IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v15y2024i1d10.1038_s41467-024-52091-1.html
   My bibliography  Save this article

Small LEA proteins mitigate air-water interface damage to fragile cryo-EM samples during plunge freezing

Author

Listed:
  • Kaitlyn M. Abe

    (University of Wisconsin-Madison)

  • Gan Li

    (University of Wisconsin-Madison
    Morgridge Institute for Research)

  • Qixiang He

    (University of Wisconsin-Madison)

  • Timothy Grant

    (University of Wisconsin-Madison
    Morgridge Institute for Research)

  • Ci Ji Lim

    (University of Wisconsin-Madison)

Abstract

Air-water interface (AWI) interactions during cryo-electron microscopy (cryo-EM) sample preparation cause significant sample loss, hindering structural biology research. Organisms like nematodes and tardigrades produce Late Embryogenesis Abundant (LEA) proteins to withstand desiccation stress. Here we show that these LEA proteins, when used as additives during plunge freezing, effectively mitigate AWI damage to fragile multi-subunit molecular samples. The resulting high-resolution cryo-EM maps are comparable to or better than those obtained using existing AWI damage mitigation methods. Cryogenic electron tomography reveals that particles are localized at specific interfaces, suggesting LEA proteins form a barrier at the AWI. This interaction may explain the observed sample-dependent preferred orientation of particles. LEA proteins offer a simple, cost-effective, and adaptable approach for cryo-EM structural biologists to overcome AWI-related sample damage, potentially revitalizing challenging projects and advancing the field of structural biology.

