Free energy simulations reveal molecular mechanism for functional switch of a DNA helicase
- 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
Zaida Luthey-Schulten
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.
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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Free energy simulations reveal molecular mechanism for functional switch of a DNA helicase
eLife 7:e34186.
https://doi.org/10.7554/eLife.34186
