Abstract

Calcineurin B homologous protein 3 (CHP3) is an EF-hand Ca2+-binding protein involved in regulation of cancerogenesis, cardiac hypertrophy and neuronal development through interactions with sodium/proton exchangers (NHEs) and signalling proteins. While the importance of Ca2+ binding and myristoylation for CHP3 function has been recognized, the underlying molecular mechanism remained elusive. In this study, we demonstrate that Ca2+ binding and myristoylation independently affect the conformation and functions of human CHP3. Ca2+ binding increased local flexibility and hydrophobicity of CHP3 indicative of an open conformation. The Ca2+-bound CHP3 exhibited a higher affinity for NHE1 and associated stronger with lipid membranes compared to the Mg2+-bound CHP3, which adopted a closed conformation. Myristoylation enhanced the local flexibility of CHP3 and decreased its affinity to NHE1 independently of the bound ion, but did not affect its binding to lipid membranes. The data exclude the proposed Ca2+-myristoyl switch for CHP3. Instead, a Ca2+-independent exposure of the myristoyl moiety is induced by binding of the target peptide to CHP3 enhancing its association to lipid membranes. We name this novel regulatory mechanism 'target-myristoyl switch'. Collectively, the interplay of Ca2+ binding, myristoylation, and target binding allows for a context-specific regulation of CHP3 functions.

Data availability

All data generated or analyzed during this study are included in the manuscript. Source files have been provided for Figures 1, 4, 6, and Figure 4-figure supplement 1. Data2Dynamics Software used for EC50 and KD determination is available at GitHub (https://github.com/Data2Dynamics/d2d).

Article and author information

Author details

  1. Florian Becker

    Institute for Biochemistry and Molecular Biology, University of Freiburg, Freiburg, Germany
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5889-8728
  2. Simon Fuchs

    Institute for Biochemistry and Molecular Biology, University of Freiburg, Freiburg, Germany
    Competing interests
    No competing interests declared.
  3. Lukas Refisch

    Institute of Medical Biometry and Statistics, University of Freiburg, Freiburg, Germany
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9049-1944
  4. Friedel Drepper

    Institute of Biology II, University of Freiburg, Freiburg, Germany
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2043-5795
  5. Wolfgang Bildl

    Institute of Physiology, University of Freiburg, Freiburg, Germany
    Competing interests
    No competing interests declared.
  6. Uwe Schulte

    Institute of Physiology, University of Freiburg, Freiburg, Germany
    Competing interests
    Uwe Schulte, is an employee and shareholder of Logopharm GmbH that produces ComplexioLyte 47 used in this study..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3557-0591
  7. Shuo Liang

    Institute for Biochemistry and Molecular Biology, University of Freiburg, Freiburg, Germany
    Competing interests
    No competing interests declared.
  8. Jonas Immanuel Heinicke

    Institute for Biochemistry and Molecular Biology, University of Freiburg, Freiburg, Germany
    Competing interests
    No competing interests declared.
  9. Sierra C Hansen

    Institute for Biochemistry and Molecular Biology, University of Freiburg, Freiburg, Germany
    Competing interests
    No competing interests declared.
  10. Clemens Kreutz

    Institute of Medical Biometry and Statistics, University of Freiburg, Freiburg, Germany
    Competing interests
    No competing interests declared.
  11. Bettina Warscheid

    Institute of Biology II, University of Freiburg, Freiburg, Germany
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5096-1975
  12. Bernd Fakler

    Institute of Physiology, University of Freiburg, Freiburg, Germany
    Competing interests
    Bernd Fakler, is shareholder of Logopharm GmbH. The company provides ComplexioLyte reagents to academic institutions on a non-profit basis..
  13. Evgeny V Mymrikov

    Institute of Biochemistry and Molecular Biology, University of Freiburg, Freiburg, Germany
    For correspondence
    evgeny.mymrikov@biochemie.uni-freiburg.de
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4817-6278
  14. Carola Hunte

    Institute for Biochemistry and Molecular Biology, University of Freiburg, Freiburg, Germany
    For correspondence
    carola.hunte@biochemie.uni-freiburg.de
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0826-3986

Funding

Deutsche Forschungsgemeinschaft (EXC-2189 - 390939984)

  • Clemens Kreutz
  • Bettina Warscheid
  • Bernd Fakler
  • Evgeny V Mymrikov
  • Carola Hunte

Deutsche Forschungsgemeinschaft (SFB 1381 - 403222702)

  • Uwe Schulte
  • Bettina Warscheid
  • Carola Hunte

Deutsche Forschungsgemeinschaft (SFB 1453 - 431984000)

  • Bernd Fakler
  • Carola Hunte

Deutsche Forschungsgemeinschaft (RTG 2202 - 278002225)

  • Carola Hunte

Bundesministerium für Bildung und Forschung (FKZ031L0080)

  • Clemens Kreutz

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

Reviewing Editor

  1. M Joanne Lemieux, University of Alberta, Canada

Version history

  1. Preprint posted: September 23, 2022 (view preprint)
  2. Received: September 30, 2022
  3. Accepted: July 3, 2023
  4. Accepted Manuscript published: July 12, 2023 (version 1)
  5. Version of Record published: July 25, 2023 (version 2)

Copyright

© 2023, Becker 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. Florian Becker
  2. Simon Fuchs
  3. Lukas Refisch
  4. Friedel Drepper
  5. Wolfgang Bildl
  6. Uwe Schulte
  7. Shuo Liang
  8. Jonas Immanuel Heinicke
  9. Sierra C Hansen
  10. Clemens Kreutz
  11. Bettina Warscheid
  12. Bernd Fakler
  13. Evgeny V Mymrikov
  14. Carola Hunte
(2023)
Conformational regulation and target-myristoyl switch of calcineurin B homologous protein 3
eLife 12:e83868.
https://doi.org/10.7554/eLife.83868

Share this article

https://doi.org/10.7554/eLife.83868

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