brehm W, Chapman HN, Morgan AJ, Millane RP. Macromolecular phasing using diffraction from multiple crystal forms. Acta Crystallogr A Found Adv 2021; 77:19-35. [PMID: 33399128 PMCID: PMC7842209 DOI: 10.1107/s2053273320013650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 10/12/2020] [Indexed: 11/23/2022]
Abstract
A phasing algorithm for protein crystallography using diffraction data from multiple crystal forms is proposed. The algorithm is evaluated by simulation, and practical aspects and potential for ab initio phasing are discussed. A phasing algorithm for macromolecular crystallography is proposed that utilizes diffraction data from multiple crystal forms – crystals of the same molecule with different unit-cell packings (different unit-cell parameters or space-group symmetries). The approach is based on the method of iterated projections, starting with no initial phase information. The practicality of the method is demonstrated by simulation using known structures that exist in multiple crystal forms, assuming some information on the molecular envelope and positional relationships between the molecules in the different unit cells. With incorporation of new or existing methods for determination of these parameters, the approach has potential as a method for ab initio phasing.
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Affiliation(s)
- Markus Metz
- Department of Physics, University of Hamburg, 22761 Hamburg, Germany
| | - Romain D Arnal
- Computational Imaging Group, Department of Electrical and Computer Engineering, University of Canterbury, Christchurch, New Zealand
| | - Wolfgang Brehm
- Department of Physics, University of Hamburg, 22761 Hamburg, Germany
| | - Henry N Chapman
- Department of Physics, University of Hamburg, 22761 Hamburg, Germany
| | - Andrew J Morgan
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), 22607 Hamburg, Germany
| | - Rick P Millane
- Computational Imaging Group, Department of Electrical and Computer Engineering, University of Canterbury, Christchurch, New Zealand
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42
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Morgan AJ, Murray KT, Quiney HM, Bajt S, Chapman HN. speckle-tracking: a software suite for ptychographic X-ray speckle tracking. J Appl Crystallogr 2020; 53:1603-1612. [PMID: 33304226 PMCID: PMC7710491 DOI: 10.1107/s1600576720011991] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 08/31/2020] [Indexed: 11/13/2022] Open
Abstract
The program speckle-tracking is described, an open-source software suite for performing wavefront metrology and sample imaging from projection in-line holograms of a sample. In recent years, X-ray speckle-tracking techniques have emerged as viable tools for wavefront metrology and sample imaging applications. These methods are based on the measurement of near-field images. Thanks to their simple experimental setup, high angular sensitivity and compatibility with low-coherence sources, these methods have been actively developed for use with synchrotron and laboratory light sources. Not only do speckle-tracking techniques give the potential for high-resolution imaging, but they also provide rapid and robust characterization of aberrations of X-ray optical elements, focal spot profiles, and sample position and transmission properties. In order to realize these capabilities, software implementations are required that are equally rapid and robust. To address this need, a software suite has been developed for the ptychographic X-ray speckle-tracking technique, an X-ray speckle-based method suitable for highly divergent wavefields. The software suite is written in Python 3, with an OpenCL back end for GPU and multi-CPU core processing. It is accessible as a Python module, through the command line or through a graphical user interface, and is available as source code under Version 3 or later of the GNU General Public License.
