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Biophys J. 2018 May 22;114(10):2386-2396. doi: 10.1016/j.bpj.2017.11.3743. Epub 2017 Dec 13.

Protein Flexibility and Synergy of HMG Domains Underlie U-Turn Bending of DNA by TFAM in Solution.

Author information

1
Structural MitoLab, Department of Structural Biology, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona, Spain.
2
Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Institute for Research in Biomedicine, Barcelona, Spain; Joint BSC-IRB Program in Computational Biology, Institute for Research in Biomedicine, Barcelona, Spain.
3
Deutsches Krebsforschungszentrum, Division Biophysics of Macromolecules, Heidelberg, Germany.
4
Centre de Biochimie Structurale (CBS), Inserm, CNRS and Université de Montpellier, France.
5
Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Institute for Research in Biomedicine, Barcelona, Spain; Joint BSC-IRB Program in Computational Biology, Institute for Research in Biomedicine, Barcelona, Spain; Department of Biochemistry and Biomedicine, Faculty of Biology, University of Barcelona, Barcelona, Spain.
6
Deutsches Krebsforschungszentrum, Division Biophysics of Macromolecules, Heidelberg, Germany. Electronic address: kt@dkfz-heidelberg.de.
7
Structural MitoLab, Department of Structural Biology, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona, Spain. Electronic address: maria.sola@ibmb.csic.es.

Abstract

Human 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.

PMID:
29248151
PMCID:
PMC6028807
DOI:
10.1016/j.bpj.2017.11.3743
[Indexed for MEDLINE]
Free PMC Article

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