ArticleThe journal of physical chemistry. B2021
What Are the Molecular Requirements for Protein Sliding along DNA?
Article in The journal of physical chemistry. B, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Collision-induced transfer enhances ligand-binding kinetics in guanine quadruplex DNA.Nucleic acids research · 2026Article
- Interactions of proteins with heparan sulfate.Essays in biochemistry · 2024Review
- Sodium Ion-Induced Structural Transition on the Surface of a DNA-Interacting Protein.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Thymine DNA glycosylase combines sliding, hopping, and nucleosome interactions to efficiently search for 5-formylcytosine.Nature communications · 2024Article
- 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
- Extensive Bioinformatics Analyses Reveal a Phylogenetically Conserved Winged Helix (WH) Domain (Zτ) of Topoisomerase IIα, Elucidating Its Very High Affinity for Left-Handed Z-DNA and Suggesting Novel Putative Functions.International journal of molecular sciences · 2023Article
- Negatively charged, intrinsically disordered regions can accelerate target search by DNA-binding proteins.Nucleic acids research · 2023Article
- Conformational Analysis of Charged Homo-Polypeptides.Biomolecules · 2023Article
- Conformational Change of Transcription Factors from Search to Specific Binding: AThe journal of physical chemistry. B · 2022Article
- Salt Dependence of DNA Binding Activity of Human Transcription Factor Dlx3.International journal of molecular sciences · 2022Article
- Article
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3 authors.
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Abstract
DNA-binding proteins rely on linear diffusion along the longitudinal DNA axis, supported by their nonspecific electrostatic affinity for DNA, to search for their target recognition sites. One may therefore expect that the ability to engage in linear diffusion along DNA is universal to all DNA-binding proteins, with the detailed biophysical characteristics of that diffusion differing between proteins depending on their structures and functions. One key question is whether the linear diffusion mechanism is defined by translation coupled with rotation, a mechanism that is often termed sliding. We conduct coarse-grained and atomistic molecular dynamics simulations to investigate the minimal requirements for protein sliding along DNA. We show that coupling, while widespread, is not universal. DNA-binding proteins that slide along DNA transition to uncoupled translation-rotation (i.e., hopping) at higher salt concentrations. Furthermore, and consistently with experimental reports, we find that the sliding mechanism is the less dominant mechanism for some DNA-binding proteins, even at low salt concentrations. In particular, the toroidal PCNA protein is shown to follow the hopping rather than the sliding mechanism.
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