ArticleBiophysical journal2014
The role of histone tails in the nucleosome: a computational study.
Article in Biophysical journal, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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52 citing papers in PubMed, 86 citations in OpenAlex.
- Molecular dynamics guided all-atom reconstruction of cryo-ET maps reveals mechanisms of histone tail mediated chromatin compaction.Nature communications · 2026Article
- H2A.Z facilitates Sox2-nucleosome interaction by promoting DNA and histone H3 tail mobility.Nucleic acids research · 2026Article
- Selective binding of divalent cations reshapes nucleosome mechanics and unlocks histone tail dynamics.Communications biology · 2026Article
- Unveiling the Conformational Dynamics of the Histone Tails Using Markov State Modeling.Journal of chemical theory and computation · 2025Article
- Unveiling nucleosome dynamics: A comparative study using all-atom and coarse-grained simulations enhanced by principal component analysis.The Journal of chemical physics · 2025Article
- Unveiling Nucleosome Dynamics: A Comparative Study Using All-Atom and Coarse-Grained Simulations Enhanced by Principal Component Analysis.bioRxiv : the preprint server for biology · 2024Article
- On the Roles of Protein Intrinsic Disorder in the Origin of Life and Evolution.Life (Basel, Switzerland) · 2024Review
- Determining mesoscale chromatin structure parameters from spatially correlated cleavage data using a coarse-grained oligonucleosome model.bioRxiv : the preprint server for biology · 2024Article
- 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
- Mesenchymal stem cells under epigenetic control - the role of epigenetic machinery in fate decision and functional properties.Cell death & disease · 2023Review
- Post-translational modifications of histones: Mechanisms, biological functions, and therapeutic targets.MedComm · 2023Review
- Machines on Genes through the Computational Microscope.Journal of chemical theory and computation · 2023Review
- The Role of PARP1 and PAR in ATP-Independent Nucleosome Reorganisation during the DNA Damage Response.Genes · 2022Review
- Role of Histone Deacetylases in T-Cell Development and Function.International journal of molecular sciences · 2022Review
- Tuning Formation of Protein-DNA Coacervates by Sequence and Environment.The journal of physical chemistry. B · 2022Article
- Peptide Dynamics and Metadynamics: Leveraging Enhanced Sampling Molecular Dynamics to Robustly Model Long-Timescale Transitions.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Molecular dynamics analysis of biomolecular systems including nucleic acids.Biophysics and physicobiology · 2022Article
- Non-enzymatic Covalent Modifications as a New Chapter in the Histone Code.Trends in biochemical sciences · 2021Review
- Histone Tail Conformations: A Fuzzy Affair with DNA.Trends in biochemical sciences · 2021Review
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Histone tails play an important role in gene transcription and expression. We present here a systematic computational study of the role of histone tails in the nucleosome, using replica exchange molecular dynamics simulations with an implicit solvent model and different well-established force fields. We performed simulations for all four histone tails, H4, H3, H2A, and H2B, isolated and with inclusion of the nucleosome. The results confirm predictions of previous theoretical studies for the secondary structure of the isolated tails but show a strong dependence on the force field used. In the presence of the entire nucleosome for all force fields, the secondary structure of the histone tails is destabilized. Specific contacts are found between charged lysine and arginine residues and DNA phosphate groups and other binding sites in the minor and major DNA grooves. Using cluster analysis, we found a single dominant configuration of binding to DNA for the H4 and H2A histone tails, whereas H3 and H2B show multiple binding configurations with an equal probability. The leading stabilizing contribution for those binding configurations is the attractive interaction between the positively charged lysine and arginine residues and the negatively charged phosphate groups, and thus the resulting charge neutralization. Finally, we present results of molecular dynamics simulations in explicit solvent to confirm our conclusions. Results from both implicit and explicit solvent models show that large portions of the histone tails are not bound to DNA, supporting the complex role of these tails in gene transcription and expression and making them possible candidates for binding sites of transcription factors, enzymes, and other proteins.
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