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Cited by 14Enzyme Structure and FunctionAdvanced X-ray Imaging TechniquesCrystal structures of chemical compounds

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A multi-reservoir extruder for time-resolved serial protein crystallography and compound screening at X-ray free-electron lasers

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Wranik, Maximilian, Kepa, Michal W., Beale, Emma V., James, Daniel, Bertrand, Quentin, Weinert, Tobias, Furrer, Antonia, Glover, Hannah, Gashi, Dardan, Carrillo, Melissa, Kondo, Yasushi, Stipp, Robin T., Khusainov, Georgii, Nass, Karol, Ozerov, Dmitry, Cirelli, Claudio, Johnson, Philip J. M., Dworkowski, Florian, Beale, John H., Stubbs, Scott, Zamofing, Thierry, Schneider, Marco, Krauskopf, Kristina, Gao, Li, Thorn-Seshold, Oliver, Bostedt, Christoph, Bacellar, Camila, Steinmetz, Michel O., Milne, Christopher, Standfuss, Jörg·2023·Nature Communications
DOI 10.1038/s41467-023-43523-5PMC PMC10693631

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Abstract

Serial crystallography at X-ray free-electron lasers (XFELs) permits the determination of radiation-damage free static as well as time-resolved protein structures at room temperature. Efficient sample delivery is a key factor for such experiments. Here, we describe a multi-reservoir, high viscosity extruder as a step towards automation of sample delivery at XFELs. Compared to a standard single extruder, sample exchange time was halved and the workload of users was greatly reduced. In-built temperature control of samples facilitated optimal extrusion and supported sample stability. After commissioning the device with lysozyme crystals, we collected time-resolved data using crystals of a membrane-bound, light-driven sodium pump. Static data were also collected from the soluble protein tubulin that was soaked with a series of small molecule drugs. Using these data, we identify low occupancy (as little as 30%) ligands using a minimal amount of data from a serial crystallography experiment, a result that could be exploited for structure-based drug design.

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Research works printed but not linked: 84

