1. Computational and Systems Biology
  2. Structural Biology and Molecular Biophysics
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Functional cross-talk between allosteric effects of activating and inhibiting ligands underlies PKM2 regulation

  1. Jamie A Macpherson
  2. Alina Theisen
  3. Laura Masino
  4. Louise Fets
  5. Paul C Driscoll
  6. Vesela Encheva
  7. Ambrosius P Snijders
  8. Stephen R. Martin
  9. Jens Kleinjung
  10. Perdita E Barran
  11. Franca Fraternali  Is a corresponding author
  12. Dimitrios Anastasiou  Is a corresponding author
  1. The Francis Crick Institute, United Kingdom
  2. University of Manchester, United Kingdom
  3. King's College London, United Kingdom
Research Article
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Cite this article as: eLife 2019;8:e45068 doi: 10.7554/eLife.45068

Abstract

Several enzymes can simultaneously interact with multiple intracellular metabolites, however, how the allosteric effects of distinct ligands are integrated to coordinately control enzymatic activity remains poorly understood. We addressed this question using, as a model system, the glycolytic enzyme pyruvate kinase M2 (PKM2). We show that the PKM2 activator fructose 1,6-bisphosphate (FBP) alone promotes tetramerisation and increases PKM2 activity, but addition of the inhibitor L-phenylalanine (Phe) prevents maximal activation of FBP-bound PKM2 tetramers. We developed a method, AlloHubMat, that uses eigenvalue decomposition of mutual information derived from molecular dynamics trajectories to identify residues that mediate FBP-induced allostery. Experimental mutagenesis of these residues identified PKM2 variants in which activation by FBP remains intact but cannot be attenuated by Phe. Our findings reveal residues involved in FBP-induced allostery that enable the integration of allosteric input from Phe and provide a paradigm for the coordinate regulation of enzymatic activity by simultaneous allosteric inputs.

Article and author information

Author details

  1. Jamie A Macpherson

    Cancer Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  2. Alina Theisen

    Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0216-8582
  3. Laura Masino

    Structural Biology Science Technology Platform, The Francis Crick Institute, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  4. Louise Fets

    Cancer Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  5. Paul C Driscoll

    Metabolomics Science Technology Platform, The Francis Crick Institute, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  6. Vesela Encheva

    Proteomics Science Technology Platform, The Francis Crick Institute, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  7. Ambrosius P Snijders

    Proteomics Science Technology Platform, The Francis Crick Institute, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  8. Stephen R. Martin

    Structural Biology Science Technology Platform, The Francis Crick Institute, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  9. Jens Kleinjung

    Computational Biology Science Technology Platform, The Francis Crick Institute, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  10. Perdita E Barran

    Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  11. Franca Fraternali

    Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
    For correspondence
    franca.fraternali@kcl.ac.uk
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3143-6574
  12. Dimitrios Anastasiou

    Cancer Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
    For correspondence
    dimitrios.anastasiou@crick.ac.uk
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1269-843X

Funding

Cancer Research UK (FC001033)

  • Dimitrios Anastasiou

Wellcome (FC001033)

  • Dimitrios Anastasiou

Medical Research Council (FC001033)

  • Dimitrios Anastasiou

Francis Crick Institute (FC001033)

  • Dimitrios Anastasiou

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

Reviewing Editor

  1. Nir Ben-Tal, Tel Aviv University, Israel

Publication history

  1. Received: January 20, 2019
  2. Accepted: July 1, 2019
  3. Accepted Manuscript published: July 2, 2019 (version 1)

Copyright

© 2019, Macpherson 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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