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Protein flexibility and synergy of HMG domains underlie U-turn bending of DNA by TFAM in solution

AuthorsRubio-Cosials, Anna ; Battistini, Federica; Gansen, Alexander; Cuppari, Anna ; Bernadó, Pau; Orozco, Modesto; Langowski, Jörg; Tóth, Katalin; Solà, Maria
Issue Date22-May-2018
PublisherBiophysical Society
CitationBiophysical Journal 14(10): 2386-2396 (2018)
AbstractHuman mitochondrial transcription factor A (TFAM) distorts DNA into a U-turn, as shown by crystallographic studies. The relevance of this U-turn is associated with transcription initiation at the mitochondrial light strand promoter (LSP). However, it has not been yet discerned whether a tight U-turn or an alternative conformation, such as a V-shape, is formed in solution. Here, single-molecule FRET experiments on freely diffusing TFAM/LSP complexes containing different DNA lengths show that a DNA U-turn is induced by progressive and cooperative binding of the two TFAM HMG-box domains and the linker between them. SAXS studies further show compaction of the protein upon complex formation. Finally, molecular dynamics simulations reveal that TFAM/LSP complexes are dynamic entities, and the HMG boxes induce the U-turn against the tendency of the DNA to adopt a straighter conformation. This tension is resolved by reversible unfolding of the linker, which is a singular mechanism that allows a flexible protein to stabilize a tight bending of DNA.
Publisher version (URL)http://dx.doi.org/10.1016/j.bpj.2017.11.3743
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