Abstract
The organization of genomes in space and time dimension plays an important role in gene expression and regulation. Chromatin folding occurs in a dynamic, structured way that is subject to biophysical rules and biological processes. Nucleosomes are the basic unit of chromatin in living cells, and here we report on the effective interactions between two nucleosomes in physiological conditions using explicit-solvent all-atom simulations. Free energy landscapes derived from umbrella sampling simulations agree well with recent experimental and simulation results. Our simulations reveal the atomistic details of the interactions between nucleosomes in solution and can be used for constructing the coarse-grained model for chromatin in a bottom-up manner.
Highlights
Chromatin is highly compacted and condensed into the small space of the nucleus (Goloborodko et al, 2016b; Finn and Misteli, 2019)
The organization and folding processes of chromatin can be mainly divided into four layers: 1) The antiparallel double helical and right-handed B-DNA structure with each base pair rising up about 3.4 Å along the helical axis, which makes DNA very stable while it provides potential for the binding of proteins
The binding between DNA and histone core was very stable as indicated by their root mean square deviations (RMSDs) being around 4 Å with respect to the initial structures (Supplementary Figure S3)
Summary
Chromatin is highly compacted and condensed into the small space of the nucleus (Goloborodko et al, 2016b; Finn and Misteli, 2019). The organization and folding processes of chromatin can be mainly divided into four layers: 1) The antiparallel double helical and right-handed B-DNA structure with each base pair rising up about 3.4 Å along the helical axis, which makes DNA very stable while it provides potential for the binding of proteins. 2) About 146 base pairs wrap around a histone octamer ( called histone core), including two copies each of the four histone core proteins (H2A, H2B, H3, and H4) in a lefthanded superhelix, which constitute a nucleosome. Nucleosomes are the basic units of chromatin and provide controlled accessibility for DNA-binding proteins such as transcription machines and structural maintenance of chromosome (SMC) complexes. About 75–90% of the genome are organized in the form of nucleosomes (Field et al, 2008). 3) Under the view of electron microscopes, chromatin appears as “beads on a string,” in which beads correspond to nucleosomes and the string between beads
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