IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v16y2025i1d10.1038_s41467-025-65173-5.html
   My bibliography  Save this article

Sample delivery methods for protein X-ray crystallography with a special focus on sample consumption

Author

Listed:
  • Abhik Manna

    (Arizona State University
    Arizona State University)

  • Diandra Doppler

    (Arizona State University
    Arizona State University)

  • Manasa P. Sripati

    (Arizona State University)

  • Mukul Sonker

    (Arizona State University
    Arizona State University)

  • Alexandra Ros

    (Arizona State University
    Arizona State University)

Abstract

Serial crystallography (SX) has revolutionized structural biology by enabling high-resolution structure determination for important classes of proteins, including the study of relevant biomolecular reaction mechanisms. However, one of the ongoing challenges in this field remains the efficient use of precious macromolecule samples whose availability is often limited. Reducing sample consumption is thus critical in maximizing the potential of SX conducted at powerful X-ray sources such as synchrotrons and X-ray free-electron lasers (XFEL) to expand to a broader range of significant biological samples, gaining insights into unraveled biological reaction mechanisms. This review focuses on three primary sample delivery systems: fixed-targets, liquid injection, and hybrid methods, each with distinct advantages and limitations concerning sample consumption. The progress and challenges associated with these methods, highlighting advancements in reducing sample consumption and thus enabling the study of more diverse biological samples, are summarized. We compare the currently reported sample delivery methods in view of the minimum amount of sample required to obtain a full data set and discuss how the current approaches compare to this theoretical minimum. With this overview, we aim to provide a critical and comprehensive assessment of the current methods and experimental realizations for sample delivery in SX with proteins.

