Conformational Flexibility of Nucleosomes: A Molecular Dynamics Study

Armeev, G.A.; Shaitan, K.V.; Shaytan, A.K.

Авторы: Armeev G.A., Shaitan K.V., Shaytan and A.K
Журнал: Moscow University Biological Sciences Bulletin
Том: 70
Номер: 3
Год издания: 2015
Издательство: Allerton Press
Местоположение издательства: New York, N.Y., United States
Первая страница: 147
Последняя страница: 151
DOI: 10.3103/S0096392515030025
Аннотация: 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 expres sion, 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 Xray 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 polymor phism 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 500ns 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 mol ecules in the system, and assumed the role of intranucleosomal water. Keywords: nucleosome, chromatin, molecular dynamics, epigenetics
Добавил в систему: Шайтан Константин Вольдемарович

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Conformational Flexibility of Nucleosomes: A Molecular Dynamics Studyстатья

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