Nucleosome structure relaxation during DNA unwrapping: Molecular dynamics simulations study
In this paper we consider the effects of relaxation of the nucleosome local structure after DNA unwrapping from the histone octamer. We study the role of the charge distribution in histones during DNA rewrapping. We employ molecular dynamics simulations to show that ionic environment rapidly stabilizes during the relaxation of the system. In the case of simulations with preliminary relaxation of solvent and non-backbone atoms for a short period of time, a rapid irreversible restoration of the structure similar to crystal was observed. Rewrapping of DNA did not occur in case when the solvent was allowed to relax for a longer time period, despite no apparent differences in the ionic environment of DNA. The change of the quadrupole moment during relaxation of the system was shown.