IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v14y2023i1d10.1038_s41467-023-43931-7.html
   My bibliography  Save this article

Proximity extracellular protein-protein interaction analysis of EGFR using AirID-conjugated fragment of antigen binding

Author

Listed:
  • Kohdai Yamada

    (Ehime University)

  • Ryouhei Shioya

    (Ehime University)

  • Kohei Nishino

    (Tokushima University)

  • Hirotake Furihata

    (Ehime University)

  • Atsushi Hijikata

    (Tokyo University of Pharmacy and Life Sciences)

  • Mika K. Kaneko

    (Tohoku University Graduate School of Medicine
    Tohoku University Graduate School of Medicine)

  • Yukinari Kato

    (Tohoku University Graduate School of Medicine
    Tohoku University Graduate School of Medicine)

  • Tsuyoshi Shirai

    (Nagahama Institute of BioScience and Technology)

  • Hidetaka Kosako

    (Tokushima University)

  • Tatsuya Sawasaki

    (Ehime University)

Abstract

Receptor proteins, such as epidermal growth factor receptor (EGFR), interact with other proteins in the extracellular region of the cell membrane to drive intracellular signalling. Therefore, analysis of extracellular protein-protein interactions (exPPIs) is important for understanding the biological function of receptor proteins. Here, we present an approach using a proximity biotinylation enzyme (AirID) fusion fragment of antigen binding (FabID) to analyse the proximity exPPIs of EGFR. AirID was C-terminally fused to the Fab fragment against EGFR (EGFR-FabID), which could then biotinylate the extracellular region of EGFR in several cell lines. Liquid Chromatography-Mass Spectrometry (LC-MS/MS) analysis indicated that many known EGFR interactors were identified as proximity exPPIs, along with many unknown candidate interactors, using EGFR-FabID. Interestingly, these proximity exPPIs were influenced by treatment with EGF ligand and its specific kinase inhibitor, gefitinib. These results indicate that FabID provides accurate proximity exPPI analysis of target receptor proteins on cell membranes with ligand and drug responses.

