LRET-derived HADDOCK structural models describe the conformational heterogeneity required for DNA cleavage by the Mre11-Rad50 DNA damage repair complex
Abstract
The Mre11-Rad50-Nbs1 protein complex is one of the first responders to DNA double strand breaks. Studies have shown that the catalytic activities of the evolutionarily conserved Mre11-Rad50 (MR) core complex depend on an ATP-dependent global conformational change that takes the macromolecule from an open, extended structure in the absence of ATP to a closed, globular structure when ATP is bound. We have previously identified an additional ‘partially open’ conformation using Luminescence Resonance Energy Transfer (LRET) experiments. Here, a combination of LRET and the molecular docking program HADDOCK was used to further investigate this partially open state and identify three conformations of MR in solution: closed, partially open, and open, which are in addition to the extended, apo conformation. Mutants disrupting specific Mre11-Rad50 interactions within each conformation were used in nuclease activity assays on a variety of DNA substrates to help put the three states into a functional perspective. LRET data collected on MR bound to DNA demonstrate that the three conformations also exist when nuclease substrates are bound. These models were further supported with SAXS data which corroborate the presence of multiple states in solution. Together, the data suggest a mechanism for the nuclease activity of the MR complex along the DNA.
Data availability
All data generated or analysed during this study are available from the DRYAD database under the doi: https://doi.org/10.5061/dryad.qfttdz0h6
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Data from: LRET-derived HADDOCK structural models describe the conformational heterogeneity required for processivity of the Mre11-Rad50 DNA damage repair complexDryad Digital Repository, doi:10.5061/dryad.qfttdz0h6.
Article and author information
Author details
Funding
National Institute of General Medical Sciences (1R35GM128906)
- Michael Latham
Cancer Prevention and Research Institute of Texas (RP180553)
- Michael Latham
Welch Foundation (D-1876)
- Michael Latham
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Maria Spies, University of Iowa, United States
Version history
- Received: April 20, 2021
- Preprint posted: August 4, 2021 (view preprint)
- Accepted: January 26, 2022
- Accepted Manuscript published: January 27, 2022 (version 1)
- Version of Record published: February 8, 2022 (version 2)
- Version of Record updated: February 22, 2022 (version 3)
Copyright
© 2022, Canny & Latham
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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