1. Structural Biology and Molecular Biophysics

Inhibition of the proton-activated chloride channel PAC by PIP2

  1. Ljubica Mihaljevic
  2. Zheng Ruan
  3. James Osei-Owusu
  4. Wei Lü  Is a corresponding author
  5. Zhaozhu Qiu  Is a corresponding author
  1. Johns Hopkins Medicine, United States
  2. Van Andel Institute, United States
https://doi.org/10.7554/eLife.83935
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  1. Ljubica Mihaljevic
  2. Zheng Ruan
  3. James Osei-Owusu
  4. Wei Lü
  5. Zhaozhu Qiu
(2023)
Inhibition of the proton-activated chloride channel PAC by PIP2
eLife 12:e83935.
https://doi.org/10.7554/eLife.83935
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Abstract

Proton-Activated Chloride (PAC) channel is a ubiquitously expressed pH-sensing ion channel, encoded by PACC1 (TMEM206). PAC regulates endosomal acidification and macropinosome shrinkage by releasing chloride from the organelle lumens. It is also found at the cell surface, where it is activated under pathological conditions related to acidosis and contributes to acid-induced cell death. However, the pharmacology of the PAC channel is poorly understood. Here, we report that phosphatidylinositol (4,5)-bisphosphate (PIP2) potently inhibits PAC channel activity. We solved the cryo-electron microscopy structure of PAC with PIP2 at pH 4.0 and identified its putative binding site, which, surprisingly, locates on the extracellular side of the transmembrane domain (TMD). While the overall conformation resembles the previously resolved PAC structure in the desensitized state, the TMD undergoes remodeling upon PIP2-binding. Structural and electrophysiological analyses suggest that PIP2 inhibits the PAC channel by stabilizing the channel in a desensitized-like conformation. Our findings identify PIP2 as a new pharmacological tool for the PAC channel and lay the foundation for future drug discovery targeting this channel.

Data availability

The cryo-EM density map and atomic models have been deposited in the EMDB (Electron Microscopy Data Bank) and the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCS-PDB), respectively, under accession numbers EMD-28535 and PDB 8EQ4.

The following data sets were generated

Article and author information

Author details

  1. Ljubica Mihaljevic

    Department of Physiology, Johns Hopkins Medicine, Baltimore, United States
    Competing interests
    The authors declare that no competing interests exist.

  2. Zheng Ruan

    Department of Structural Biology, Van Andel Institute, Grand Rapids, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4412-4916

  3. James Osei-Owusu

    Department of Physiology, Johns Hopkins Medicine, Baltimore, United States
    Competing interests
    The authors declare that no competing interests exist.

  4. Wei Lü

    Department of Structural Biology, Van Andel Institute, Grand Rapids, United States
    For correspondence
    wei.lu@vai.org
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3009-1025

  5. Zhaozhu Qiu

    Department of Physiology, Johns Hopkins Medicine, Baltimore, United States
    For correspondence
    zhaozhu@jhmi.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9122-6077

Funding

Boehringer Ingelheim Fonds (Graduate Student Fellowship)

  • Ljubica Mihaljevic

National Institutes of Health (grant R35GM124824)

  • Zhaozhu Qiu

National Institutes of Health (grant R01NS118014)

  • Zhaozhu Qiu

National Institute of General Medical Sciences (T32 GM007445 Graduate Training Program)

  • Ljubica Mihaljevic

American Heart Association (Postdoctoral Fellowship grant 20POST35120556)

  • Zheng Ruan

National Institutes of Health (grant K99NS128258)

  • Zheng Ruan

American Heart Association (Predoctoral Fellowship grant 18PRE34060025)

  • James Osei-Owusu

National Institutes of Health (grant R01NS112363)

  • Wei Lü

McKnight Foundation (McKnight Scholar Award)

  • Zhaozhu Qiu

Alfred P. Sloan Foundation (Sloan Research Fellowship)

  • Zhaozhu Qiu

Esther A. and Joseph Klingenstein Fund (Klingenstein-Simons Fellowship)

  • Zhaozhu Qiu

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Andrés Jara-Oseguera, The University of Texas at Austin, United States

Version history

  1. Received: October 4, 2022
  2. Preprint posted: October 7, 2022 (view preprint)
  3. Accepted: December 18, 2022
  4. Accepted Manuscript published: January 12, 2023 (version 1)
  5. Version of Record published: January 25, 2023 (version 2)

Copyright

© 2023, Mihaljevic et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Ljubica Mihaljevic
  2. Zheng Ruan
  3. James Osei-Owusu
  4. Wei Lü
  5. Zhaozhu Qiu
(2023)
Inhibition of the proton-activated chloride channel PAC by PIP2
eLife 12:e83935.
https://doi.org/10.7554/eLife.83935

Share this article

https://doi.org/10.7554/eLife.83935

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