1. Structural Biology and Molecular Biophysics
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A putative structural mechanism underlying the antithetic effect of homologous RND1 and RhoD GTPases in mammalian plexin regulation

  1. Yanyan Liu
  2. Pu Ke
  3. Yi-Chun Kuo
  4. Yuxiao Wang
  5. Xuewu Zhang  Is a corresponding author
  6. Chen Song  Is a corresponding author
  7. Yibing Shan  Is a corresponding author
  1. Peking University, China
  2. Beijing Computational Science Research Center, China
  3. University of Texas Southwest Medical Center, United States
  4. University of Texas Southwestern Medical Center, United States
  5. Antidote Health Foundation, United States
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Cite this article as: eLife 2021;10:e64304 doi: 10.7554/eLife.64304

Abstract

Plexins are semaphorin receptors that play essential roles in mammalian neuronal axon guidance and in many other important mammalian biological processes. Plexin signaling depends on a semaphorin-induced dimerization mechanism, and is modulated by small GTPases of the Rho family, of which RND1 serves as a plexin activator yet its close homolog RhoD an inhibitor. Using molecular dynamics (MD) simulations we showed that RND1 reinforces the plexin dimerization interface whereas RhoD destabilizes it due to their differential interaction with the cell membrane. Upon binding plexin at the Rho-GTPase binding domain (RBD), RND1 and RhoD interact differently with the inner leaflet of the cell membrane, and exert opposite effects on the dimerization interface via an allosteric network involving the RBD, RBD linkers, and a buttress segment adjacent to the dimerization interface. The differential membrane interaction is attributed to the fact that, unlike RND1, RhoD features a short C-terminal tail and a positively charged membrane interface.

Data availability

Diffraction data have been deposited in PDB under the accession code 7KDC.Simulation data have been deposited in ZONODO database.

The following data sets were generated

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Author details

  1. Yanyan Liu

    Center for Quantitative Biology, Peking University, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.

  2. Pu Ke

    Complex System, Beijing Computational Science Research Center, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.

  3. Yi-Chun Kuo

    University of Texas Southwest Medical Center, Dallas, TX, United States
    Competing interests
    The authors declare that no competing interests exist.

  4. Yuxiao Wang

    University of Texas Southwest Medical Center, Dallas, TX, United States
    Competing interests
    The authors declare that no competing interests exist.

  5. Xuewu Zhang

    Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States
    For correspondence
    xuewu.zhang@utsouthwestern.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3634-6711

  6. Chen Song

    Center for Quantitative Biology, Peking University, Beijing, China
    For correspondence
    c.song@pku.edu.cn
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9730-3216

  7. Yibing Shan

    Chemistry, Antidote Health Foundation, Morristown, United States
    For correspondence
    ybshan@gmail.com
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3865-8110

Funding

National Natural Science Foundation of China (21806004)

  • Yanyan Liu

NSAF Joint Fund (U1430237)

  • Yanyan Liu

National Institutes of Health (R35GM130289)

  • Xuewu Zhang

Welch Foundation (I-1702)

  • Chen Song

National Natural Science Foundation of China (21873006)

  • Chen Song

National Natural Science Foundation of China (32071251)

  • Chen Song

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

Reviewing Editor

  1. Aaron Frank, University of Michigan, United States

Publication history

  1. Received: October 24, 2020
  2. Accepted: June 10, 2021
  3. Accepted Manuscript published: June 11, 2021 (version 1)
  4. Version of Record published: June 22, 2021 (version 2)

Copyright

© 2021, Liu 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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