ArticleBiophysical journal2006
Computer modeling demonstrates that electrostatic attraction of nucleosomal DNA is mediated by histone tails.
Article in Biophysical journal, 2006. 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 18 papers.
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Who cites it
18 citing papers in PubMed, 71 citations in OpenAlex.
- A Bottom-Up Coarse-Grained Model for Nucleosome-Nucleosome Interactions with Explicit Ions.Journal of chemical theory and computation · 2022Article
- A systematic analysis of nucleosome core particle and nucleosome-nucleosome stacking structure.Scientific reports · 2018Article
- H4 Tails Potentially Produce the Diversity in the Orientation of Two Nucleosomes.Biophysical journal · 2017Article
- The chromatin fiber: multiscale problems and approaches.Current opinion in structural biology · 2015Review
- Histone H3 and H4 N-terminal tails in nucleosome arrays at cellular concentrations probed by magic angle spinning NMR spectroscopy.Journal of the American Chemical Society · 2013Article
- Article
- Structural role of RKS motifs in chromatin interactions: a molecular dynamics study of HP1 bound to a variably modified histone tail.Biophysical journal · 2012Article
- A universal description for the experimental behavior of salt-(in)dependent oligocation-induced DNA condensation.Nucleic acids research · 2012Article
- Unwrapping of nucleosomal DNA ends: a multiscale molecular dynamics study.Biophysical journal · 2012Article
- Modeling studies of chromatin fiber structure as a function of DNA linker length.Journal of molecular biology · 2010Article
- Chromatin ionic atmosphere analyzed by a mesoscale electrostatic approach.Biophysical journal · 2010Article
- Electrostatic origin of salt-induced nucleosome array compaction.Biophysical journal · 2010Article
- A universal description for the experimental behavior of salt-(in)dependent oligocation-induced DNA condensation.Nucleic acids research · 2009Article
- Molecular dynamics simulations of DNA-polycation complex formation.Biophysical journal · 2009Article
- A tale of tails: how histone tails mediate chromatin compaction in different salt and linker histone environments.The journal of physical chemistry. A · 2009Article
- Computer modeling reveals that modifications of the histone tail charges define salt-dependent interaction of the nucleosome core particles.Biophysical journal · 2009Article
- Structure and phase diagram of nucleosome core particles aggregated by multivalent cations.Biophysical journal · 2007Article
- H3 and H4 histone tails play a central role in the interactions of recombinant NCPs.Biophysical journal · 2007Article
Corrections and comments
- Erratum issued
Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We conducted molecular dynamics computer simulations of charged histone tail-DNA interactions in systems mimicking nucleosome core particles (NCP) . In a coarse-grained model, the NCP is modeled as a negatively charged spherical particle with flexible polycationic histone tails attached to it in a dielectric continuum with explicit mobile counterions and added salt. The size, charge, and distribution of the tails relative to the core were built to mimick real NCP. In this way, we incorporate attractive ion-ion correlation effects due to fluctuations in the ion cloud and the attractive entropic and energetic tail-bridging effects. In agreement with experimental data, increase of monovalent salt content from salt-free to physiological concentration leads to the formation of NCP aggregates; likewise, in the presence of MgCl2, the NCPs form condensed systems via histone-tail bridging and accumulation of counterions. More detailed mechanisms of the histone tail-DNA interactions and dynamics have been obtained from all-atom molecular dynamics simulations (including water), comprising three DNA 22-mers and 14 short fragments of the H4 histone tail (amino acids 5-12) carrying three positive charges on lysine+ interacting with DNA. We found correlation of the DNA-DNA distance with the presence and association of the histone tail between the DNA molecules.
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