Membrane interactions of the globular domain and the hypervariable region of KRAS4b define its unique diffusion behavior

  1. Debanjan Goswami
  2. De Chen
  3. Yue Yang
  4. Prabhakar R Gudla
  5. John Columbus
  6. Karen Worthy
  7. Megan Rigby
  8. Madeline Wheeler
  9. Suman Mukhopadhyay
  10. Katie Powell
  11. William Burgan
  12. Vanessa Wall
  13. Dominic Esposito
  14. Dhirendra Simanshu
  15. Felice C Lightstone
  16. Dwight V Nissley
  17. Frank McCormick
  18. Thomas Turbyville  Is a corresponding author
  1. Frederick National Laboratory for Cancer Research, United States
  2. Lawrence Livermore National Laboratory, United States
  3. University of California, San Francisco, United States

Abstract

The RAS proteins are GTP-dependent switches that regulate signaling pathways and are frequently mutated in cancer. RAS proteins concentrate in the plasma membrane via lipid-tethers and hypervariable side-chain interactions in distinct nano-domains. However, little is known about RAS membrane dynamics and the details of RAS activation of downstream signaling. Here we characterize RAS in live human and mouse cells using single molecule tracking methods and estimate RAS mobility parameters. KRAS4b exhibits confined mobility with three diffusive states distinct from the other RAS isoforms (KRAS4a, NRAS, and HRAS); and although most of the amino acid differences between RAS isoforms lie within the hypervariable region, the additional confinement of KRAS4b is largely determined by the protein's globular domain. To understand the altered mobility of an oncogenic KRAS4b we used complementary experimental and molecular dynamic simulation approaches to reveal a detailed mechanism.

Data availability

For the molecular dynamic simulations, trajectories and inputs have been provided on the webpage at https://bbs.llnl.gov/KRAS4b-simulation-data.html.For the images, we will access a suitable repository, and make the data freely available.

Article and author information

Author details

  1. Debanjan Goswami

    RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5910-3811
  2. De Chen

    RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Yue Yang

    Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Prabhakar R Gudla

    RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. John Columbus

    RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Karen Worthy

    RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Megan Rigby

    RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Madeline Wheeler

    RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Suman Mukhopadhyay

    RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
    Competing interests
    The authors declare that no competing interests exist.
  10. Katie Powell

    RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
    Competing interests
    The authors declare that no competing interests exist.
  11. William Burgan

    RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
    Competing interests
    The authors declare that no competing interests exist.
  12. Vanessa Wall

    RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
    Competing interests
    The authors declare that no competing interests exist.
  13. Dominic Esposito

    RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
    Competing interests
    The authors declare that no competing interests exist.
  14. Dhirendra Simanshu

    RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
    Competing interests
    The authors declare that no competing interests exist.
  15. Felice C Lightstone

    Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1465-426X
  16. Dwight V Nissley

    RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
    Competing interests
    The authors declare that no competing interests exist.
  17. Frank McCormick

    UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, United States
    Competing interests
    The authors declare that no competing interests exist.
  18. Thomas Turbyville

    RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
    For correspondence
    turbyvillet@mail.nih.gov
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2638-9520

Funding

National Cancer Institute (NIH Contract HHSN261200800001E)

  • De Chen
  • Prabhakar R Gudla
  • John Columbus
  • Karen Worthy
  • Megan Rigby
  • Suman Mukhopadhyay
  • Katie Powell
  • William Burgan
  • Vanessa Wall
  • Dominic Esposito
  • Dhirendra Simanshu
  • Dwight V Nissley
  • Thomas Turbyville

U.S. Department of Energy (Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. LLNL-JRNL-771099-DRAFT)

  • Yue Yang
  • Felice C Lightstone

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

Reviewing Editor

  1. Roger J Davis, University of Massachusetts Medical School, United States

Publication history

  1. Received: April 12, 2019
  2. Accepted: January 2, 2020
  3. Accepted Manuscript published: January 20, 2020 (version 1)
  4. Version of Record published: March 6, 2020 (version 2)

Copyright

This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

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  1. Debanjan Goswami
  2. De Chen
  3. Yue Yang
  4. Prabhakar R Gudla
  5. John Columbus
  6. Karen Worthy
  7. Megan Rigby
  8. Madeline Wheeler
  9. Suman Mukhopadhyay
  10. Katie Powell
  11. William Burgan
  12. Vanessa Wall
  13. Dominic Esposito
  14. Dhirendra Simanshu
  15. Felice C Lightstone
  16. Dwight V Nissley
  17. Frank McCormick
  18. Thomas Turbyville
(2020)
Membrane interactions of the globular domain and the hypervariable region of KRAS4b define its unique diffusion behavior
eLife 9:e47654.
https://doi.org/10.7554/eLife.47654

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