  1. Brändén, G. & Neutze, R. Advances and challenges in time-resolved macromolecular crystallography. Science 373, eaba0954 (2021). · DOI
  2. Barends, T. R. M., Stauch, B., Cherezov, V. & Schlichting, I. Serial femtosecond crystallography. Nat. Rev. Methods Prim. 2, 59 (2022). · DOI
  3. Orville, A. M. Recent results in time resolved serial femtosecond crystallography at XFELs. Curr. Opin. Struct. Biol. 65, 193–208 (2020). · DOI
  4. Standfuss, J. Membrane protein dynamics studied by X-ray lasers – or why only time will tell. Curr. Opin. Struct. Biol. 57, 63–71 (2019). · DOI
  5. Gati, C. et al. Atomic structure of granulin determined from native nanocrystalline granulovirus using an X-ray free-electron laser. PNAS 114, 2247–2252 (2017). · DOI
  6. Nass, K. et al. Structural dynamics in proteins induced by and probed with X-ray free-electron laser pulses. Nat. Commun. 11, 1–9 (2020). · DOI
  7. Neutze, R., Wouts, R. & Spoel, D. Van Der & Weckert, E. Potential for biomolecular imaging with femtosecond X-ray pulses. Nature 406, 752–757 (2000). · DOI · Paper page
  8. Chapman, H. N., Caleman, C. & Timneanu, N. Diffraction before destruction. Philos. Trans. R. Soc. B 369, 20130313 (2014). · DOI
  9. Nass, K. Radiation damage in protein crystallography at X-ray free-electron lasers research papers. Acta Cryst. D. 75, 211–218 (2019). · DOI
  10. Fischer, M. Macromolecular room temperature crystallography. Q. Rev. Biophys. 54, 1–15 (2021). · DOI
  11. Pande, K. et al. Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein. Science 352, 725–729 (2016). · DOI
  12. Nogly, P. et al. Retinal isomerization in bacteriorhodopsin captured by a femtosecond x-ray laser. Science 361, eaat0094 (2018). · DOI
  13. Barends, T. R. M. et al. Direct observation of ultrafast collective motions in CO myoglobin upon ligand dissociation. Science 350, 445–450 (2015). · DOI
  14. Chapman, H. N. et al. Femtosecond X-ray protein nanocrystallography. Nature 470, 73–78 (2011). · DOI
  15. Weierstall, U. et al. Lipidic cubic phase injector facilitates membrane protein serial femtosecond crystallography. Nat. Commun. 5, 3309 (2014). · DOI
  16. Hunter, M. S. et al. Fixed-target protein serial microcrystallography with an X-ray free electron laser. Sci. Rep. 4, 1–5 (2014). · DOI
  17. Roessler, C. G. et al. Acoustic Injectors for Drop-On-Demand Serial Femtosecond Crystallography. Structure 24, 631–640 (2016). · DOI
  18. Grünbein, M. L. & Kovacs, G. N. Sample delivery for serial crystallography at free-electron lasers and synchrotrons. Acta Cryst. D75, 178–191 (2019).
  19. Cheng, R. K. Y. Towards an optimal sample delivery method for serial crystallography at XFEL. Crystals 10, 1–27 (2020). · DOI
  20. Martiel, I., Müller-Werkmeister, H. M. & Cohen, A. E. Strategies for sample delivery for femtosecond crystallography. Acta Cryst. D75, 160–177 (2019).
  21. Nogly, P. et al. Lipidic cubic phase serial millisecond crystallography using synchrotron radiation. IUCrJ 2, 168–176 (2015). · DOI
  22. Weinert, T. et al. Serial millisecond crystallography for routine room-temperature structure determination at synchrotrons. Nat. Commun. 8, 542 (2017). · DOI
  23. Botha, S. et al. Room-temperature serial crystallography at synchrotron X-ray sources using slowly flowing free-standing high-viscosity microstreams. Acta Cryst. D71, 387–397 (2015).
  24. Weinert, T. et al. Proton uptake mechanism in bacteriorhodopsin captured by serial synchrotron crystallography. Science 364, 61–65 (2019). · DOI
  25. Nogly, P. et al. Lipidic cubic phase injector is a viable crystal delivery system for time-resolved serial crystallography. Nat. Commun. 7, 1–9 (2016). · DOI
  26. Schneider, Di. K. et al. FMX - The Frontier Microfocusing Macromolecular Crystallography Beamline at the National Synchrotron Light Source II. J. Synchrotron Radiat. 28, 650–665 (2021). · DOI
  27. Schroer, C. G. et al. The synchrotron radiation source PETRA III and its future ultra-low-emittance upgrade PETRA IV. Eur. Phys. J. 137, 1312 (2022).
  28. Shimazu, Y. et al. High-viscosity sample-injection device for serial femtosecond crystallography at atmospheric pressure. J. Appl. Crystallogr. 52, 1280–1288 (2019). · DOI
  29. Abela, R. et al. Perspective: Opportunities for ultrafast science at SwissFEL. Struct. Dyn. 4, 061602 (2017). · DOI
  30. Skopintsev, P. et al. Femtosecond-to-millisecond structural changes in a light-driven sodium pump. Nature 583, 314–318 (2020). · DOI
  31. Mous, S. et al. Dynamics and mechanism of a light-driven chloride pump. Science 375, 845–851 (2022). · DOI
  32. Blake, C. et al. Crystallographic studies of the activity of hen egg-white lysozyme. Proc. R. Soc. L. B Biol. Sci. 167, 378–388 (1967).
  33. Boutet, S. et al. High-Resolution Protein Structure Determination by Serial Femtosecond Crystallography. Science 337, 362–364 (2012). · DOI
  34. Barends, T., Foucar, L. & Botha, S. De novo protein crystal structure determination from X-ray free-electron laser data. Nature 505, 244–247 (2014). · DOI
  35. Cherezov, V. Crystallizing membrane proteins using lipidic mesophases. Nat. Protoc. 4, 706–731 (2009). · DOI
  36. Wranik, M. et al. Watching the release of a photo- pharmacological drug from tubulin using time-resolved serial crystallography. Nat. Commun. 14, 903 (2023). · DOI
  37. Cellini, A. et al. Structural basis of the radical pair state in photolyases and cryptochromes. Chem. Commun. 58, 4889–4892 (2022). · DOI
  38. Zhao, F. et al. A guide to sample delivery systems for serial crystallography. FEBS 286, 4402–4417 (2019). · DOI
  39. Nam, K. H. Sample Delivery Media for Serial Crystallography. Int. J. Mol. Sci. 20, 1094 (2019). · DOI
  40. Caffrey, M. A comprehensive review of the lipid cubic phase or in meso method for crystallizing membrane and soluble proteins and complexes. Acta Cryst. F71, 3–18 (2015).
  41. Qiu, H. & Caffrey, M. The phase diagram of the monoolein/water system: Metastability and equilibrium aspects. Biomaterials 21, 223–234 (2000). · DOI
  42. De Zitter, E., Coquelle, N., Oeser, P., Barends, T. R. M. & Colletier, J. P. Xtrapol8 enables automatic elucidation of low-occupancy intermediate-states in crystallographic studies. Commun. Biol. 5, 1–11 (2022). · DOI
