ArticleBiophysical journal2017
H4 Tails Potentially Produce the Diversity in the Orientation of Two Nucleosomes.
Article in Biophysical journal, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed, 28 citations in OpenAlex.
- 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
- Machines on Genes through the Computational Microscope.Journal of chemical theory and computation · 2023Review
- Genome modeling: From chromatin fibers to genes.Current opinion in structural biology · 2023Review
- OCT4 interprets and enhances nucleosome flexibility.Nucleic acids research · 2022Article
- Molecular dynamics analysis of biomolecular systems including nucleic acids.Biophysics and physicobiology · 2022Article
- 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
- Interactions Between Nucleosomes: From Atomistic Simulation to Polymer Model.Frontiers in molecular biosciences · 2021Article
- A multiscale analysis of DNA phase separation: from atomistic to mesoscale level.Nucleic acids research · 2019Article
- Frozen-hydrated chromatin from metaphase chromosomes has an interdigitated multilayer structure.The EMBO journal · 2019Article
- Free energy profile for unwrapping outer superhelical turn of CENP-A nucleosome.Biophysics and physicobiology · 2019Article
- Cryo-EM of nucleosome core particle interactions in trans.Scientific reports · 2018Article
- Free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA.PLoS computational biology · 2018Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Histone tails play an important role in internucleosomal interaction and chromatin compaction. To understand how the H4 tails are involved in the internucleosomal interaction, an adaptively biased molecular dynamics simulation of 63 models of two stacked nucleosomes, each with the H4 tails in different locations, was carried out. This simulation generated a variety of orientations of the separated nucleosomes depending on the formation of the H4 tail bridge between the H4 tails and the DNA of the neighboring nucleosomes. For the models that showed distinctive orientations of the two nucleosomes, the free energies of the separation of the nucleosomes were further investigated using umbrella sampling simulations. The attractive force between the nucleosomes was estimated from the free energies; the force when two H4 tail bridges formed varied from 36 to 63 pN, depending on the formation of the H4 tail-bridge and the interfacial interaction, whereas the force reduced to 15-18 pN after either one of the H4 tail bridges had broken, regardless of the conformation of the H4 tail. Additional simulations of the nucleosomes show that when the H4 tail was truncated, the force between the nucleosomes became repulsive (from-3 to -7 pN). We concluded that the H4 tails potentially produce the diversity in the orientation of the two nucleosomes, which would contribute to the polymorphism of the chromatin structure.
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