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Affiliation(s)
- Andrew J Morgan
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany.,ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, University of Melbourne, Parkville, Victoria 3010, Australia
| | | | - Harry M Quiney
- ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Saša Bajt
- DESY, Notkestrasse 85, 22607 Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Henry N Chapman
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany.,Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
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43
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Li H, Nazari R, Abbey B, Alvarez R, Aquila A, Ayyer K, Barty A, Berntsen P, Bielecki J, Pietrini A, Bucher M, Carini G, Chapman HN, Contreras A, Daurer BJ, DeMirci H, Flűckiger L, Frank M, Hajdu J, Hantke MF, Hogue BG, Hosseinizadeh A, Hunter MS, Jönsson HO, Kirian RA, Kurta RP, Loh D, Maia FRNC, Mancuso AP, Morgan AJ, McFadden M, Muehlig K, Munke A, Reddy HKN, Nettelblad C, Ourmazd A, Rose M, Schwander P, Marvin Seibert M, Sellberg JA, Sierra RG, Sun Z, Svenda M, Vartanyants IA, Walter P, Westphal D, Williams G, Xavier PL, Yoon CH, Zaare S. Diffraction data from aerosolized Coliphage PR772 virus particles imaged with the Linac Coherent Light Source. Sci Data 2020; 7:404. [PMID: 33214568 PMCID: PMC7678860 DOI: 10.1038/s41597-020-00745-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/29/2020] [Indexed: 11/18/2022] Open
Abstract
Single Particle Imaging (SPI) with intense coherent X-ray pulses from X-ray free-electron lasers (XFELs) has the potential to produce molecular structures without the need for crystallization or freezing. Here we present a dataset of 285,944 diffraction patterns from aerosolized Coliphage PR772 virus particles injected into the femtosecond X-ray pulses of the Linac Coherent Light Source (LCLS). Additional exposures with background information are also deposited. The diffraction data were collected at the Atomic, Molecular and Optical Science Instrument (AMO) of the LCLS in 4 experimental beam times during a period of four years. The photon energy was either 1.2 or 1.7 keV and the pulse energy was between 2 and 4 mJ in a focal spot of about 1.3 μm x 1.7 μm full width at half maximum (FWHM). The X-ray laser pulses captured the particles in random orientations. The data offer insight into aerosolised virus particles in the gas phase, contain information relevant to improving experimental parameters, and provide a basis for developing algorithms for image analysis and reconstruction.
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Affiliation(s)
- Haoyuan Li
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025, USA
- Physics Department, Stanford University, 450 Serra Mall, Stanford, California, 94305, USA
| | - Reza Nazari
- Arizona State University, 1001S. McAllister Avenue, Tempe, AZ, 85287, USA
| | - Brian Abbey
- ARC Centre of Excellence in Advanced Molecular Imaging, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Roberto Alvarez
- Arizona State University, 1001S. McAllister Avenue, Tempe, AZ, 85287, USA
| | - Andrew Aquila
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025, USA.
| | - Kartik Ayyer
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Anton Barty
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
- DESY, Photon Science, Notkestrasse 85, 22607, Hamburg, Germany
| | - Peter Berntsen
- ARC Centre of Excellence in Advanced Molecular Imaging, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Johan Bielecki
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24, Uppsala, Sweden
| | - Alberto Pietrini
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24, Uppsala, Sweden
| | - Maximilian Bucher
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025, USA
| | - Gabriella Carini
- Brookhaven National Laboratory, Bldg 535B, Upton, NY, 11973, USA
| | - Henry N Chapman
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Alice Contreras
- Arizona State University, 1001S. McAllister Avenue, Tempe, AZ, 85287, USA
| | - Benedikt J Daurer
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24, Uppsala, Sweden
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, OX11 0DE, United Kingdom
| | - Hasan DeMirci
- Stanford PULSE Institute, 2575 Sand Hill Road, Menlo Park, California, 94025, USA
- Koc University, Rumelifeneri, Sariyer Rumeli Feneri Yolu, 34450, Sariyer/Istanbul, Turkey
| | - Leonie Flűckiger
- ARC Centre of Excellence in Advanced Molecular Imaging, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Matthias Frank
- Lawrence Livermore National Laboratory, 7000 East Avenue, L-452, Livermore, California, 94550, USA
| | - Janos Hajdu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24, Uppsala, Sweden
- The European Extreme Light Infrastructure, Institute of Physics, Academy of Sciences of the Czech Republic, Za Radnicic 835, 25241, Dolní Břežany, Czech Republic
| | - Max F Hantke
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24, Uppsala, Sweden
| | - Brenda G Hogue
- Arizona State University, 1001S. McAllister Avenue, Tempe, AZ, 85287, USA
| | - Ahmad Hosseinizadeh
- University of Wisconsin Milwaukee, 3135N. Maryland Ave, Milwaukee, Wisconsin, 53211, USA
| | - Mark S Hunter
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025, USA
| | - H Olof Jönsson
- Department of Applied Physics, KTH Royal Institute of Technology, AlbaNova University Center, KTH Royal Institute of Technology, S-106 91, Stockholm, Sweden
| | - Richard A Kirian
- Arizona State University, 1001S. McAllister Avenue, Tempe, AZ, 85287, USA
| | | | - Duane Loh
- Department of Physics, National University of Singapore, 14 Science Drive 4, Blk S1A, Level 2, S1A-02-07, Lee Wee Kheng Building, Singapore, 117557, Singapore
| | - Filipe R N C Maia
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24, Uppsala, Sweden
| | - Adrian P Mancuso
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia
| | - Andrew J Morgan
- ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, University of Melbourne, Parkville, Victoria, 3010, Australia.
