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

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


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biomechanical Phenomena
  • DNA / chemistry*
  • DNA / metabolism*
  • DNA-Binding Proteins / chemistry*
  • DNA-Binding Proteins / metabolism*
  • Diffusion
  • Humans
  • Mechanical Phenomena*
  • Mitochondrial Proteins / chemistry*
  • Mitochondrial Proteins / metabolism*
  • Molecular Dynamics Simulation
  • Nucleic Acid Conformation
  • Protein Domains
  • Solutions
  • Transcription Factors / chemistry*
  • Transcription Factors / metabolism*


  • DNA-Binding Proteins
  • Mitochondrial Proteins
  • Solutions
  • Transcription Factors
  • mitochondrial transcription factor A
  • DNA