Abstract
Histone tails play an important role in nucleosome structure and dynamics. Here we investigate the effect of truncation of histone tails H3, H4, H2A and H2B on nucleosome structure with 100 ns all-atom molecular dynamics simulations. Tail domains of H3 and H2B show propensity of -helics formation during the intact nucleosome simulation. On truncation of H4 or H2B tails no structural change occurs in histones. However, H3 or H2A tail truncation results in structural alterations in the histone core domain, and in both the cases the structural change occurs in the H2A3 domain. We also find that the contacts between the histone H2A C terminal docking domain and surrounding residues are destabilized upon H3 tail truncation. The relation between the present observations and corresponding experiments is discussed.
Highlights
Eukaryotic DNA is organized into nucleosomes [1], in which about 150 bp of DNA are wrapped in left-handed superhelical turns around an octameric histone protein complex [2]
The histone octamer has a tripartite structure composed of a (H3{H4)2 tetramer flanked by two H2A–H2B dimers
Our study revealed that truncation of H3 or H2A tail results in structural alterations in the nucleosome core whereas truncation of H4 or H2B tail does not
Summary
Eukaryotic DNA is organized into nucleosomes [1], in which about 150 bp of DNA are wrapped in left-handed superhelical turns around an octameric histone protein complex [2]. The histone octamer has a tripartite structure composed of a (H3{H4) tetramer flanked by two H2A–H2B dimers. In the structure the four histone dimers (two each of H3, H4, H2A and H2B) are arranged about a twofold dyad symmetry axis, which intersects with the middle of the DNA fragment. Each of the histone proteins consists of a structured core and a unstructured tail domain. The core domains consist of three a-helices (a1, a2 and a3), connected by short loops L1 and L2 and are composed mainly of basic residues, except for an acidic patch of H2A near the center of the nucleosome. Positively-charged histone tails make specific interactions with negatively-charged DNA [2]. There are 14 positions on the nucleosomal DNA at which histone residues make contact with DNA by hydrogen bond formation.
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