NUCLEOSOME STRUCTURE RELAXATION DURING DNA UNWRAPPING: MOLECULAR DYNAMICS SIMULATIONS STUDY
Abstract
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.
About the Authors
G. A. Armeev
Department of Bioengineering, School of Biology, Lomonosov Moscow State University
Russian Federation
Russian Federation
K. V. Shaitan
Department of Bioengineering, School of Biology, Lomonosov Moscow State University
Russian Federation
Russian Federation
A. K. Shaytan
Department of Bioengineering, School of Biology, Lomonosov Moscow State University
Russian Federation
Russian Federation
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Review
For citations:
Armeev G.A., Shaitan K.V., Shaytan A.K. NUCLEOSOME STRUCTURE RELAXATION DURING DNA UNWRAPPING: MOLECULAR DYNAMICS SIMULATIONS STUDY. Vestnik Moskovskogo universiteta. Seriya 16. Biologiya. 2016;(3):34-37. (In Russ.)
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