1. Structural Biology and Molecular Biophysics
  2. Computational and Systems Biology
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Pi-Pi contacts are an overlooked protein feature relevant to phase separation

Research Article
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Cite this article as: eLife 2018;7:e31486 doi: 10.7554/eLife.31486

Abstract

Protein phase separation is implicated in formation of membraneless organelles, signaling puncta and the nuclear pore. Multivalent interactions of modular binding domains and their target motifs can drive phase separation. However, forces promoting the more common phase separation of intrinsically disordered regions are less understood, with suggested roles for multivalent cation-pi, pi-pi, and charge interactions and the hydrophobic effect. Known phase-separating proteins are enriched in pi-orbital containing residues and thus we analyzed pi-interactions in folded proteins. We found that pi-pi interactions involving non-aromatic groups are widespread, underestimated by force-fields used in structure calculations and correlated with solvation and lack of regular secondary structure, properties associated with disordered regions. We present a phase separation predictive algorithm based on pi interaction frequency, highlighting proteins involved in biomaterials and RNA processing.

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The following previously published data sets were used

Article and author information

Author details

  1. Robert McCoy Vernon

    Program in Molecular Medicine, Hospital for Sick Children, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  2. Paul Andrew Chong

    Program in Molecular Medicine, Hospital for Sick Children, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  3. Brian Tsang

    Program in Molecular Medicine, Hospital for Sick Children, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  4. Tae Hun Kim

    Program in Molecular Medicine, Hospital for Sick Children, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  5. Alaji Bah

    Program in Molecular Medicine, Hospital for Sick Children, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  6. Patrick Farber

    Program in Molecular Medicine, Hospital for Sick Children, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  7. Hong Lin

    Program in Molecular Medicine, Hospital for Sick Children, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  8. Julie Deborah Forman-Kay

    Program in Molecular Medicine, Hospital for Sick Children, Toronto, Canada
    For correspondence
    forman@sickkids.ca
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8265-972X

Funding

Canadian Institutes of Health Research (114985)

  • Julie Deborah Forman-Kay

Natural Sciences and Engineering Research Council of Canada (6718)

  • Julie Deborah Forman-Kay

Canadian Cancer Society Research Institute (703477)

  • Julie Deborah Forman-Kay

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

Reviewing Editor

  1. Yibing Shan, DE Shaw Research, United States

Publication history

  1. Received: August 24, 2017
  2. Accepted: February 8, 2018
  3. Accepted Manuscript published: February 9, 2018 (version 1)
  4. Version of Record published: March 12, 2018 (version 2)

Copyright

© 2018, Vernon 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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