Journal Article H4 tails potentially produce the diversity in the orientation of two nucleosomes

H., Ishida,  ,  H., Kono,

113 ( 5 )  , pp.978 - 990 , 2017-09
Histone tails play an important role in internucleosomal interaction and chromatin compaction. To understand how the H4 tails are involved in the internucleosomal interaction, an adaptively biased molecular dynamics (ABMD) simulation of 63 models of stacked two nucleosomes each with the H4 tails in different locations, was carried out. This simulation generated a variety of orientations of the separated NCPs depending on the formation of the H4 tail bridge between the H4 tails and the DNA of the neighboring NCP. For the models which showed distinctive orientations of the two NCPs, the free-energies of the separation of the NCPs were further investigated using umbrella sampling simulations. The attractive force between the NCPs was estimated from the free-energies; the force when two H4 tail bridges formed varied from 36 to 63 pN, depending on the formation of the H4 tail-bridge and the interfacial interaction, while the force reduced to 15–18 pN after either one of the H4 tail bridges had broken regardless of the conformations of the H4 tail. Additional simulations of the NCPs show that when the H4 tail was truncated the force between the NCPs became repulsive (from −3 to −7 pN). We concluded that the H4 tails potentially produce the diversity in the orientation of the two NCPs, which would contribute to the polymorphism of the chromatin structure.

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