ArticleJournal of the American Chemical Society2016
Molecular Mechanism of Facilitated Dissociation of Fis Protein from DNA.
Article in Journal of the American Chemical Society, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 53 citations in OpenAlex.
- Exploring Abeta42 monomer diffusion dynamics on fibril surfaces through molecular simulations.Protein science : a publication of the Protein Society · 2025Article
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- Modeling the compaction of bacterial chromosomes by biomolecular crowding and the cross-linking protein H-NS.Scientific reports · 2024Article
- Brewing COFFEE: A sequence-specific coarse-grained energy function for simulations of DNA-protein complexes.bioRxiv : the preprint server for biology · 2023Article
- Interdomain dynamics in human Replication Protein A regulates kinetics and thermodynamics of its binding to ssDNA.PloS one · 2023Article
- Spatiotemporal Coupling of DNA Supercoiling and Genomic Sequence Organization-A Timing Chain for the Bacterial Growth Cycle?Biomolecules · 2022Review
- Facilitated dissociation of nucleoid-associated proteins from DNA in the bacterial confinement.Biophysical journal · 2022Article
- Exploring the folding energy landscapes of heme proteins using a hybrid AWSEM-heme model.Journal of biological physics · 2022Article
- The molecular basis of allostery in a facilitated dissociation process.Structure (London, England : 1993) · 2021Article
- Binding Dynamics of Disordered Linker Histone H1 with a Nucleosomal Particle.Journal of molecular biology · 2021Article
- Fibril Surface-Dependent Amyloid Precursors Revealed by Coarse-Grained Molecular Dynamics Simulation.Frontiers in molecular biosciences · 2021Article
- How to assess the structural dynamics of transcription factors by integrating sparse NMR and EPR constraints with molecular dynamics simulations.Computational and structural biotechnology journal · 2021Review
- Balance between asymmetry and abundance in multi-domain DNA-binding proteins may regulate the kinetics of their binding to DNA.PLoS computational biology · 2020Article
- Structural Basis of Enhanced Facilitated Diffusion of DNA-Binding Protein in Crowded Cellular Milieu.Biophysical journal · 2020Article
- 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
- Recycling of single-stranded DNA-binding protein by the bacterial replisome.Nucleic acids research · 2019Article
- Structural and Dynamical Order of a Disordered Protein: Molecular Insights into Conformational Switching of PAGE4 at the Systems Level.Biomolecules · 2019Article
- Polarized displacement by transcription activator-like effectors for regulatory circuits.Nature chemical biology · 2019Article
- AWSEM-IDP: A Coarse-Grained Force Field for Intrinsically Disordered Proteins.The journal of physical chemistry. B · 2018Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 1 country.
Funding
Abstract
Fis protein is a nucleoid-associated protein that plays many roles in transcriptional regulation and DNA site-specific recombination. In contrast to the naïve expectation based on stoichiometry, recent single-molecule studies have shown that the dissociation of Fis protein from DNA is accelerated by increasing the concentration of the Fis protein. Because the detailed molecular mechanism of facilitated dissociation is still not clear, in this study, we employ computational methods to explore the binding landscapes of Fis:DNA complexes with various stoichiometries. When two Fis molecules are present, simulations uncover a ternary complex, where the originally bound Fis protein is partially dissociated from DNA. The simulations support a three-state sequential kinetic model (N ⇄ I → D) for facilitated dissociation, thus explaining the concentration-dependent dissociation.
Identifiers
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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.