Suggested Citation

  • Kohdai Yamada & Ryouhei Shioya & Kohei Nishino & Hirotake Furihata & Atsushi Hijikata & Mika K. Kaneko & Yukinari Kato & Tsuyoshi Shirai & Hidetaka Kosako & Tatsuya Sawasaki, 2023. "Proximity extracellular protein-protein interaction analysis of EGFR using AirID-conjugated fragment of antigen binding," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-43931-7
    DOI: 10.1038/s41467-023-43931-7
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-023-43931-7
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-023-43931-7?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. Kathryn Tunyasuvunakool & Jonas Adler & Zachary Wu & Tim Green & Michal Zielinski & Augustin Žídek & Alex Bridgland & Andrew Cowie & Clemens Meyer & Agata Laydon & Sameer Velankar & Gerard J. Kleywegt, 2021. "Highly accurate protein structure prediction for the human proteome," Nature, Nature, vol. 596(7873), pages 590-596, August.
    2. Giovanna Scapin & Venkata P. Dandey & Zhening Zhang & Winifred Prosise & Alan Hruza & Theresa Kelly & Todd Mayhood & Corey Strickland & Clinton S. Potter & Bridget Carragher, 2018. "Structure of the insulin receptor–insulin complex by single-particle cryo-EM analysis," Nature, Nature, vol. 556(7699), pages 122-125, April.
    3. John Jumper & Richard Evans & Alexander Pritzel & Tim Green & Michael Figurnov & Olaf Ronneberger & Kathryn Tunyasuvunakool & Russ Bates & Augustin Žídek & Anna Potapenko & Alex Bridgland & Clemens Me, 2021. "Highly accurate protein structure prediction with AlphaFold," Nature, Nature, vol. 596(7873), pages 583-589, August.
    4. Keiichirou Nemoto & Abdelaziz Ramadan & Gen-ichiro Arimura & Kenichiro Imai & Kentaro Tomii & Kazuo Shinozaki & Tatsuya Sawasaki, 2017. "Tyrosine phosphorylation of the GARU E3 ubiquitin ligase promotes gibberellin signalling by preventing GID1 degradation," Nature Communications, Nature, vol. 8(1), pages 1-15, December.
    5. Christopher D. Go & James D. R. Knight & Archita Rajasekharan & Bhavisha Rathod & Geoffrey G. Hesketh & Kento T. Abe & Ji-Young Youn & Payman Samavarchi-Tehrani & Hui Zhang & Lucie Y. Zhu & Evelyn Pop, 2021. "A proximity-dependent biotinylation map of a human cell," Nature, Nature, vol. 595(7865), pages 120-124, July.
    6. Satoshi Yamanaka & Yuto Horiuchi & Saya Matsuoka & Kohki Kido & Kohei Nishino & Mayaka Maeno & Norio Shibata & Hidetaka Kosako & Tatsuya Sawasaki, 2022. "A proximity biotinylation-based approach to identify protein-E3 ligase interactions induced by PROTACs and molecular glues," Nature Communications, Nature, vol. 13(1), pages 1-17, 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. Jasjot Singh & Hadeer Elhabashy & Pathma Muthukottiappan & Markus Stepath & Martin Eisenacher & Oliver Kohlbacher & Volkmar Gieselmann & Dominic Winter, 2022. "Cross-linking of the endolysosomal system reveals potential flotillin structures and cargo," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    2. Cristina M. Viola & Orsolya Frittmann & Huw T. Jenkins & Talha Shafi & Pierre Meyts & Andrzej M. Brzozowski, 2023. "Structural conservation of insulin/IGF signalling axis at the insulin receptors level in Drosophila and humans," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    3. Robert A. Saxton & Nathanael A. Caveney & Maria Dolores Moya-Garzon & Karsten D. Householder & Grayson E. Rodriguez & Kylie A. Burdsall & Jonathan Z. Long & K. Christopher Garcia, 2023. "Structural insights into the mechanism of leptin receptor activation," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    4. Stella Vitt & Simone Prinz & Martin Eisinger & Ulrich Ermler & Wolfgang Buckel, 2022. "Purification and structural characterization of the Na+-translocating ferredoxin: NAD+ reductase (Rnf) complex of Clostridium tetanomorphum," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    5. Deyun Qiu & Jinxin V. Pei & James E. O. Rosling & Vandana Thathy & Dongdi Li & Yi Xue & John D. Tanner & Jocelyn Sietsma Penington & Yi Tong Vincent Aw & Jessica Yi Han Aw & Guoyue Xu & Abhai K. Tripa, 2022. "A G358S mutation in the Plasmodium falciparum Na+ pump PfATP4 confers clinically-relevant resistance to cipargamin," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    6. Shuo-Shuo Liu & Tian-Xia Jiang & Fan Bu & Ji-Lan Zhao & Guang-Fei Wang & Guo-Heng Yang & Jie-Yan Kong & Yun-Fan Qie & Pei Wen & Li-Bin Fan & Ning-Ning Li & Ning Gao & Xiao-Bo Qiu, 2024. "Molecular mechanisms underlying the BIRC6-mediated regulation of apoptosis and autophagy," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    7. Justin N. Vaughn & Sandra E. Branham & Brian Abernathy & Amanda M. Hulse-Kemp & Adam R. Rivers & Amnon Levi & William P. Wechter, 2022. "Graph-based pangenomics maximizes genotyping density and reveals structural impacts on fungal resistance in melon," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    8. Eliza S. Nieweglowska & Axel F. Brilot & Melissa Méndez-Moran & Claire Kokontis & Minkyung Baek & Junrui Li & Yifan Cheng & David Baker & Joseph Bondy-Denomy & David A. Agard, 2023. "The ϕPA3 phage nucleus is enclosed by a self-assembling 2D crystalline lattice," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    9. Sash Lopaticki & Robyn McConville & Alan John & Niall Geoghegan & Shihab Deen Mohamed & Lisa Verzier & Ryan W. J. Steel & Cindy Evelyn & Matthew T. O’Neill & Niccolay Madiedo Soler & Nichollas E. Scot, 2022. "Tryptophan C-mannosylation is critical for Plasmodium falciparum transmission," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    10. Radoslaw Pluta & Eric Aragón & Nicholas A. Prescott & Lidia Ruiz & Rebeca A. Mees & Blazej Baginski & Julia R. Flood & Pau Martin-Malpartida & Joan Massagué & Yael David & Maria J. Macias, 2022. "Molecular basis for DNA recognition by the maternal pioneer transcription factor FoxH1," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    11. Xiaoke Yang & Mingqi Zhu & Xue Lu & Yuxin Wang & Junyu Xiao, 2024. "Architecture and activation of human muscle phosphorylase kinase," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    12. Kristy Rochon & Brianna L. Bauer & Nathaniel A. Roethler & Yuli Buckley & Chih-Chia Su & Wei Huang & Rajesh Ramachandran & Maria S. K. Stoll & Edward W. Yu & Derek J. Taylor & Jason A. Mears, 2024. "Structural basis for regulated assembly of the mitochondrial fission GTPase Drp1," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    13. Fan Lu & Liang Zhu & Thomas Bromberger & Jun Yang & Qiannan Yang & Jianmin Liu & Edward F. Plow & Markus Moser & Jun Qin, 2022. "Mechanism of integrin activation by talin and its cooperation with kindlin," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
    14. Kiran Krishnamachari & Dylan Lu & Alexander Swift-Scott & Anuar Yeraliyev & Kayla Lee & Weitai Huang & Sim Ngak Leng & Anders Jacobsen Skanderup, 2022. "Accurate somatic variant detection using weakly supervised deep learning," Nature Communications, Nature, vol. 13(1), pages 1-8, December.
    15. Martin F. Peter & Christian Gebhardt & Rebecca Mächtel & Gabriel G. Moya Muñoz & Janin Glaenzer & Alessandra Narducci & Gavin H. Thomas & Thorben Cordes & Gregor Hagelueken, 2022. "Cross-validation of distance measurements in proteins by PELDOR/DEER and single-molecule FRET," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
    16. Olga V. Kochenova & Sirisha Mukkavalli & Malavika Raman & Johannes C. Walter, 2022. "Cooperative assembly of p97 complexes involved in replication termination," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    17. Andy M. Lau & Shaun M. Kandathil & David T. Jones, 2023. "Merizo: a rapid and accurate protein domain segmentation method using invariant point attention," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    18. Xiuqing Lv & Kaixuan Gao & Jia Nie & Xin Zhang & Shuhao Zhang & Yinhang Ren & Xiaoou Sun & Qi Li & Jingrui Huang & Lijuan Liu & Xiaowen Zhang & Weishe Zhang & Xiangyu Liu, 2023. "Structures of human prostaglandin F2α receptor reveal the mechanism of ligand and G protein selectivity," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    19. Guizhen Fan & Mariah R. Baker & Lara E. Terry & Vikas Arige & Muyuan Chen & Alexander B. Seryshev & Matthew L. Baker & Steven J. Ludtke & David I. Yule & Irina I. Serysheva, 2022. "Conformational motions and ligand-binding underlying gating and regulation in IP3R channel," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    20. Daniel Flam-Shepherd & Kevin Zhu & Alán Aspuru-Guzik, 2022. "Language models can learn complex molecular distributions," Nature Communications, Nature, vol. 13(1), pages 1-10, 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:14:y:2023:i:1:d:10.1038_s41467-023-43931-7. 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.