Free energy simulations reveal molecular mechanism for functional switch of a DNA helicase

  1. Wen Ma
  2. Kevin D Whitley
  3. Yann R Chemla  Is a corresponding author
  4. Zaida Luthey-Schulten  Is a corresponding author
  5. Klaus Schulten
  1. University of Illinois at Urbana-Champaign, United States

Abstract

Helicases play key roles in genome maintenance, yet it remains elusive how these enzymes change conformations and how transitions between different conformational states regulate nucleic acid reshaping. Here we developed a computational technique combining structural bioinformatics approaches and atomic-level free energy simulations to characterize how the E. coli DNA repair enzyme UvrD changes its conformation at the fork junction to switch its function from unwinding to rezipping DNA. The lowest free energy path shows that UvrD opens the interface between two domains, allowing the bound ssDNA to escape. The simulation results predict a key metastable 'tilted' state during ssDNA strand switching. By simulating FRET distributions with fluorophores attached to UvrD, we show that the new state is supported quantitatively by single-molecule measurements. The present study deciphers key elements for the 'hyper-helicase' behavior of a mutant, and provides an effective framework to characterize directly structure-function relationships in molecular machines.

Data availability

The PDB file of our predicted structure (tilted state) has been uploaded as Supplementary File 1.

Article and author information

Author details

  1. Wen Ma

    Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Kevin D Whitley

    Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Yann R Chemla

    Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, United States
    For correspondence
    ychemla@illinois.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9167-0234
  4. Zaida Luthey-Schulten

    Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, United States
    For correspondence
    zan@illinois.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9749-8367
  5. Klaus Schulten

    Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, United States
    Competing interests
    The authors declare that no competing interests exist.

Funding

National Institute of General Medical Sciences (9P41GM104601)

  • Zaida Luthey-Schulten
  • Klaus Schulten

National Science Foundation (PHY-1430124)

  • Yann R Chemla
  • Zaida Luthey-Schulten
  • Klaus Schulten

National Institute of General Medical Sciences (R01 GM120353)

  • Yann R Chemla

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: December 26, 2017
  2. Accepted: April 16, 2018
  3. Accepted Manuscript published: April 17, 2018 (version 1)
  4. Version of Record published: May 29, 2018 (version 2)

Copyright

© 2018, Ma 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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  1. Wen Ma
  2. Kevin D Whitley
  3. Yann R Chemla
  4. Zaida Luthey-Schulten
  5. Klaus Schulten
(2018)
Free energy simulations reveal molecular mechanism for functional switch of a DNA helicase
eLife 7:e34186.
https://doi.org/10.7554/eLife.34186

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