MersV1, Main, Exploration, bibRecord, 002D44

Computer modeling demonstrates that electrostatic attraction of nucleosomal DNA is mediated by histone tails.

Identifieur interne : 002D44 ( Main/Exploration ); précédent : 002D43; suivant : 002D45

Computer modeling demonstrates that electrostatic attraction of nucleosomal DNA is mediated by histone tails.

Auteurs : Nikolay Korolev [Singapour] ; Alexander P. Lyubartsev ; Lars Nordenskiöld

Source :

Biophysical journal [ 0006-3495 ] ; 2006.

RBID : pubmed:16565063

Descripteurs français

English descriptors

KwdEn :
- Binding Sites, Computer Simulation, DNA (chemistry), HMGN Proteins (chemistry), Histones (chemistry), Models, Chemical, Models, Molecular, Nucleic Acid Conformation, Nucleosomes (chemistry), Protein Binding, Static Electricity, Stress, Mechanical.
MESH :
- chemical , chemistry : DNA, HMGN Proteins, Histones, Nucleosomes.
- Binding Sites, Computer Simulation, Models, Chemical, Models, Molecular, Nucleic Acid Conformation, Protein Binding, Static Electricity, Stress, Mechanical.

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.

DOI: 10.1529/biophysj.105.080226
PubMed: 16565063

Affiliations:

Singapour

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<front><div type="abstract" xml:lang="en">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.</div>
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Computer modeling demonstrates that electrostatic attraction of nucleosomal DNA is mediated by histone tails.

Computer modeling demonstrates that electrostatic attraction of nucleosomal DNA is mediated by histone tails.

Source :

Descripteurs français

English descriptors

Abstract

Links toward previous steps (curation, corpus...)

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

Pour générer des pages wiki

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