ArticleThe European physical journal. E, Soft matter2013
Rigid-body molecular dynamics of DNA inside a nucleosome.
Article in The European physical journal. E, Soft matter, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- The role of transcript regions and amino acid choice in nucleosome positioning.NAR genomics and bioinformatics · 2023Article
- The kinetic landscape of nucleosome assembly: A coarse-grained molecular dynamics study.PLoS computational biology · 2021Article
- Ensembles of Breathing Nucleosomes: A Computational Study.Biophysical journal · 2020Article
- The base pair-scale diffusion of nucleosomes modulates binding of transcription factors.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- The implication of DNA bending energy for nucleosome positioning and sliding.Scientific reports · 2018Article
- DNA sliding in nucleosomes via twist defect propagation revealed by molecular simulations.Nucleic acids research · 2018Article
- The role of DNA sequence in nucleosome breathing.The European physical journal. E, Soft matter · 2017Article
- In silico evidence for sequence-dependent nucleosome sliding.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Benchmarking and refining probability-based models for nucleosome-DNA interaction.BMC bioinformatics · 2017Article
- Article
- Computational study of remodeling in a nucleosomal array.The European physical journal. E, Soft matter · 2015Article
- Partial Unwrapping and Histone Tail Dynamics in Nucleosome Revealed by Coarse-Grained Molecular Simulations.PLoS computational biology · 2015Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The majority of eukaryotic DNA, about three quarter, is wrapped around histone proteins forming so-called nucleosomes. To study nucleosomal DNA we introduce a coarse-grained molecular dynamics model based on sequence-dependent harmonic rigid base pair step parameters of DNA and nucleosomal binding sites. Mixed parametrization based on all-atom molecular dynamics and crystallographic data of protein-DNA structures is used for the base pair step parameters. The binding site parameters are adjusted by experimental B-factor values of the nucleosome crystal structure. The model is then used to determine the energy cost for placing a twist defect into the nucleosomal DNA which allows us to use Kramers theory to calculate nucleosome sliding caused by such defects. It is shown that the twist defect scenario together with the sequence-dependent elasticity of DNA can explain the slow time scales observed for nucleosome mobility along DNA. With this method we also show how the twist defect mechanism leads to a higher mobility of DNA in the presence of sin mutations near the dyad axis. Finally, by performing simulations on 5s rDNA, 601, and telomeric base pair sequences, it is demonstrated that the current model is a powerful tool to predict nucleosome positioning.
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