Suggested Citation

  • Abhik Manna & Diandra Doppler & Manasa P. Sripati & Mukul Sonker & Alexandra Ros, 2025. "Sample delivery methods for protein X-ray crystallography with a special focus on sample consumption," Nature Communications, Nature, vol. 16(1), pages 1-29, December.
  • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-65173-5
    DOI: 10.1038/s41467-025-65173-5
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-025-65173-5
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-025-65173-5?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Iris D. Young & Mohamed Ibrahim & Ruchira Chatterjee & Sheraz Gul & Franklin D. Fuller & Sergey Koroidov & Aaron S. Brewster & Rosalie Tran & Roberto Alonso-Mori & Thomas Kroll & Tara Michels-Clark & , 2016. "Structure of photosystem II and substrate binding at room temperature," Nature, Nature, vol. 540(7633), pages 453-457, December.
    2. Agata Butryn & Philipp S. Simon & Pierre Aller & Philip Hinchliffe & Ramzi N. Massad & Gabriel Leen & Catherine L. Tooke & Isabel Bogacz & In-Sik Kim & Asmit Bhowmick & Aaron S. Brewster & Nicholas E., 2021. "An on-demand, drop-on-drop method for studying enzyme catalysis by serial crystallography," Nature Communications, Nature, vol. 12(1), pages 1-7, December.
    3. Jan Kern & Rosalie Tran & Roberto Alonso-Mori & Sergey Koroidov & Nathaniel Echols & Johan Hattne & Mohamed Ibrahim & Sheraz Gul & Hartawan Laksmono & Raymond G. Sierra & Richard J. Gildea & Guangye H, 2014. "Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy," Nature Communications, Nature, vol. 5(1), pages 1-11, September.
    4. Richard Neutze & Remco Wouts & David van der Spoel & Edgar Weckert & Janos Hajdu, 2000. "Potential for biomolecular imaging with femtosecond X-ray pulses," Nature, Nature, vol. 406(6797), pages 752-757, August.
    5. Rana Hussein & Mohamed Ibrahim & Asmit Bhowmick & Philipp S. Simon & Ruchira Chatterjee & Louise Lassalle & Margaret Doyle & Isabel Bogacz & In-Sik Kim & Mun Hon Cheah & Sheraz Gul & Casper Lichtenber, 2021. "Structural dynamics in the water and proton channels of photosystem II during the S2 to S3 transition," Nature Communications, Nature, vol. 12(1), pages 1-16, December.
    6. Tobias Weinert & Natacha Olieric & Robert Cheng & Steffen Brünle & Daniel James & Dmitry Ozerov & Dardan Gashi & Laura Vera & May Marsh & Kathrin Jaeger & Florian Dworkowski & Ezequiel Panepucci & Shi, 2017. "Serial millisecond crystallography for routine room-temperature structure determination at synchrotrons," Nature Communications, Nature, vol. 8(1), pages 1-11, December.
    7. Yanyong Kang & X. Edward Zhou & Xiang Gao & Yuanzheng He & Wei Liu & Andrii Ishchenko & Anton Barty & Thomas A. White & Oleksandr Yefanov & Gye Won Han & Qingping Xu & Parker W. de Waal & Jiyuan Ke & , 2015. "Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser," Nature, Nature, vol. 523(7562), pages 561-567, July.
    8. Izumi Ishigami & Raymond G. Sierra & Zhen Su & Ariana Peck & Cong Wang & Frederic Poitevin & Stella Lisova & Brandon Hayes & Frank R. Moss & Sébastien Boutet & Robert E. Sublett & Chun Hong Yoon & Syu, 2023. "Structural insights into functional properties of the oxidized form of cytochrome c oxidase," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    9. Uwe Weierstall & Daniel James & Chong Wang & Thomas A. White & Dingjie Wang & Wei Liu & John C. H. Spence & R. Bruce Doak & Garrett Nelson & Petra Fromme & Raimund Fromme & Ingo Grotjohann & Christoph, 2014. "Lipidic cubic phase injector facilitates membrane protein serial femtosecond crystallography," Nature Communications, Nature, vol. 5(1), pages 1-6, May.
    10. Henry N. Chapman & Petra Fromme & Anton Barty & Thomas A. White & Richard A. Kirian & Andrew Aquila & Mark S. Hunter & Joachim Schulz & Daniel P. DePonte & Uwe Weierstall & R. Bruce Doak & Filipe R. N, 2011. "Femtosecond X-ray protein nanocrystallography," Nature, Nature, vol. 470(7332), pages 73-77, February.
    11. J. R. Stagno & Y. Liu & Y. R. Bhandari & C. E. Conrad & S. Panja & M. Swain & L. Fan & G. Nelson & C. Li & D. R. Wendel & T. A. White & J. D. Coe & M. O. Wiedorn & J. Knoska & D. Oberthuer & R. A. Tuc, 2017. "Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography," Nature, Nature, vol. 541(7636), pages 242-246, January.
    12. Joyce Woodhouse & Gabriela Nass Kovacs & Nicolas Coquelle & Lucas M. Uriarte & Virgile Adam & Thomas R. M. Barends & Martin Byrdin & Eugenio Mora & R. Bruce Doak & Mikolaj Feliks & Martin Field & Fran, 2020. "Photoswitching mechanism of a fluorescent protein revealed by time-resolved crystallography and transient absorption spectroscopy," Nature Communications, Nature, vol. 11(1), pages 1-11, December.