| | - Matthew McFadden
- Arizona State University, 1001S. McAllister Avenue, Tempe, AZ, 85287, USA
| | - Kerstin Muehlig
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24, Uppsala, Sweden
| | - Anna Munke
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24, Uppsala, Sweden
| | - Hemanth Kumar Narayana Reddy
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24, Uppsala, Sweden
| | - Carl Nettelblad
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24, Uppsala, Sweden
| | - Abbas Ourmazd
- University of Wisconsin Milwaukee, 3135N. Maryland Ave, Milwaukee, Wisconsin, 53211, USA
| | - Max Rose
- DESY, Photon Science, Notkestrasse 85, 22607, Hamburg, Germany
| | - Peter Schwander
- University of Wisconsin Milwaukee, 3135N. Maryland Ave, Milwaukee, Wisconsin, 53211, USA
| | - M Marvin Seibert
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24, Uppsala, Sweden
| | - Jonas A Sellberg
- Department of Applied Physics, KTH Royal Institute of Technology, AlbaNova University Center, KTH Royal Institute of Technology, S-106 91, Stockholm, Sweden
| | - Raymond G Sierra
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025, USA
| | - Zhibin Sun
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025, USA
- Photon Science Division, Paul Scherrer Institute, CH-5232, Villigen PSI, Switzerland
| | - Martin Svenda
- Department of Applied Physics, KTH Royal Institute of Technology, AlbaNova University Center, KTH Royal Institute of Technology, S-106 91, Stockholm, Sweden
| | - Ivan A Vartanyants
- DESY, Photon Science, Notkestrasse 85, 22607, Hamburg, Germany
- NRNU MEPhI, Kashirskoe shosse 31, 115409, Moscow, Russia
| | - Peter Walter
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025, USA
| | - Daniel Westphal
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24, Uppsala, Sweden
| | - Garth Williams
- Brookhaven National Laboratory, Bldg 535B, Upton, NY, 11973, USA
| | - P Lourdu Xavier
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025, USA
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Chun Hong Yoon
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025, USA
| | - Sahba Zaare
- Arizona State University, 1001S. McAllister Avenue, Tempe, AZ, 85287, USA
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44
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Echelmeier A, Cruz Villarreal J, Messerschmidt M, Kim D, Coe JD, Thifault D, Botha S, Egatz-Gomez A, Gandhi S, Brehm G, Conrad CE, Hansen DT, Madsen C, Bajt S, Meza-Aguilar JD, Oberthür D, Wiedorn MO, Fleckenstein H, Mendez D, Knoška J, Martin-Garcia JM, Hu H, Lisova S, Allahgholi A, Gevorkov Y, Ayyer K, Aplin S, Ginn HM, Graafsma H, Morgan AJ, Greiffenberg D, Klujev A, Laurus T, Poehlsen J, Trunk U, Mezza D, Schmidt B, Kuhn M, Fromme R, Sztuk-Dambietz J, Raab N, Hauf S, Silenzi A, Michelat T, Xu C, Danilevski C, Parenti A, Mekinda L, Weinhausen B, Mills G, Vagovic P, Kim Y, Kirkwood H, Bean R, Bielecki J, Stern S, Giewekemeyer K, Round AR, Schulz J, Dörner K, Grant TD, Mariani V, Barty A, Mancuso AP, Weierstall U, Spence JCH, Chapman HN, Zatsepin N, Fromme P, Kirian RA, Ros A. Segmented flow generator for serial crystallography at the European X-ray free electron laser. Nat Commun 2020; 11:4511. [PMID: 32908128 PMCID: PMC7481229 DOI: 10.1038/s41467-020-18156-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 07/23/2020] [Indexed: 12/14/2022] Open
Abstract
Serial femtosecond crystallography (SFX) with X-ray free electron lasers (XFELs) allows structure determination of membrane proteins and time-resolved crystallography. Common liquid sample delivery continuously jets the protein crystal suspension into the path of the XFEL, wasting a vast amount of sample due to the pulsed nature of all current XFEL sources. The European XFEL (EuXFEL) delivers femtosecond (fs) X-ray pulses in trains spaced 100 ms apart whereas pulses within trains are currently separated by 889 ns. Therefore, continuous sample delivery via fast jets wastes >99% of sample. Here, we introduce a microfluidic device delivering crystal laden droplets segmented with an immiscible oil reducing sample waste and demonstrate droplet injection at the EuXFEL compatible with high pressure liquid delivery of an SFX experiment. While achieving ~60% reduction in sample waste, we determine the structure of the enzyme 3-deoxy-D-manno-octulosonate-8-phosphate synthase from microcrystals delivered in droplets revealing distinct structural features not previously reported.
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Affiliation(s)
- Austin Echelmeier
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Jorvani Cruz Villarreal
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Marc Messerschmidt
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA.,European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Daihyun Kim
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Jesse D Coe
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Darren Thifault
