ArticleNucleic acids research2016
Conformational selection and dynamic adaptation upon linker histone binding to the nucleosome.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 42 citations in OpenAlex.
- One chromatin, many structures: From ensemble contact maps to single-cell 3D organization.Biophysical journal · 2026Article
- One Chromatin, Many Structures: From Ensemble Contact Maps to Single-Cell 3D Organization.bioRxiv : the preprint server for biology · 2026Article
- Regulation of chromatin architecture by protein binding: insights from molecular modeling.Biophysical reviews · 2024Review
- 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
- How acidic amino acid residues facilitate DNA target site selection.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- OCT4 interprets and enhances nucleosome flexibility.Nucleic acids research · 2022Article
- Structure, dynamics, and stability of the globular domain of human linker histone H1.0 and the role of positive charges.Protein science : a publication of the Protein Society · 2022Article
- DNA sequence-dependent positioning of the linker histone in a nucleosome: A single-pair FRET study.Biophysical journal · 2021Article
- Histone tails cooperate to control the breathing of genomic nucleosomes.PLoS computational biology · 2021Article
- Binding Dynamics of Disordered Linker Histone H1 with a Nucleosomal Particle.Journal of molecular biology · 2021Article
- Distinct Structures and Dynamics of Chromatosomes with Different Human Linker Histone Isoforms.Molecular cell · 2021Article
- DNA binds to a specific site of the adhesive blood-protein von Willebrand factor guided by electrostatic interactions.Nucleic acids research · 2020Article
- Protein disorder-to-order transition enhances the nucleosome-binding affinity of H1.Nucleic acids research · 2020Article
- Ensembles of Breathing Nucleosomes: A Computational Study.Biophysical journal · 2020Article
- Nucleosomal DNA Dynamics Mediate Oct4 Pioneer Factor Binding.Biophysical journal · 2020Article
- Elucidating the influence of linker histone variants on chromatosome dynamics and energetics.Nucleic acids research · 2020Article
- Emergence of chromatin hierarchical loops from protein disorder and nucleosome asymmetry.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Sensitive effect of linker histone binding mode and subtype on chromatin condensation.Nucleic acids research · 2019Article
- Molecular recognition of nucleosomes by binding partners.Current opinion in structural biology · 2019Review
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Linker histones are essential for DNA compaction in chromatin. They bind to nucleosomes in a 1:1 ratio forming chromatosomes. Alternative configurations have been proposed in which the globular domain of the linker histone H5 (gH5) is positioned either on- or off-dyad between the nucleosomal and linker DNAs. However, the dynamic pathways of chromatosome assembly remain elusive. Here, we studied the conformational plasticity of gH5 in unbound and off-dyad nucleosome-bound forms with classical and accelerated molecular dynamics simulations. We find that the unbound gH5 converts between open and closed conformations, preferring the closed form. However, the open gH5 contributes to a more rigid chromatosome and restricts the motion of the nearby linker DNA through hydrophobic interactions with thymidines. Moreover, the closed gH5 opens and reorients in accelerated simulations of the chromatosome. Brownian dynamics simulations of chromatosome assembly, accounting for a range of amplitudes of nucleosome opening and different nucleosome DNA sequences, support the existence of both on- and off-dyad binding modes of gH5 and reveal alternative, sequence and conformation-dependent chromatosome configurations. Taken together, these findings suggest that the conformational dynamics of linker histones and nucleosomes facilitate alternative chromatosome configurations through an interplay between induced fit and conformational selection.
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