Suggested Citation

  • Kaitlyn M. Abe & Gan Li & Qixiang He & Timothy Grant & Ci Ji Lim, 2024. "Small LEA proteins mitigate air-water interface damage to fragile cryo-EM samples during plunge freezing," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-52091-1
    DOI: 10.1038/s41467-024-52091-1
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-024-52091-1
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-024-52091-1?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. Yun-Tao Liu & Heng Zhang & Hui Wang & Chang-Lu Tao & Guo-Qiang Bi & Z. Hong Zhou, 2022. "Isotropic reconstruction for electron tomography with deep learning," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    2. Qixiang He & Xiuhua Lin & Bianca L. Chavez & Sourav Agrawal & Benjamin L. Lusk & Ci Ji Lim, 2022. "Structures of the human CST-Polα–primase complex bound to telomere templates," Nature, Nature, vol. 608(7924), pages 826-832, August.
    3. Katerina Naydenova & Christopher J. Russo, 2017. "Measuring the effects of particle orientation to improve the efficiency of electron cryomicroscopy," Nature Communications, Nature, vol. 8(1), pages 1-5, December.
    4. Ye Lu & Nan Liu & Yongbo Liu & Liming Zheng & Junhao Yang & Jia Wang & Xia Jia & Qinru Zi & Hailin Peng & Yu Rao & Hong-Wei Wang, 2022. "Functionalized graphene grids with various charges for single-particle cryo-EM," Nature Communications, Nature, vol. 13(1), pages 1-8, December.
    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. Un Seng Chio & Eugene Palovcak & Anton A. A. Smith & Henriette Autzen & Elise N. Muñoz & Zanlin Yu & Feng Wang & David A. Agard & Jean-Paul Armache & Geeta J. Narlikar & Yifan Cheng, 2024. "Functionalized graphene-oxide grids enable high-resolution cryo-EM structures of the SNF2h-nucleosome complex without crosslinking," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    2. Radostin Danev & Matthew Belousoff & Yi-Lynn Liang & Xin Zhang & Fabian Eisenstein & Denise Wootten & Patrick M. Sexton, 2021. "Routine sub-2.5 Å cryo-EM structure determination of GPCRs," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
    3. Tim Schulte & Antonio Chaves-Sanjuan & Valentina Speranzini & Kevin Sicking & Melissa Milazzo & Giulia Mazzini & Paola Rognoni & Serena Caminito & Paolo Milani & Chiara Marabelli & Alessandro Corbelli, 2024. "Helical superstructures between amyloid and collagen in cardiac fibrils from a patient with AL amyloidosis," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    4. Fred E. Fregoso & Malgorzata Boczkowska & Grzegorz Rebowski & Peter J. Carman & Trevor Eeuwen & Roberto Dominguez, 2023. "Mechanism of synergistic activation of Arp2/3 complex by cortactin and WASP-family proteins," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    5. Simon Wiedemann & Reinhard Heckel, 2024. "A deep learning method for simultaneous denoising and missing wedge reconstruction in cryogenic electron tomography," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    6. Xueming Meng & Cong Xu & Jiawei Li & Benhua Qiu & Jiajun Luo & Qin Hong & Yujie Tong & Chuyu Fang & Yanyan Feng & Rui Ma & Xiangyi Shi & Cheng Lin & Chen Pan & Xueliang Zhu & Xiumin Yan & Yao Cong, 2024. "Multi-scale structures of the mammalian radial spoke and divergence of axonemal complexes in ependymal cilia," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    7. Anjie Li & Tingting You & Xiaojie Pang & Yidi Wang & Lijin Tian & Xiaobo Li & Zhenfeng Liu, 2024. "Structural basis for an early stage of the photosystem II repair cycle in Chlamydomonas reinhardtii," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    8. Bryan S. Sibert & Joseph Y. Kim & Jie E. Yang & Zunlong Ke & Christopher C. Stobart & Martin L. Moore & Elizabeth R. Wright, 2024. "Assembly of respiratory syncytial virus matrix protein lattice and its coordination with fusion glycoprotein trimers," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    9. Zhen Hou & Frank Nightingale & Yanan Zhu & Craig MacGregor-Chatwin & Peijun Zhang, 2023. "Structure of native chromatin fibres revealed by Cryo-ET in situ," Nature Communications, Nature, vol. 14(1), pages 1-7, December.
    10. Tomáš Kovaľ & Nabajyoti Borah & Petra Sudzinová & Barbora Brezovská & Hana Šanderová & Viola Vaňková Hausnerová & Alena Křenková & Martin Hubálek & Mária Trundová & Kristýna Adámková & Jarmila Dušková, 2024. "Mycobacterial HelD connects RNA polymerase recycling with transcription initiation," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
    11. Conny Leistner & Martin Wilkinson & Ailidh Burgess & Megan Lovatt & Stanley Goodbody & Yong Xu & Susan Deuchars & Sheena E. Radford & Neil A. Ranson & René A. W. Frank, 2023. "The in-tissue molecular architecture of β-amyloid pathology in the mammalian brain," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    12. Liming Zheng & Jie Xu & Weihua Wang & Xiaoyin Gao & Chao Zhao & Weijun Guo & Luzhao Sun & Hang Cheng & Fanhao Meng & Buhang Chen & Weiyu Sun & Xia Jia & Xiong Zhou & Kai Wu & Zhongfan Liu & Feng Ding , 2024. "Self-assembled superstructure alleviates air-water interface effect in cryo-EM," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    13. Clément Madru & Markel Martínez-Carranza & Sébastien Laurent & Alessandra C. Alberti & Maelenn Chevreuil & Bertrand Raynal & Ahmed Haouz & Rémy A. Meur & Marc Delarue & Ghislaine Henneke & Didier Flam, 2023. "DNA-binding mechanism and evolution of replication protein A," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    14. Yitang Zhang & Maofei Chen & Xudong Chen & Minghui Zhang & Jian Yin & Zi Yang & Xin Gao & Sensen Zhang & Maojun Yang, 2024. "Molecular architecture of the mammalian 2-oxoglutarate dehydrogenase complex," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    15. Iskander Khusainov & Natalie Romanov & Camille Goemans & Beata Turoňová & Christian E. Zimmerli & Sonja Welsch & Julian D. Langer & Athanasios Typas & Martin Beck, 2024. "Bactericidal effect of tetracycline in E. coli strain ED1a may be associated with ribosome dysfunction," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    16. Michelle M. Shimogawa & Angeline S. Wijono & Hui Wang & Jiayan Zhang & Jihui Sha & Natasha Szombathy & Sabeeca Vadakkan & Paula Pelayo & Keya Jonnalagadda & James Wohlschlegel & Z. Hong Zhou & Kent L., 2023. "FAP106 is an interaction hub for assembling microtubule inner proteins at the cilium inner junction," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    17. Rebeccah A. Warmack & Ailiena O. Maggiolo & Andres Orta & Belinda B. Wenke & James B. Howard & Douglas C. Rees, 2023. "Structural consequences of turnover-induced homocitrate loss in nitrogenase," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    18. Zuanning Yuan & Roxana Georgescu & Huilin Li & Michael E. O’Donnell, 2023. "Molecular choreography of primer synthesis by the eukaryotic Pol α-primase," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    19. Haonan Zhang & Yan Li & Yanan Liu & Dongyu Li & Lin Wang & Kai Song & Keyan Bao & Ping Zhu, 2023. "A method for restoring signals and revealing individual macromolecule states in cryo-ET, REST," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    20. Rhianna J. Rowland & Svitlana Korolchuk & Marco Salamina & Natalie J. Tatum & James R. Ault & Sam Hart & Johan P. Turkenburg & James N. Blaza & Martin E. M. Noble & Jane A. Endicott, 2024. "Cryo-EM structure of the CDK2-cyclin A-CDC25A complex," Nature Communications, Nature, vol. 15(1), pages 1-14, 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:15:y:2024:i:1:d:10.1038_s41467-024-52091-1. 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.