Facilitated dissociation of transcription factors from single DNA binding sites

Ramsey I. Kamar, Edward J. Banigan, Aykut Erbas, Rebecca D. Giuntoli, Monica Olvera De La Cruz, Reid C. Johnson, John F. Marko*

*Corresponding author for this work

Research output: Contribution to journalArticle

24 Scopus citations

Abstract

The binding of transcription factors (TFs) to DNA controls most aspects of cellular function, making the understanding of their binding kinetics imperative. The standard description of bimolecular interactions posits that TF off rates are independent of TF concentration in solution. However, recent observations have revealed that proteins in solution can accelerate the dissociation of DNA-bound proteins. To study the molecular basis of facilitated dissociation (FD), we have used single-molecule imaging to measure dissociation kinetics of Fis, a key Escherichia coli TF and major bacterial nucleoid protein, from single dsDNA binding sites. We observe a strong FD effect characterized by an exchange rate ∼1×104 M-1s-1, establishing that FD of Fis occurs at the single-binding site level, and we find that the off rate saturates at large Fis concentrations in solution. Although spontaneous (i.e., competitor-free) dissociation shows a strong salt dependence, we find that FD depends only weakly on salt. These results are quantitatively explained by a model in which partially dissociated bound proteins are susceptible to invasion by competitor proteins in solution. We also report FD of NHP6A, a yeast TF with structure that differs significantly from Fis. We further perform molecular dynamics simulations, which indicate that FD can occur for molecules that interact far more weakly than those that we have studied. Taken together, our results indicate that FD is a general mechanism assisting in the local removal of TFs from their binding sites and does not necessarily require cooperativity, clustering, or binding site overlap.

Original languageEnglish (US)
Pages (from-to)E3251-E3257
JournalProceedings of the National Academy of Sciences of the United States of America
Volume114
Issue number16
DOIs
StatePublished - Apr 18 2017

Keywords

  • Biomolecule binding
  • Chemical kinetics
  • DNA-protein interactions
  • Facilitated dissociation
  • Transcription factor

ASJC Scopus subject areas

  • General

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