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Conformational flexibility of nucleosomes: A molecular dynamics study

Conformational flexibility of nucleosomes: A molecular dynamics study 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. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Moscow University Biological Sciences Bulletin Springer Journals

Conformational flexibility of nucleosomes: A molecular dynamics study

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References (23)

Publisher
Springer Journals
Copyright
Copyright © 2015 by Allerton Press, Inc.
Subject
Life Sciences; Biochemistry, general; Cell Biology; Life Sciences, general; Plant Sciences; Zoology
ISSN
0096-3925
eISSN
1934-791X
DOI
10.3103/S0096392515030025
Publisher site
See Article on Publisher Site

Abstract

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.

Journal

Moscow University Biological Sciences BulletinSpringer Journals

Published: Sep 23, 2015

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