IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v15y2024i1d10.1038_s41467-024-48823-y.html
   My bibliography  Save this article

Atomistic mechanism of coupling between cytosolic sensor domain and selectivity filter in TREK K2P channels

Author

Listed:
  • Berke Türkaydin

    (Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
    Technical University of Berlin)

  • Marcus Schewe

    (Kiel University)

  • Elena Barbara Riel

    (Kiel University
    Weill Cornell Medical College)

  • Friederike Schulz

    (Kiel University)

  • Johann Biedermann

    (Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP))

  • Thomas Baukrowitz

    (Kiel University)

  • Han Sun

    (Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
    Technical University of Berlin)

Abstract

The two-pore domain potassium (K2P) channels TREK-1 and TREK-2 link neuronal excitability to a variety of stimuli including mechanical force, lipids, temperature and phosphorylation. This regulation involves the C-terminus as a polymodal stimulus sensor and the selectivity filter (SF) as channel gate. Using crystallographic up- and down-state structures of TREK-2 as a template for full atomistic molecular dynamics (MD) simulations, we reveal that the SF in down-state undergoes inactivation via conformational changes, while the up-state structure maintains a stable and conductive SF. This suggests an atomistic mechanism for the low channel activity previously assigned to the down state, but not evident from the crystal structure. Furthermore, experimentally by using (de-)phosphorylation mimics and chemically attaching lipid tethers to the proximal C-terminus (pCt), we confirm the hypothesis that moving the pCt towards the membrane induces the up-state. Based on MD simulations, we propose two gating pathways by which movement of the pCt controls the stability (i.e., conductivity) of the filter gate. Together, these findings provide atomistic insights into the SF gating mechanism and the physiological regulation of TREK channels by phosphorylation.

Suggested Citation

  • Berke Türkaydin & Marcus Schewe & Elena Barbara Riel & Friederike Schulz & Johann Biedermann & Thomas Baukrowitz & Han Sun, 2024. "Atomistic mechanism of coupling between cytosolic sensor domain and selectivity filter in TREK K2P channels," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-48823-y
    DOI: 10.1038/s41467-024-48823-y
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-024-48823-y
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-024-48823-y?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. 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.
    3. Charles R. Harris & K. Jarrod Millman & Stéfan J. Walt & Ralf Gommers & Pauli Virtanen & David Cournapeau & Eric Wieser & Julian Taylor & Sebastian Berg & Nathaniel J. Smith & Robert Kern & Matti Picu, 2020. "Array programming with NumPy," Nature, Nature, vol. 585(7825), pages 357-362, September.
    4. Baobin Li & Robert A. Rietmeijer & Stephen G. Brohawn, 2020. "Structural basis for pH gating of the two-pore domain K+ channel TASK2," Nature, Nature, vol. 586(7829), pages 457-462, October.
    5. Wojciech Kopec & Brad S. Rothberg & Bert L. Groot, 2019. "Molecular mechanism of a potassium channel gating through activation gate-selectivity filter coupling," Nature Communications, Nature, vol. 10(1), pages 1-15, December.
    6. Stephen G. Brohawn & Ernest B. Campbell & Roderick MacKinnon, 2014. "Physical mechanism for gating and mechanosensitivity of the human TRAAK K+ channel," Nature, Nature, vol. 516(7529), pages 126-130, 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. Toby S. Turney & Vivian Li & Stephen G. Brohawn, 2022. "Structural Basis for pH-gating of the K+ channel TWIK1 at the selectivity filter," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    2. 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.
    3. Akshay J. Maheshwari & Jonathan Calles & Sean K. Waterton & Drew Endy, 2023. "Engineering tRNA abundances for synthetic cellular systems," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    4. Gabriele Orlando & Daniele Raimondi & Ramon Duran-Romaña & Yves Moreau & Joost Schymkowitz & Frederic Rousseau, 2022. "PyUUL provides an interface between biological structures and deep learning algorithms," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    5. Kevin E. Wu & Kevin K. Yang & Rianne Berg & Sarah Alamdari & James Y. Zou & Alex X. Lu & Ava P. Amini, 2024. "Protein structure generation via folding diffusion," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    6. Josie L. Ferreira & Vojtěch Pražák & Daven Vasishtan & Marc Siggel & Franziska Hentzschel & Annika M. Binder & Emma Pietsch & Jan Kosinski & Friedrich Frischknecht & Tim W. Gilberger & Kay Grünewald, 2023. "Variable microtubule architecture in the malaria parasite," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    7. Zhihui He & Yonghui Zhao & Michael J. Rau & James A. J. Fitzpatrick & Rajan Sah & Hongzhen Hu & Peng Yuan, 2023. "Structural and functional analysis of human pannexin 2 channel," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    8. Maximilian Seidel & Natalie Romanov & Agnieszka Obarska-Kosinska & Anja Becker & Nayara Trevisan Doimo de Azevedo & Jan Provaznik & Sankarshana R. Nagaraja & Jonathan J. M. Landry & Vladimir Benes & M, 2023. "Co-translational binding of importins to nascent proteins," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    9. Friederike M. C. Benning & Simon Jenni & Coby Y. Garcia & Tran H. Nguyen & Xuewu Zhang & Luke H. Chao, 2024. "Helical reconstruction of VP39 reveals principles for baculovirus nucleocapsid assembly," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    10. Ye Yuan & Lei Chen & Kexu Song & Miaomiao Cheng & Ling Fang & Lingfei Kong & Lanlan Yu & Ruonan Wang & Zhendong Fu & Minmin Sun & Qian Wang & Chengjun Cui & Haojue Wang & Jiuyang He & Xiaonan Wang & Y, 2024. "Stable peptide-assembled nanozyme mimicking dual antifungal actions," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    11. Ivica Odorčić & Mohamed Belal Hamed & Sam Lismont & Lucía Chávez-Gutiérrez & Rouslan G. Efremov, 2024. "Apo and Aβ46-bound γ-secretase structures provide insights into amyloid-β processing by the APH-1B isoform," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    12. Léon Faure & Bastien Mollet & Wolfram Liebermeister & Jean-Loup Faulon, 2023. "A neural-mechanistic hybrid approach improving the predictive power of genome-scale metabolic models," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    13. 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.
    14. Pierre Azoulay & Joshua Krieger & Abhishek Nagaraj, 2024. "Old Moats for New Models: Openness, Control, and Competition in Generative AI," NBER Chapters, in: Entrepreneurship and Innovation Policy and the Economy, volume 4, National Bureau of Economic Research, Inc.
    15. Riya Shah & Thomas C. Panagiotou & Gregory B. Cole & Trevor F. Moraes & Brigitte D. Lavoie & Christopher A. McCulloch & Andrew Wilde, 2024. "The DIAPH3 linker specifies a β-actin network that maintains RhoA and Myosin-II at the cytokinetic furrow," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    16. Bret M. Boyd & Ian James & Kevin P. Johnson & Robert B. Weiss & Sarah E. Bush & Dale H. Clayton & Colin Dale, 2024. "Stochasticity, determinism, and contingency shape genome evolution of endosymbiotic bacteria," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    17. 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.
    18. 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.
    19. 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.
    20. 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.

    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_s41467-024-48823-y. 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.