ArticlePLoS computational biology2016
H3 Histone Tail Conformation within the Nucleosome and the Impact of K14 Acetylation Studied Using Enhanced Sampling Simulation.
Article in PLoS computational biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
- Linker histone H1 represses H3 tail acetylation induced by H4 tail acetylation and alters its dynamics.Communications biology · 2026Article
- In vitro reconstitution of heterochromatin compartments reveals the spontaneous formation of tunable liquid-liquid interfaces.Nucleic acids research · 2026Article
- Feasibility of Combining Biomolecular Conformational Sampling Techniques for Molecular Dynamics Simulation.Journal of computational chemistry · 2025Article
- Unveiling the Conformational Dynamics of the Histone Tails Using Markov State Modeling.Journal of chemical theory and computation · 2025Article
- HP1a promotes chromatin liquidity and drives spontaneous heterochromatin compartmentalization.bioRxiv : the preprint server for biology · 2025Article
- A virtual system-coupled molecular dynamics simulation free from experimental knowledge on binding sites: Application to RNA-ligand binding free-energy landscape.Biophysics and physicobiology · 2025Article
- Conformational Dynamics of the Nucleosomal Histone H2B Tails Revealed by Molecular Dynamics Simulations.Journal of chemical information and modeling · 2024Article
- Sequence Dependence in Nucleosome Dynamics.The journal of physical chemistry. B · 2024Article
- Article
- Molecular basis for PHF7-mediated ubiquitination of histone H3.Genes & development · 2023Article
- The effects of RNA.DNA-DNA triple helices on nucleosome structures and dynamics.Biophysical journal · 2023Article
- Studies of the Mechanism of Nucleosome Dynamics: A Review on Multifactorial Regulation from Computational and Experimental Cases.Polymers · 2023Review
- Methylation of recombinant mononucleosomes by DNMT3A demonstrates efficient linker DNA methylation and a role of H3K36me3.Communications biology · 2022Article
- Extended ensemble simulations of a SARS-CoV-2 nsp1-5'-UTR complex.PLoS computational biology · 2022Article
- Targeting Epigenetic Regulatory Enzymes for Cancer Therapeutics: Novel Small-Molecule Epidrug Development.Frontiers in oncology · 2022Review
- AnPeerJ · 2022Article
- Molecular dynamics analysis of biomolecular systems including nucleic acids.Biophysics and physicobiology · 2022Article
- Molecular dynamics simulations reveal how H3K56 acetylation impacts nucleosome structure to promote DNA exposure for lesion sensing.DNA repair · 2021Article
- Binding of regulatory proteins to nucleosomes is modulated by dynamic histone tails.Nature communications · 2021Article
- Histone Tail Conformations: A Fuzzy Affair with DNA.Trends in biochemical sciences · 2021Review
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Acetylation of lysine residues in histone tails is associated with gene transcription. Because histone tails are structurally flexible and intrinsically disordered, it is difficult to experimentally determine the tail conformations and the impact of acetylation. In this work, we performed simulations to sample H3 tail conformations with and without acetylation. The results show that irrespective of the presence or absence of the acetylation, the H3 tail remains in contact with the DNA and assumes an α-helix structure in some regions. Acetylation slightly weakened the interaction between the tail and DNA and enhanced α-helix formation, resulting in a more compact tail conformation. We inferred that this compaction induces unwrapping and exposure of the linker DNA, enabling DNA-binding proteins (e.g., transcription factors) to bind to their target sequences. In addition, our simulation also showed that acetylated lysine was more often exposed to the solvent, which is consistent with the fact that acetylation functions as a post-translational modification recognition site marker.
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