  43. Pecqueur, L. et al. A designed ankyrin repeat protein selected to bind to tubulin caps the microtubule plus end. Proc. Natl Acad. Sci. Usa. 109, 12011–12016 (2012). · DOI
  44. Prota, A. E. et al. Molecular Mechanism of Action of Microtubule-Stabilizing Anticancer Agents. Science 339, 587–591 (2013). · DOI
  45. Prota, A. E. et al. Structural basis of tubulin tyrosination by tubulin tyrosine ligase. J. Cell Biol. 200, 259–270 (2013). · DOI
  46. Dumontet, C. & Jordan, M. A. Microtubule-binding agents: A dynamic field of cancer therapeutics. Nat. Rev. Drug Discov. 9, 790–803 (2010). · DOI
  47. Steinmetz, M. O. & Prota, A. E. Microtubule-Targeting Agents: Strategies To Hijack the Cytoskeleton. Trends Cell Biol. 28, 776–792 (2018). · DOI
  48. Dalbeth, N., Lauterio, T. J. & Wolfe, H. R. Mechanism of Action of Colchicine in the Treatment of Gout. Clin. Ther. 36, 1465–1479 (2014). · DOI
  49. Barnette, K. G. et al. Oral Sabizabulin for High-Risk, Hospitalized Adults with Covid-19: Interim Analysis. NEJM Evid. 1, 1–11 (2022). · DOI
  50. Mühlethaler, T. et al. Comprehensive Analysis of Binding Sites in Tubulin. Angew. Chem. Int. Ed. 60, 13331–13342 (2021). · DOI
  51. Gao, L. et al. In Vivo Photocontrol of Microtubule Dynamics and Integrity, Migration and Mitosis, by the Potent GFP-Imaging-Compatible Photoswitchable Reagents SBTubA4P and SBTub2M. J. Am. Chem. Soc. 144, 5614–5628 (2022). · DOI
  52. Verlinde, C. et al. Fragment-Based Cocktail Crystallography by the Medical Structural Genomics of Pathogenic Protozoa Consortium. Curr. Top. Med. Chem. 9, 1678–1687 (2009). · DOI
  53. Kirsch, P., Hartman, A. M., Hirsch, A. K. H. & Empting, M. Concepts and core principles of fragment-based drug design. Molecules 24, 4309 (2019). · DOI
  54. Murray, C. W. & Rees, D. C. The rise of fragment-based drug discovery. Nat. Chem. 1, 187–192 (2009). · DOI
  55. Pearce, N. M. et al. Partial-occupancy binders identified by the Pan-Dataset Density Analysis method offer new chemical opportunities and reveal cryptic binding sites. Struct. Dyn. 4, 032104 (2017). · DOI
  56. Schulz, E. C., Yorke, B. A., Pearson, A. R. & Mehrabi, P. Best practices for time-resolved serial synchrotron crystallography. Acta Cryst. D78, 14–29 (2022).
  57. Moreno-Chicano, T. et al. High-throughput structures of protein-ligand complexes at room temperature using serial femtosecond crystallography. IUCrJ 6, 1074–1085 (2019). · DOI
  58. Schmidt, M. Time-Resolved Macromolecular Crystallography at Pulsed X-ray Sources. Int. J. Mol. Sci. 20, 1401 (2019). · DOI
  59. Poddar, H. et al. A Guide to time-resolved structural analysis of light-activated proteins. FEBS J. 289, 576–595 (2021). · DOI
  60. Pandey, S. et al. Time-resolved serial femtosecond crystallography at the European XFEL. Nat. Methods 17, 73–78 (2020). · DOI
  61. Frank, J. Time-resolved Cryo-Electron Microscopy: Recent Progress. J. Struct. Biol. 200, 303–306 (2018). · DOI
  62. Dandey, V. P. et al. Time-resolved cryo-EM using Spotiton. Nat. Methods 17, 897–900 (2020). · DOI
  63. Mäeots, M. E. et al. Modular microfluidics enables kinetic insight from time-resolved cryo-EM. Nat. Commun. 11, 1–14 (2020). · DOI
  64. Perrakis, A. & Sixma, T. K. AI revolutions in biology. EMBO Rep. 22, 1–6 (2021). · DOI · Paper page
  65. Douangamath, A. et al. Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source. J. Vis. Exp. 171, e62414 (2021).
  66. Lima, G. M. A. et al. FragMAX: The fragment-screening platform at the MAX IV Laboratory. Acta Cryst. D76, 771–777 (2020).
  67. Lima, G. M. A. et al. FragMAXapp: Crystallographic fragment-screening data-analysis and project-management system. Acta Crystallogr. Sect. D. Struct. Biol. 77, 799–808 (2021).
  68. Cornaciu, I. et al. The Automated Crystallography Pipelines at the EMBL HTX Facility in Grenoble. J. Vis. Exp. 172, e62491 (2021).
  69. Kaminski, J. W. et al. Fast fragment- and compound-screening pipeline at the Swiss Light Source. Acta Cryst. D78, 328–336 (2022).
  70. Ishchenko, A., Gati, C. & Cherezov, V. Structural Biology of G Protein-Coupled Receptors: new opportunities from XFELs and cryoEM. Curr. Opin. Struct. Biol. 51, 44–52 (2018). · DOI
  71. Mishin, A. et al. An outlook on using serial femtosecond crystallography in drug discovery. Expert. Opin. Drug Discov. 14, 933–945 (2020). · DOI
  72. Nass Kovacs, G. Potential of X-ray free-electron lasers for challenging targets in structure-based drug discovery. Drug Discov. Today Technol. 39, 101–110 (2021). · DOI
  73. Zhu, L., Chen, X., Abola, E. E., Jing, L. & Liu, W. Serial Crystallography for Structure-Based Drug Discovery. Trends Pharmacol. Sci. 41, 830–839 (2020). · DOI
  74. Cheng, R. K. Y., Abela, R. & Hennig, M. X-ray free electron laser: Opportunities for drug discovery. Essays Biochem 61, 529–542 (2017). · DOI
  75. Huang, C. Y. et al. Probing ligand binding of endothiapepsin by ‘temperature-resolved’ macromolecular crystallography. Acta Cryst. D78, 964–974 (2022).
  76. James, D. et al. Improving High Viscosity Extrusion of Microcrystals for Time-resolved Serial Femtosecond Crystallography at X-ray Lasers. J. Vis. Exp. 144, e59087 (2019).
  77. Muhlethaler, Tobias et al. Crystallization Systems for the High-Resolution Structural Analysis of Tubulin–Ligand Complexes. Methods Mol. Biol. 2430, 349 (2022). · DOI
  78. White, T. A. et al. CrystFEL: A software suite for snapshot serial crystallography. J. Appl. Crystallogr. 45, 335–341 (2012). · DOI
  79. White, T. A. et al. Recent developments in CrystFEL. J. Appl. Crystallogr. 49, 680–689 (2016). · DOI
  80. Adams, P. D. et al. PHENIX: Building new software for automated crystallographic structure determination. Acta Cryst. D58, 1948–1954 (2002).
  81. Emsley, P. & Cowtan, K. Coot: Model-building tools for molecular graphics. Acta Cryst. D60, 2126–2132 (2004).
  82. Gevorkov, Y. et al. XGANDALF - Extended gradient descent algorithm for lattice finding. Acta Cryst. A75, 694–704 (2019).
  83. Tickle, I. J. et al. STARANISO. Global Phasing Ltd, Cambridge, United Kingdom.
  84. Moriarty, N. W., Grosse-Kunstleve, R. W. & Adams, P. D. Electronic ligand builder and optimization workbench (eLBOW): A tool for ligand coordinate and restraint generation. Acta Cryst. D65, 1074–1080 (2009).

