ArticleNucleic acids research2019
Quantifying the two-state facilitated diffusion model of protein-DNA interactions.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Collision-induced transfer enhances ligand-binding kinetics in guanine quadruplex DNA.Nucleic acids research · 2026Article
- Mechanisms of enhanced or impaired DNA target selectivity driven by protein dimerization.PNAS nexus · 2026Article
- Electrostatic properties of disordered regions control transcription factor search and pioneer activity.Nature communications · 2026Article
- Article
- Theory on the Design Principles of Protein Molecular Oscillatory Machines.The journal of physical chemistry. B · 2025Article
- Mechanisms of enhanced or impaired DNA target selectivity driven by protein dimerization.bioRxiv : the preprint server for biology · 2025Article
- Mechanisms for DNA Interplay in Eukaryotic Transcription Factors.Annual review of biophysics · 2025Review
- Protein target search diffusion-association/dissociation free energy landscape around DNA binding site with flanking sequences.Biophysical journal · 2025Article
- Article
- Skipping events impose repeated binding attempts: profound kinetic implications of protein-DNA conformational changes.Nucleic acids research · 2024Article
- Nonspecific vs. specific DNA binding free energetics of a transcription factor domain protein.Biophysical journal · 2023Article
- Conformational Change of Transcription Factors from Search to Specific Binding: AThe journal of physical chemistry. B · 2022Article
- Function and regulation of transcription factors during mitosis-to-G1 transition.Open biology · 2022Review
- Investigating the Conformational Dynamics of a Y-Family DNA Polymerase during Its Folding and Binding to DNA and a Nucleotide.JACS Au · 2022Article
- Dynamics of Proteins and Macromolecular Machines in Escherichia coli.EcoSal Plus · 2021Review
- Overview of theBiophysical reviews · 2021Article
- Direct visualization of the effect of DNA structure and ionic conditions on HU-DNA interactions.Scientific reports · 2021Article
- Regulator-dependent temporal dynamics of a restriction-modification system's gene expression upon entering new host cells: single-cell and population studies.Nucleic acids research · 2021Article
- What Are the Molecular Requirements for Protein Sliding along DNA?The journal of physical chemistry. B · 2021Article
- Discrete-state stochastic kinetic models for target DNA search by proteins: Theory and experimental applications.Biophysical chemistry · 2021Review
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The current report extends the facilitated diffusion model to account for conflict between the search and recognition binding modes adopted by DNA-binding proteins (DBPs) as they search DNA and subsequently recognize and bind to their specific binding site. The speed of the search dynamics is governed by the energetic ruggedness of the protein-DNA landscape, whereas the rate for the recognition process is mostly dictated by the free energy barrier for the transition between the DBP's search and recognition binding modes. We show that these two modes are negatively coupled, such that fast 1D sliding and rapid target site recognition probabilities are unlikely to coexist. Thus, a tradeoff occurs between optimizing the timescales for finding and binding the target site. We find that these two kinetic properties can be balanced to produce a fast timescale for the total target search and recognition process by optimizing frustration. Quantification of the facilitated diffusion model by including a frustration term enables it to explain several experimental observations concerning search and recognition speeds. The extended model captures experimental estimate of the energetic ruggedness of the protein-DNA landscape and predicts how various molecular properties of protein-DNA binding affect recognition kinetics. Particularly, point mutations may change the frustration and so affect protein association with DNA, thus providing a means to modulate protein-DNA affinity by manipulating the protein's association or dissociation reactions.
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