ArticlePLoS computational biology2018
Free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA.
Article in PLoS computational biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 29 citations in OpenAlex.
- DNA Sequence and Histone Variant H2A.Z Jointly Govern Nucleosome Unwrapping Pathways.bioRxiv : the preprint server for biology · 2026Article
- Unveiling the Conformational Dynamics of the Histone Tails Using Markov State Modeling.Journal of chemical theory and computation · 2025Article
- Conformational Dynamics of the Nucleosomal Histone H2B Tails Revealed by Molecular Dynamics Simulations.Journal of chemical information and modeling · 2024Article
- Beyond the Usual Suspects: Examining the Role of Understudied Histone Variants in Breast Cancer.International journal of molecular sciences · 2024Review
- Structural and Dynamic Changes of Nucleosome upon GATA3 Binding.Journal of molecular biology · 2023Article
- Brewing COFFEE: A sequence-specific coarse-grained energy function for simulations of DNA-protein complexes.bioRxiv : the preprint server for biology · 2023Article
- Machines on Genes through the Computational Microscope.Journal of chemical theory and computation · 2023Review
- Histone variant H2A.Z modulates nucleosome dynamics to promote DNA accessibility.Nature communications · 2023Article
- 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
- The kinetic landscape of nucleosome assembly: A coarse-grained molecular dynamics study.PLoS computational biology · 2021Article
- Histone tails cooperate to control the breathing of genomic nucleosomes.PLoS computational biology · 2021Article
- Torsional stress can regulate the unwrapping of two outer half superhelical turns of nucleosomal DNA.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Ensembles of Breathing Nucleosomes: A Computational Study.Biophysical journal · 2020Article
- Big data science at AMED-BINDS.Biophysical reviews · 2020Article
- The role of histone tails in nucleosome stability: An electrostatic perspective.Computational and structural biotechnology journal · 2020Article
- Correction: Free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA.PLoS computational biology · 2019Article
- Free energy profile for unwrapping outer superhelical turn of CENP-A nucleosome.Biophysics and physicobiology · 2019Article
- Dynamics of Chromatin Fibers: Comparison of Monte Carlo Simulations with Force Spectroscopy.Biophysical journal · 2018Article
Corrections and comments
- Erratum issued
Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The eukaryotic genome is packaged into a nucleus in the form of chromatin. The fundamental structural unit of chromatin is a protein-DNA complex, the nucleosome, where 146 or 147 base pairs of DNA wrap 1.75 times around a histone core. To function in cellular processes, however, nucleosomal DNA must be unwrapped. Although this unwrapping has been experimentally investigated, details of the process at an atomic level are not yet well understood. Here, we used molecular dynamics simulation with an enhanced sampling method to calculate the free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA. A free energy change of about 11.5 kcal/mol for the unwrapping agrees well with values obtained in single molecule experiments. This simulation revealed a variety of conformational states, indicating there are many potential paths to outer superhelicdal turn unwrapping, but the dominant path is likely asymmetric. At one end of the DNA, the first five bps unwrap, after which a second five bps unwrap at the same end with no increase in free energy. The unwrapping then starts at the other end of the DNA, where 10 bps are unwrapped. During further unwrapping of 15 bps, the unwrapping advances at one of the ends, after which the other end of the DNA unwraps to complete the unwrapping of the outer superhelical turn. These results provide insight into the construction, disruption, and repositioning of nucleosomes, which are continuously ongoing during cellular processes.
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