Metadata

Authors
Wranik, M., Kepa, M. W., Beale, E. V., James, D., Bertrand, Q., Weinert, T., Furrer, A., Glover, H., Gashi, D., Carrillo, M., Kondo, Y., Stipp, R. T., Khusainov, G., Nass, K., Ozerov, D., Cirelli, C., Johnson, P. J. M., Dworkowski, F., Beale, J. H., Stubbs, S., Zamofing, T., Schneider, M., Krauskopf, K., Gao, L., Thorn-Seshold, O., Bostedt, C., Bacellar, C., Steinmetz, M. O., Milne, C., & Standfuss, J.
Affiliations
  • Paul Scherrer Institute (CH)
  • Ludwig-Maximilians-Universität München (DE)
  • University of Basel (CH)
  • European X-Ray Free-Electron Laser (DE)
Corresponding author
  • Wranik, Maximilian
  • Kepa, Michal W.
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2023-12-02
Volume
14
Issue
1
Pages
7956-7956
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/s41467-023-43523-5
PMC
PMC10693631
OpenAlex
W4389264817
Cited by
14
References
2
Citations by year
2026: 5 · 2025: 6 · 2024: 3
FWCI
1.03
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by)
  • Research Square (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DORA PSI (Paul Scherrer Institute) (submittedVersion, cc-by)
  • Infoscience (Ecole Polytechnique Fédérale de Lausanne) (submittedVersion, cc-by-nc-nd)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • European XFEL (submittedVersion, cc-by)
Funders
  • National Science Foundation
  • Deutsche Forschungsgemeinschaft (TH2231/1-1, 400324123)
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (207462, 179351, 192566, 310030)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
  • Physical Sciences › Physics and Astronomy › Radiation › Advanced X-ray Imaging Techniques
  • Physical Sciences › Chemistry › Inorganic Chemistry › Crystal structures of chemical compounds
Keywords
time-resolved serial crystallography, X-ray free-electron laser, protein crystallography, sample temperature control, lysozyme crystals, membrane proteins, tubulin, ligand occupancy, structure-based drug design, compound screening
MeSH terms
Crystallography, Electrons, Lasers, Proteins, Synchrotrons, Crystallography, X-Ray

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