ArticleNucleic acids research2014
Multiple-binding-site mechanism explains concentration-dependent unbinding rates of DNA-binding proteins.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
40 citing papers in PubMed.
- Article
- Exploring TRF2-Dependent DNA Distortion Through Single-DNA Manipulation Studies.Communications biology · 2024Article
- Embracing Heterogeneity: Challenging the Paradigm of Replisomes as Deterministic Machines.Chemical reviews · 2023Review
- Multiple RNA- and DNA-binding proteins exhibit direct transfer of polynucleotides with implications for target-site search.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- PRC2 direct transfer from G-quadruplex RNA to dsDNA has implications for RNA-binding chromatin modifiers.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Facilitated dissociation of nucleoid-associated proteins from DNA in the bacterial confinement.Biophysical journal · 2022Article
- The Role of Ligand Rebinding and Facilitated Dissociation on the Characterization of Dissociation Rates by Surface Plasmon Resonance (SPR) and Benchmarking Performance Metrics.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Single-Molecule Fluorescence Methods to Study Protein Exchange Kinetics in Supramolecular Complexes.Methods in molecular biology (Clifton, N.J.) · 2021Article
- 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
- Kinetically distinct phases of tau on microtubules regulate kinesin motors and severing enzymes.Nature cell biology · 2019Article
- The emergence of the two cell fates and their associated switching for a negative auto-regulating gene.BMC biology · 2019Article
- Recycling of single-stranded DNA-binding protein by the bacterial replisome.Nucleic acids research · 2019Article
- Receptor-Ligand Rebinding Kinetics in Confinement.Biophysical journal · 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 Unbinding via Multivalency-Enabled Ternary Complexes: New Paradigm for Protein-DNA Interactions.Accounts of chemical research · 2018Review
- Force-extension behavior of DNA in the presence of DNA-bending nucleoid associated proteins.The Journal of chemical physics · 2018Article
- Understanding non-linear effects from Hill-type dynamics with application to decoding of p53 signaling.Scientific reports · 2018Article
- Effects of electrostatic interactions on ligand dissociation kinetics.Physical review. E · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Recent work has demonstrated concentration-dependent unbinding rates of proteins from DNA, using fluorescence visualization of the bacterial nucleoid protein Fis [Graham et al. (2011) (Concentration-dependent exchange accelerates turnover of proteins bound to double-stranded DNA. Nucleic Acids Res., 39:2249)]. The physical origin of this concentration-dependence is unexplained. We use a combination of coarse-grained simulation and theory to demonstrate that this behavior can be explained by taking into account the dimeric nature of the protein, which permits partial dissociation and exchange with other proteins in solution. Concentration-dependent unbinding is generated by this simple model, quantitatively explaining experimental data. This effect is likely to play a major role in determining binding lifetimes of proteins in vivo where there are very high concentrations of solvated molecules.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.