    13. Christopher Kupitz & Shibom Basu & Ingo Grotjohann & Raimund Fromme & Nadia A. Zatsepin & Kimberly N. Rendek & Mark S. Hunter & Robert L. Shoeman & Thomas A. White & Dingjie Wang & Daniel James & Jay-, 2014. "Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser," Nature, Nature, vol. 513(7517), pages 261-265, September.
    14. Petr Skopintsev & David Ehrenberg & Tobias Weinert & Daniel James & Rajiv K. Kar & Philip J. M. Johnson & Dmitry Ozerov & Antonia Furrer & Isabelle Martiel & Florian Dworkowski & Karol Nass & Gregor K, 2020. "Femtosecond-to-millisecond structural changes in a light-driven sodium pump," Nature, Nature, vol. 583(7815), pages 314-318, July.
    15. Austin Echelmeier & Jorvani Cruz Villarreal & Marc Messerschmidt & Daihyun Kim & Jesse D. Coe & Darren Thifault & Sabine Botha & Ana Egatz-Gomez & Sahir Gandhi & Gerrit Brehm & Chelsie E. Conrad & Deb, 2020. "Segmented flow generator for serial crystallography at the European X-ray free electron laser," Nature Communications, Nature, vol. 11(1), pages 1-10, December.
    16. Susannah Holmes & Henry J. Kirkwood & Richard Bean & Klaus Giewekemeyer & Andrew V. Martin & Marjan Hadian-Jazi & Max O. Wiedorn & Dominik Oberthür & Hugh Marman & Luigi Adriano & Nasser Al-Qudami & S, 2022. "Megahertz pulse trains enable multi-hit serial femtosecond crystallography experiments at X-ray free electron lasers," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    17. Chris Gisriel & Jesse Coe & Romain Letrun & Oleksandr M. Yefanov & Cesar Luna-Chavez & Natasha E. Stander & Stella Lisova & Valerio Mariani & Manuela Kuhn & Steve Aplin & Thomas D. Grant & Katerina Dö, 2019. "Membrane protein megahertz crystallography at the European XFEL," Nature Communications, Nature, vol. 10(1), pages 1-11, December.
    18. Asmit Bhowmick & Rana Hussein & Isabel Bogacz & Philipp S. Simon & Mohamed Ibrahim & Ruchira Chatterjee & Margaret D. Doyle & Mun Hon Cheah & Thomas Fransson & Petko Chernev & In-Sik Kim & Hiroki Maki, 2023. "Structural evidence for intermediates during O2 formation in photosystem II," Nature, Nature, vol. 617(7961), pages 629-636, May.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Susannah Holmes & Henry J. Kirkwood & Richard Bean & Klaus Giewekemeyer & Andrew V. Martin & Marjan Hadian-Jazi & Max O. Wiedorn & Dominik Oberthür & Hugh Marman & Luigi Adriano & Nasser Al-Qudami & S, 2022. "Megahertz pulse trains enable multi-hit serial femtosecond crystallography experiments at X-ray free electron lasers," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    2. Maximilian Wranik & Michal W. Kepa & Emma V. Beale & Daniel James & Quentin Bertrand & Tobias Weinert & Antonia Furrer & Hannah Glover & Dardan Gashi & Melissa Carrillo & Yasushi Kondo & Robin T. Stip, 2023. "A multi-reservoir extruder for time-resolved serial protein crystallography and compound screening at X-ray free-electron lasers," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    3. Basudev Maity & Mitsuo Shoji & Fangjia Luo & Takanori Nakane & Satoshi Abe & Shigeki Owada & Jungmin Kang & Kensuke Tono & Rie Tanaka & Thuc Toan Pham & Mariko Kojima & Yuki Hishikawa & Junko Tanaka &, 2024. "Real-time observation of a metal complex-driven reaction intermediate using a porous protein crystal and serial femtosecond crystallography," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    4. Maximilian Wranik & Tobias Weinert & Chavdar Slavov & Tiziana Masini & Antonia Furrer & Natacha Gaillard & Dario Gioia & Marco Ferrarotti & Daniel James & Hannah Glover & Melissa Carrillo & Demet Keki, 2023. "Watching the release of a photopharmacological drug from tubulin using time-resolved serial crystallography," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    5. Quentin Bertrand & Przemyslaw Nogly & Eriko Nango & Demet Kekilli & Georgii Khusainov & Antonia Furrer & Daniel James & Florian Dworkowski & Petr Skopintsev & Sandra Mous & Isabelle Martiel & Per Börj, 2024. "Structural effects of high laser power densities on an early bacteriorhodopsin photocycle intermediate," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    6. Hannah Glover & Torben Saßmannshausen & Quentin Bertrand & Matilde Trabuco & Chavdar Slavov & Arianna Bacchin & Fabio Andres & Yasushi Kondo & Robin Stipp & Maximilian Wranik & Georgii Khusainov & Mel, 2024. "Photoswitch dissociation from a G protein-coupled receptor resolved by time-resolved serial crystallography," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    7. Robert Bosman & Giorgia Ortolani & Swagatha Ghosh & Daniel James & Per Norder & Greger Hammarin & Tinna Björg Úlfarsdóttir & Lucija Ostojić & Tobias Weinert & Florian Dworkowski & Takashi Tomizaki & J, 2025. "Structural basis for the prolonged photocycle of sensory rhodopsin II revealed by serial synchrotron crystallography," Nature Communications, Nature, vol. 16(1), pages 1-12, December.
