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One of the major problems of molecular biology is studying the underlying principles of chromatin work. This problem is associated with understanding the processes of epigenetic regulation of gene expression, DNA repair, and heredity mechanisms. The basic unit of chromatin organization is the nucleosome, which consists of DNA and histone proteins. For a long time, the nucleosome structure obtained by X-ray crystallography was considered as the ultimate and main conformational state of nucleosomes; however, more and more experimental data indicate that chromatin functions depend on the conformational polymorphism and dynamics of nucleosomes. Nevertheless, there is no detailed understanding of the conformational dynamics of nucleosomes at the atomistic level. In this study, we have addressed this problem using molecular dynamics simulations of the nucleosome in an explicit solvent. We have investigated the dynamics of the nucleosome on a 500-ns time interval, performed covariance analysis of the trajectory of molecular dynamics of the system with subsequent analysis of the derived collective motions, studied the distribution of water molecules in the system, and assumed the role of intranucleosomal water.
Moscow University Biological Sciences Bulletin – Springer Journals
Published: Sep 23, 2015
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