ArticleBiophysical journal2012
Unwrapping of nucleosomal DNA ends: a multiscale molecular dynamics study.
Article in Biophysical journal, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- Unveiling the Conformational Dynamics of the Histone Tails Using Markov State Modeling.Journal of chemical theory and computation · 2025Article
- Multiscale modeling reveals the ion-mediated phase separation of nucleosome core particles.Biophysical journal · 2024Article
- Role of the histone tails in histone octamer transfer.Nucleic acids research · 2023Article
- A Bottom-Up Coarse-Grained Model for Nucleosome-Nucleosome Interactions with Explicit Ions.Journal of chemical theory and computation · 2022Article
- Histone Tail Conformations: A Fuzzy Affair with DNA.Trends in biochemical sciences · 2021Review
- Dynamics of the nucleosomal histone H3 N-terminal tail revealed by high precision single-molecule FRET.Nucleic acids research · 2020Article
- Nucleosome Crowding in Chromatin Slows the Diffusion but Can Promote Target Search of Proteins.Biophysical journal · 2019Article
- Molecular Mechanism of Spontaneous Nucleosome Unraveling.Journal of molecular biology · 2019Article
- Histone Tail Dynamics in Partially Disassembled Nucleosomes During Chromatin Remodeling.Frontiers in molecular biosciences · 2019Article
- Free energy profile for unwrapping outer superhelical turn of CENP-A nucleosome.Biophysics and physicobiology · 2019Article
- Mechanical evolution of DNA double-strand breaks in the nucleosome.PLoS computational biology · 2018Article
- Open-Boundary Molecular Dynamics of a DNA Molecule in a Hybrid Explicit/Implicit Salt Solution.Biophysical journal · 2018Article
- Interactions of HP1 Bound to H3K9me3 Dinucleosome by Molecular Simulations and Biochemical Assays.Biophysical journal · 2018Article
- Chromatin Fiber Folding Directed by Cooperative Histone Tail Acetylation and Linker Histone Binding.Biophysical journal · 2018Article
- Major Determinants of Nucleosome Positioning.Biophysical journal · 2018Review
- Constitutive centromere-associated network contacts confer differential stability on CENP-A nucleosomes in vitro and in the cell.Molecular biology of the cell · 2018Article
- Free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA.PLoS computational biology · 2018Article
- Jörg Langowski: his scientific legacy and the future it promises.BMC biophysics · 2018Article
- Linking Chromatin Fibers to Gene Folding by Hierarchical Looping.Biophysical journal · 2017Review
- Distinct Roles of Histone H3 and H2A Tails in Nucleosome Stability.Scientific reports · 2016Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
To permit access to DNA-binding proteins involved in the control and expression of the genome, the nucleosome undergoes structural remodeling including unwrapping of nucleosomal DNA segments from the nucleosome core. Here we examine the mechanism of DNA dissociation from the nucleosome using microsecond timescale coarse-grained molecular dynamics simulations. The simulations exhibit short-lived, reversible DNA detachments from the nucleosome and long-lived DNA detachments not reversible on the timescale of the simulation. During the short-lived DNA detachments, 9 bp dissociate at one extremity of the nucleosome core and the H3 tail occupies the space freed by the detached DNA. The long-lived DNA detachments are characterized by structural rearrangements of the H3 tail including the formation of a turn-like structure at the base of the tail that sterically impedes the rewrapping of DNA on the nucleosome surface. Removal of the H3 tails causes the long-lived detachments to disappear. The physical consistency of the CG long-lived open state was verified by mapping a CG structure representative of this state back to atomic resolution and performing molecular dynamics as well as by comparing conformation-dependent free energies. Our results suggest that the H3 tail may stabilize the nucleosome in the open state during the initial stages of the nucleosome remodeling process.
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