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Sabine Botha
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA.,Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Ana Egatz-Gomez
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Sahir Gandhi
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Gerrit Brehm
- Institute for X-Ray Physics, University of Göttingen, Friedrich-Hund-Platz 1, 37077, Göttingen, Germany
| | - Chelsie E Conrad
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Debra T Hansen
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Caleb Madsen
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA.,Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Saša Bajt
- Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany.,Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | | | - Dominik Oberthür
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Max O Wiedorn
- Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.,Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Holger Fleckenstein
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Derek Mendez
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA.,Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Juraj Knoška
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany.,Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Jose M Martin-Garcia
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Hao Hu
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA.,Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Stella Lisova
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA.,Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Aschkan Allahgholi
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Yaroslav Gevorkov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany.,Hamburg University of Technology, Vision Systems E-2, Harburger Schloßstraße 20, 21079, Hamburg, Germany
| | - Kartik Ayyer
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Steve Aplin
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Helen Mary Ginn
- Division of Structural Biology, University of Oxford, Oxford, OX1 2JD, United Kingdom.,Diamond Light Source Ltd, Didcot, Oxfordshire, OX11 0DE, United Kingdom
| | - Heinz Graafsma
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Andrew J Morgan
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | | | - Alexander Klujev
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Torsten Laurus
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Jennifer Poehlsen
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Ulrich Trunk
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Davide Mezza
- Paul Scherrer Institute, Forschungsstrasse 111, 5232, Villigen, Switzerland
| | - Bernd Schmidt
- Paul Scherrer Institute, Forschungsstrasse 111, 5232, Villigen, Switzerland
| | - Manuela Kuhn
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Raimund Fromme
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | | | - Natascha Raab
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Steffen Hauf
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | | | - Chen Xu
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | | | | | | | - Grant Mills
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Yoonhee Kim
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Richard Bean
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Stephan Stern
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany.,Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | | | - Adam R Round
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany.,School of Chemical and Physical Sciences, Keele University, Staffordshire, ST5 5AZ, United Kingdom
| | | | | | - Thomas D Grant
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, 955 Main St, Buffalo, NY, 14203, USA
| | - Valerio Mariani
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Adrian P Mancuso
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany.,Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Uwe Weierstall
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA.,Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - John C H Spence
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA.,Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Henry N Chapman
- Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.,Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany.,Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Nadia Zatsepin
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA.,Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA.,ARC Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Petra Fromme
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA
| | - Richard A Kirian
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA.,Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Alexandra Ros
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA. .,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-7401, USA.
