ArticleMolecules (Basel, Switzerland)2018
Mechanisms of Protein Search for Targets on DNA: Theoretical Insights.
Article in Molecules (Basel, Switzerland), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Protein-Protein Interactions Can Accelerate Transcription Factor Target Search on DNA.The journal of physical chemistry letters · 2026Article
- Retroviral intasome architecture shapes the dynamics of target DNA search and integration.PLoS pathogens · 2026Article
- Mechanisms of enhanced or impaired DNA target selectivity driven by protein dimerization.PNAS nexus · 2026Article
- 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
- Stochastic nucleosome disassembly mediated by remodelers and histone fragmentation.The Journal of chemical physics · 2023Article
- smFRET Detection of Cis and Trans DNA Interactions by the BfiI Restriction Endonuclease.The journal of physical chemistry. B · 2023Article
- Repetitive DNA symmetry elements negatively regulate gene expression in embryonic stem cells.Biophysical journal · 2022Article
- Surface-facilitated trapping by active sites: From catalysts to viruses.The Journal of chemical physics · 2021Article
- Kinetic Analysis of the Interaction of Nicking Endonuclease BspD6I with DNA.Biomolecules · 2021Article
- Revealing atomic-scale molecular diffusion of a plant-transcription factor WRKY domain protein along DNA.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Crowding breaks the forward/backward symmetry of transition times in biased random walks.The Journal of chemical physics · 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
- Understanding the Robustness of Protein Diffusion on DNA and Microtubules.Biophysical journal · 2020Article
- Quantifying the two-state facilitated diffusion model of protein-DNA interactions.Nucleic acids research · 2019Article
- Laying Tracks for Poison Delivery to "Kiss of Death": Search for Immune Synapse by Microtubules.Biophysical journal · 2019Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Protein-DNA interactions are critical for the successful functioning of all natural systems. The key role in these interactions is played by processes of protein search for specific sites on DNA. Although it has been studied for many years, only recently microscopic aspects of these processes became more clear. In this work, we present a review on current theoretical understanding of the molecular mechanisms of the protein target search. A comprehensive discrete-state stochastic method to explain the dynamics of the protein search phenomena is introduced and explained. Our theoretical approach utilizes a first-passage analysis and it takes into account the most relevant physical-chemical processes. It is able to describe many fascinating features of the protein search, including unusually high effective association rates, high selectivity and specificity, and the robustness in the presence of crowders and sequence heterogeneity.
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