    8. Kevin M. Dalton & Jack B. Greisman & Doeke R. Hekstra, 2022. "A unifying Bayesian framework for merging X-ray diffraction data," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    9. Yu Guo & Lanlan He & Yunxuan Ding & Lars Kloo & Dimitrios A. Pantazis & Johannes Messinger & Licheng Sun, 2024. "Closing Kok’s cycle of nature’s water oxidation catalysis," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    10. Gábor Bortel & Miklós Tegze & Marcin Sikorski & Richard Bean & Johan Bielecki & Chan Kim & Jayanath C. P. Koliyadu & Faisal H. M. Koua & Marco Ramilli & Adam Round & Tokushi Sato & Dmitrii Zabelskii &, 2024. "3D atomic structure from a single X-ray free electron laser pulse," Nature Communications, Nature, vol. 15(1), pages 1-7, December.
    11. Sarah M. Mäusle & Gianluca Parisse & Ricardo Assunção & Cristina Santis & Philipp S. Simon & Daniele Narzi & Leonardo Guidoni & Richard J. Debus & Holger Dau, 2025. "Three rate-determining protein roles in photosynthetic O2-evolution addressed by time-resolved experiments on genetically modified photosystems," Nature Communications, Nature, vol. 16(1), pages 1-17, December.
    12. Stephan Kuschel & Phay J. Ho & Andre Al Haddad & Felix F. Zimmermann & Leonie Flueckiger & Matthew R. Ware & Joseph Duris & James P. MacArthur & Alberto Lutman & Ming-Fu Lin & Xiang Li & Kazutaka Naka, 2025. "Non-linear enhancement of ultrafast X-ray diffraction through transient resonances," Nature Communications, Nature, vol. 16(1), pages 1-8, December.
    13. Mario Reiser & Anita Girelli & Anastasia Ragulskaya & Sudipta Das & Sharon Berkowicz & Maddalena Bin & Marjorie Ladd-Parada & Mariia Filianina & Hanna-Friederike Poggemann & Nafisa Begam & Mohammad Sa, 2022. "Resolving molecular diffusion and aggregation of antibody proteins with megahertz X-ray free-electron laser pulses," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    14. M. Wilamowski & D. A. Sherrell & Y. Kim & A. Lavens & R. W. Henning & K. Lazarski & A. Shigemoto & M. Endres & N. Maltseva & G. Babnigg & S. C. Burdette & V. Srajer & A. Joachimiak, 2022. "Time-resolved β-lactam cleavage by L1 metallo-β-lactamase," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    15. Rana Hussein & Mohamed Ibrahim & Asmit Bhowmick & Philipp S. Simon & Ruchira Chatterjee & Louise Lassalle & Margaret Doyle & Isabel Bogacz & In-Sik Kim & Mun Hon Cheah & Sheraz Gul & Casper Lichtenber, 2021. "Structural dynamics in the water and proton channels of photosystem II during the S2 to S3 transition," Nature Communications, Nature, vol. 12(1), pages 1-16, December.
    16. Jincong Pang & Haodi Wu & Hao Li & Tong Jin & Jiang Tang & Guangda Niu, 2024. "Reconfigurable perovskite X-ray detector for intelligent imaging," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
    17. Ziyu Zhao & Irene Vercellino & Jana Knoppová & Roman Sobotka & James W. Murray & Peter J. Nixon & Leonid A. Sazanov & Josef Komenda, 2023. "The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    18. Yasmin Aydin & Thore Böttke & Jordy Homing Lam & Stefan Ernicke & Anna Fortmann & Maik Tretbar & Barbara Zarzycka & Vsevolod V. Gurevich & Vsevolod Katritch & Irene Coin, 2023. "Structural details of a Class B GPCR-arrestin complex revealed by genetically encoded crosslinkers in living cells," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    19. Jahaun Azadmanesh & Katelyn Slobodnik & Lucas R. Struble & Jeffrey J. Lovelace & Erika A. Cone & Medhanjali Dasgupta & William E. Lutz & Siddhartha Kumar & Amarnath Natarajan & Leighton Coates & Kevin, 2025. "The role of Tyr34 in proton coupled electron transfer and product inhibition of manganese superoxide dismutase," Nature Communications, Nature, vol. 16(1), pages 1-17, December.
    20. Edda S. F. Matthees & Raphael S. Haider & Laura Klement & Mona Reichel & Nina K. Blum & Verena Weitzel & Thimea Trüpschuch & Carla Ziegler & Julia Drube & Stefan Schulz & Carsten Hoffmann, 2025. "Helix-bundle and C-terminal GPCR domains differentially influence GRK-specific functions and β-arrestin-mediated regulation," Nature Communications, Nature, vol. 16(1), pages 1-16, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-65173-5. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.