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45
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Morgan AJ, Murray KT, Prasciolu M, Fleckenstein H, Yefanov O, Villanueva-Perez P, Mariani V, Domaracky M, Kuhn M, Aplin S, Mohacsi I, Messerschmidt M, Stachnik K, Du Y, Burkhart A, Meents A, Nazaretski E, Yan H, Huang X, Chu YS, Chapman HN, Bajt S. Ptychographic X-ray speckle tracking with multi-layer Laue lens systems. J Appl Crystallogr 2020; 53:927-936. [PMID: 32788900 PMCID: PMC7401788 DOI: 10.1107/s1600576720006925] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 05/22/2020] [Indexed: 11/17/2022] Open
Abstract
The ever-increasing brightness of synchrotron radiation sources demands improved X-ray optics to utilize their capability for imaging and probing biological cells, nano-devices and functional matter on the nanometre scale with chemical sensitivity. Hard X-rays are ideal for high-resolution imaging and spectroscopic applications owing to their short wavelength, high penetrating power and chemical sensitivity. The penetrating power that makes X-rays useful for imaging also makes focusing them technologically challenging. Recent developments in layer deposition techniques have enabled the fabrication of a series of highly focusing X-ray lenses, known as wedged multi-layer Laue lenses. Improvements to the lens design and fabrication technique demand an accurate, robust, in situ and at-wavelength characterization method. To this end, a modified form of the speckle tracking wavefront metrology method has been developed. The ptychographic X-ray speckle tracking method is capable of operating with highly divergent wavefields. A useful by-product of this method is that it also provides high-resolution and aberration-free projection images of extended specimens. Three separate experiments using this method are reported, where the ray path angles have been resolved to within 4 nrad with an imaging resolution of 45 nm (full period). This method does not require a high degree of coherence, making it suitable for laboratory-based X-ray sources. Likewise, it is robust to errors in the registered sample positions, making it suitable for X-ray free-electron laser facilities, where beam-pointing fluctuations can be problematic for wavefront metrology.
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Affiliation(s)
- Andrew J. Morgan
- CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | | | | | - Holger Fleckenstein
- CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Oleksandr Yefanov
- CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | | | - Valerio Mariani
- CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Martin Domaracky
- CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | | | - Steve Aplin
- CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | | | - Marc Messerschmidt
- National Science Foundation BioXFEL Science and Technology Center, 700 Ellicott Street, Buffalo, NY 14203, USA
| | | | - Yang Du
- CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | | | - Alke Meents
- DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Evgeny Nazaretski
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Hanfei Yan
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Xiaojing Huang
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Yong S. Chu
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Henry N. Chapman
- CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Saša Bajt
- DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
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Abstract
A method is presented for the measurement of the phase gradient of a wavefront by tracking the relative motion of speckles in projection holograms as a sample is scanned across the wavefront. By removing the need to obtain an undistorted reference image of the sample, this method is suitable for the metrology of highly divergent wavefields. Such wavefields allow for large magnification factors that, according to current imaging capabilities, will allow for nanoradian angular sensitivity and nanoscale sample projection imaging. Both the reconstruction algorithm and the imaging geometry are nearly identical to that of ptychography, except that the sample is placed downstream of the beam focus and that no coherent propagation is explicitly accounted for. Like other X-ray speckle tracking methods, it is robust to low-coherence X-ray sources, making it suitable for laboratory-based X-ray sources. Likewise, it is robust to errors in the registered sample positions, making it suitable for X-ray free-electron laser facilities, where beam-pointing fluctuations can be problematic for wavefront metrology. A modified form of the speckle tracking approximation is also presented, based on a second-order local expansion of the Fresnel integral. This result extends the validity of the speckle tracking approximation and may be useful for similar approaches in the field.
