ArticlePhysical review letters2014
Stochastic ratchet mechanisms for replacement of proteins bound to DNA.
Article in Physical review letters, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Facilitated dissociation of nucleoid-associated proteins from DNA in the bacterial confinement.Biophysical journal · 2022Article
- How do DNA-bound proteins leave their binding sites? The role of facilitated dissociation.Current opinion in chemical biology · 2019Review
- Force-Dependent Facilitated Dissociation Can Generate Protein-DNA Catch Bonds.Biophysical journal · 2019Article
- The emergence of the two cell fates and their associated switching for a negative auto-regulating gene.BMC biology · 2019Article
- Polarized displacement by transcription activator-like effectors for regulatory circuits.Nature chemical biology · 2019Article
- Static Kinks or Flexible Hinges: Multiple Conformations of Bent DNA Bound to Integration Host Factor Revealed by Fluorescence Lifetime Measurements.The journal of physical chemistry. B · 2018Article
- Facilitated dissociation of transcription factors from single DNA binding sites.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Facilitated Dissociation Kinetics of Dimeric Nucleoid-Associated Proteins Follow a Universal Curve.Biophysical journal · 2017Article
- Protein dynamics of human RPA and RAD51 on ssDNA during assembly and disassembly of the RAD51 filament.Nucleic acids research · 2017Article
- Single-Stranded DNA Curtains for Studying Homologous Recombination.Methods in enzymology · 2017Article
- Molecular Mechanism of Facilitated Dissociation of Fis Protein from DNA.Journal of the American Chemical Society · 2016Article
- Facilitated Dissociation of a Nucleoid Protein from the Bacterial Chromosome.Journal of bacteriology · 2016Article
- Stability versus exchange: a paradox in DNA replication.Nucleic acids research · 2016Article
- DNA-Segment-Facilitated Dissociation of Fis and NHP6A from DNA Detected via Single-Molecule Mechanical Response.Journal of molecular biology · 2015Article
- Concentration- and chromosome-organization-dependent regulator unbinding from DNA for transcription regulation in living cells.Nature communications · 2015Article
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Authors and funding
3 authors.
Funding
Abstract
Experiments indicate that unbinding rates of proteins from DNA can depend on the concentration of proteins in nearby solution. Here we present a theory of multistep replacement of DNA-bound proteins by solution-phase proteins. For four different kinetic scenarios we calculate the dependence of protein unbinding and replacement rates on solution protein concentration. We find (1) strong effects of progressive "rezipping" of the solution-phase protein onto DNA sites liberated by "unzipping" of the originally bound protein, (2) that a model in which solution-phase proteins bind nonspecifically to DNA can describe experiments on exchanges between the nonspecific DNA-binding proteins Fis-Fis and Fis-HU, and (3) that a binding specific model describes experiments on the exchange of CueR proteins on specific binding sites.
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