1. Computational and Systems Biology
  2. Structural Biology and Molecular Biophysics
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Simulation of spontaneous G protein activation reveals a new intermediate driving GDP unbinding

  1. Xianqiang Sun
  2. Sukrit Singh
  3. Kendall Blumer
  4. Gregory R Bowman  Is a corresponding author
  1. Washington University School of Medicine, United States
Research Article
  • Cited 14
  • Views 2,782
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Cite this article as: eLife 2018;7:e38465 doi: 10.7554/eLife.38465
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Abstract

Activation of heterotrimeric G proteins is a key step in many signaling cascades. However, a complete mechanism for this process, which requires allosteric communication between binding sites that are ~30 Å apart, remains elusive. We construct an atomically-detailed model of G protein activation by combining three powerful computational methods: metadynamics, Markov state models (MSMs), and CARDS analysis of correlated motions. We uncover a mechanism that is consistent with a wide variety of structural and biochemical data. Surprisingly, the rate-limiting step for GDP release correlates with tilting rather than translation of the GPCR-binding helix 5. β-Strands 1-3 and helix 1 emerge as hubs in the allosteric network that links conformational changes in the GPCR-binding site to disordering of the distal nucleotide-binding site and consequent GDP release. Our approach and insights provide foundations for understanding disease-implicated G protein mutants, illuminating slow events in allosteric networks, and examining unbinding processes with slow off-rates.

Data availability

Summary data for all figures are made available with this manuscript. Specifically, MSM data, CARDS data, and numerical data for histograms are each provided as zipped archives. Simulation data are available upon request as there is no standard repository for such data, especially given the size of our dataset (3847 GB). The algorithms employed for calculating geometric features of protein conformations are available through MDTraj (https://github.com/mdtraj/mdtraj) and methods for building and analyzing MSMs are available through MSMBuilder (https://github.com/msmbuilder/msmbuilder) and Enspara (https://github.com/bowman-lab/enspara). The CARDS algorithm is also available through Enspara.

Article and author information

Author details

  1. Xianqiang Sun

    Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Sukrit Singh

    Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1914-4955
  3. Kendall Blumer

    Department of Cell Biology and Physiology, Washington University School of Medicine, St Louis, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Gregory R Bowman

    Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, United States
    For correspondence
    g.bowman@wustl.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2083-4892

Funding

National Institutes of Health (Grant R01GM12400701)

  • Gregory R Bowman

National Science Foundation (CAREER Award MCB-1552471)

  • Gregory R Bowman

Burroughs Wellcome Fund (Career Award at the Scientific Interface)

  • Gregory R Bowman

David and Lucile Packard Foundation (Packard Fellowship for Science and Engineering)

  • Gregory R Bowman

National Institutes of Health (Grant R01GM044592)

  • Kendall Blumer
  • Gregory R Bowman

National Institutes of Health (Grant R01GM12409301)

  • Kendall Blumer
  • Gregory R Bowman

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

Reviewing Editor

  1. José D Faraldo-Gómez, National Heart, Lung and Blood Institute, National Institutes of Health, United States

Publication history

  1. Received: May 17, 2018
  2. Accepted: October 4, 2018
  3. Accepted Manuscript published: October 5, 2018 (version 1)
  4. Version of Record published: November 8, 2018 (version 2)
  5. Version of Record updated: October 3, 2019 (version 3)

Copyright

© 2018, Sun 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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