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Affiliation(s)
- Andrew J. Morgan
- ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, University of Melbourne, Parkville, Victoria 3010, Australia
- CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Harry M. Quiney
- ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Saša Bajt
- DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Henry N. Chapman
- CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
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Gevorkov Y, Barty A, Brehm W, White TA, Tolstikova A, Wiedorn MO, Meents A, Grigat RR, Chapman HN, Yefanov O. pinkIndexer - a universal indexer for pink-beam X-ray and electron diffraction snapshots. Acta Crystallogr A Found Adv 2020; 76:121-131. [PMID: 32124850 PMCID: PMC7053222 DOI: 10.1107/s2053273319015559] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/18/2019] [Indexed: 12/15/2022] Open
Abstract
A crystallographic indexing algorithm, pinkIndexer, is presented for the analysis of snapshot diffraction patterns. It can be used in a variety of contexts including measurements made with a monochromatic radiation source, a polychromatic source or with radiation of very short wavelength. As such, the algorithm is particularly suited to automated data processing for two emerging measurement techniques for macromolecular structure determination: serial pink-beam X-ray crystallography and serial electron crystallography, which until now lacked reliable programs for analyzing many individual diffraction patterns from crystals of uncorrelated orientation. The algorithm requires approximate knowledge of the unit-cell parameters of the crystal, but not the wavelengths associated with each Bragg spot. The use of pinkIndexer is demonstrated by obtaining 1005 lattices from a published pink-beam serial crystallography data set that had previously yielded 140 indexed lattices. Additionally, in tests on experimental serial crystallography diffraction data recorded with quasi-monochromatic X-rays and with electrons the algorithm indexed more patterns than other programs tested.
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Affiliation(s)
- Yaroslav Gevorkov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
- Vision Systems, Hamburg University of Technology, 21071 Hamburg, Germany
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Wolfgang Brehm
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Thomas A. White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Aleksandra Tolstikova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Max O. Wiedorn
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Alke Meents
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Rolf-Rainer Grigat
- Vision Systems, Hamburg University of Technology, 21071 Hamburg, Germany
| | - Henry N. Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
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Kierspel T, Morgan A, Wiese J, Mullins T, Aquila A, Barty A, Bean R, Boll R, Boutet S, Bucksbaum P, Chapman HN, Christensen L, Fry A, Hunter M, Koglin JE, Liang M, Mariani V, Natan A, Robinson J, Rolles D, Rudenko A, Schnorr K, Stapelfeldt H, Stern S, Thøgersen J, Yoon CH, Wang F, Küpper J. X-ray diffractive imaging of controlled gas-phase molecules: Toward imaging of dynamics in the molecular frame. J Chem Phys 2020; 152:084307. [DOI: 10.1063/1.5133963] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Thomas Kierspel
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
- Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Andrew Morgan
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Joss Wiese
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
- Department of Chemistry, Universität Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Terry Mullins
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Andy Aquila
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Richard Bean
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
- European XFEL GmbH, 22869 Schenefeld, Germany
| | - Rebecca Boll
- Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - Sébastien Boutet
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Philip Bucksbaum
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
- SLAC National Accelerator Laboratory, PULSE Institute, Stanford, California 94305, USA
- Department of Physics, Stanford University, Stanford, California 94305, USA
| | - Henry N. Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
- Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | | | - Alan Fry
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
- SLAC National Accelerator Laboratory, PULSE Institute, Stanford, California 94305, USA
| | - Mark Hunter
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Jason E. Koglin
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Mengning Liang
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Valerio Mariani
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Adi Natan
