IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v15y2024i1d10.1038_s41467-024-51696-w.html
   My bibliography  Save this article

Self-assembled superstructure alleviates air-water interface effect in cryo-EM

Author

Listed:
  • Liming Zheng

    (Peking University)

  • Jie Xu

    (Tsinghua University
    Tsinghua University)

  • Weihua Wang

    (China Academy of Aerospace Science and Innovation)

  • Xiaoyin Gao

    (Peking University)

  • Chao Zhao

    (Shenzhen University of Advanced Technology
    Chinese Academy of Sciences
    Chinese Academy of Sciences)

  • Weijun Guo

    (Peking University)

  • Luzhao Sun

    (Beijing Graphene Institute (BGI))

  • Hang Cheng

    (Shuimu BioSciences Ltd)

  • Fanhao Meng

    (Shuimu BioSciences Ltd)

  • Buhang Chen

    (Beijing Graphene Institute (BGI))

  • Weiyu Sun

    (Peking University
    Peking University)

  • Xia Jia

    (Tsinghua University
    Tsinghua University)

  • Xiong Zhou

    (Peking University)

  • Kai Wu

    (Peking University)

  • Zhongfan Liu

    (Peking University
    Beijing Graphene Institute (BGI))

  • Feng Ding

    (Shenzhen University of Advanced Technology
    Chinese Academy of Sciences
    Chinese Academy of Sciences)

  • Nan Liu

    (Tsinghua University
    The University of Hong Kong)

  • Hong-Wei Wang

    (Tsinghua University
    Tsinghua University)

  • Hailin Peng

    (Peking University
    Beijing Graphene Institute (BGI)
    Peking University)

Abstract

Cryo-electron microscopy (cryo-EM) has been widely used to reveal the structures of proteins at atomic resolution. One key challenge is that almost all proteins are predominantly adsorbed to the air-water interface during standard cryo-EM specimen preparation. The interaction of proteins with air-water interface will significantly impede the success of reconstruction and achievable resolution. Here, we highlight the critical role of impenetrable surfactant monolayers in passivating the air-water interface problems, and develop a robust effective method for high-resolution cryo-EM analysis, by using the superstructure GSAMs which comprises surfactant self-assembled monolayers (SAMs) and graphene membrane. The GSAMs works well in enriching the orientations and improving particle utilization ratio of multiple proteins, facilitating the 3.3-Å resolution reconstruction of a 100-kDa protein complex (ACE2-RBD), which shows strong preferential orientation using traditional specimen preparation protocol. Additionally, we demonstrate that GSAMs enables the successful determinations of small proteins (

Suggested Citation

  • 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.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-51696-w
    DOI: 10.1038/s41467-024-51696-w
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-024-51696-w
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-024-51696-w?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. Liming Zheng & Yanan Chen & Ning Li & Jincan Zhang & Nan Liu & Junjie Liu & Wenhui Dang & Bing Deng & Yanbin Li & Xiaoyin Gao & Congwei Tan & Zi Yang & Shipu Xu & Mingzhan Wang & Hao Yang & Luzhao Sun, 2020. "Robust ultraclean atomically thin membranes for atomic-resolution electron microscopy," Nature Communications, Nature, vol. 11(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. 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.
    2. 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.
    3. 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.
    4. 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.
    5. 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.
    6. 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.
    7. 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.
    8. 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.
    9. 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.
    10. 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.
    11. 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.
    12. 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.
    13. Nikita Balyschew & Artsemi Yushkevich & Vasilii Mikirtumov & Ricardo M. Sanchez & Thiemo Sprink & Mikhail Kudryashev, 2023. "Streamlined structure determination by cryo-electron tomography and subtomogram averaging using TomoBEAR," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    14. Zhao Wang & Wenlin Liu & Jiaxin Shao & He Hao & Guorui Wang & Yixuan Zhao & Yeshu Zhu & Kaicheng Jia & Qi Lu & Jiawei Yang & Yanfeng Zhang & Lianming Tong & Yuqing Song & Pengzhan Sun & Boyang Mao & C, 2024. "Cyclododecane-based high-intactness and clean transfer method for fabricating suspended two-dimensional materials," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
    15. 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.
    16. 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.

    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_s41467-024-51696-w. 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.