- SLAC National Accelerator Laboratory, PULSE Institute, Stanford, California 94305, USA
| | - Joseph Robinson
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Daniel Rolles
- Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
- J. R. Macdonald Laboratory, Department of Physics, Kansas State University, Manhatten, Kansas 66506, USA
| | - Artem Rudenko
- J. R. Macdonald Laboratory, Department of Physics, Kansas State University, Manhatten, Kansas 66506, USA
| | - Kirsten Schnorr
- Max Planck Institute for Nuclear Physics, 69117 Heidelberg, Germany
| | | | - Stephan Stern
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Jan Thøgersen
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
| | - Chun Hong Yoon
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
- European XFEL GmbH, 22869 Schenefeld, Germany
| | - Fenglin Wang
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
- SLAC National Accelerator Laboratory, PULSE Institute, Stanford, California 94305, USA
| | - Jochen Küpper
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
- Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Chemistry, Universität Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
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49
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Xavier PL, Yefanov O, Ayyer K, Sha R, Knoška J, Seuring C, Boutet S, Liang M, Bushnell DA, Kornberg R, Barty A, Bajt S, Millane RP, Seeman NC, Chapman HN. DNA-Origami-Assisted Flow-Aligned Single-Particle Diffractive Imaging using XFEL Pulses. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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50
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Knoška J, Adriano L, Awel S, Beyerlein KR, Yefanov O, Oberthuer D, Peña Murillo GE, Roth N, Sarrou I, Villanueva-Perez P, Wiedorn MO, Wilde F, Bajt S, Chapman HN, Heymann M. Ultracompact 3D microfluidics for time-resolved structural biology. Nat Commun 2020; 11:657. [PMID: 32005876 PMCID: PMC6994545 DOI: 10.1038/s41467-020-14434-6] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 12/10/2019] [Indexed: 11/23/2022] Open
Abstract
To advance microfluidic integration, we present the use of two-photon additive manufacturing to fold 2D channel layouts into compact free-form 3D fluidic circuits with nanometer precision. We demonstrate this technique by tailoring microfluidic nozzles and mixers for time-resolved structural biology at X-ray free-electron lasers (XFELs). We achieve submicron jets with speeds exceeding 160 m s-1, which allows for the use of megahertz XFEL repetition rates. By integrating an additional orifice, we implement a low consumption flow-focusing nozzle, which is validated by solving a hemoglobin structure. Also, aberration-free in operando X-ray microtomography is introduced to study efficient equivolumetric millisecond mixing in channels with 3D features integrated into the nozzle. Such devices can be printed in minutes by locally adjusting print resolution during fabrication. This technology has the potential to permit ultracompact devices and performance improvements through 3D flow optimization in all fields of microfluidic engineering.
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Affiliation(s)
- Juraj Knoška
- CFEL, Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Luigi Adriano
- DESY, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
- EuXFEL, Sample Environment & Characterization Group, European XFEL Holzkoppel 4, 22869, Schenefeld, Germany
| | - Salah Awel
- CFEL, Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- CUI, Center for Ultrafast Imaging, Universität Hamburg, 22761, Hamburg, Germany
| | - Kenneth R Beyerlein
- CFEL, Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, 22761, Germany
| | - Oleksandr Yefanov
- CFEL, Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Dominik Oberthuer
- CFEL, Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Gisel E Peña Murillo
- CFEL, Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Nils Roth
- CFEL, Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Iosifina Sarrou
- CFEL, Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Pablo Villanueva-Perez
- CFEL, Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Synchrotron Radiation Research, Lund University, Box 118, SE-221 00, Lund, Sweden
| | - Max O Wiedorn
- CFEL, Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Fabian Wilde
- Helmholtz-Zentrum Geesthacht, Institut für Werkstoffforschung, Max-Planck-Straße. 1, 21502, Geesthacht, Germany
| | - Saša Bajt
- DESY, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Henry N Chapman
- CFEL, Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.
- CUI, Center for Ultrafast Imaging, Universität Hamburg, 22761, Hamburg, Germany.
| | - Michael Heymann
- CFEL, Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.
- IBBS, Institut für Biomaterialien und Biomolekulare Systeme, Universität Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany.
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