title: Dynamics of modeled oligonucleosomes and the role of histone variant proteins in nucleosome organization.
abstract: Elucidation of the structural dynamics of a nucleosome is of primary importance for understanding the molecular mechanisms that control the nucleosomal positioning. The presence of variant histone proteins in the nucleosome core raises the functional diversity of the nucleosomes in gene regulation and has the profound epigenetic consequences of great importance for understanding the fundamental issues like the assembly of variant nucleosomes, chromatin remodeling, histone posttranslational modifications, etc. Here, we report our observation of the dominant mechanisms of relaxation motions of the oligonucleosomes such as dimer, trimer, and tetramer (in the beads on a string model) with conventional core histones and role of variant histone H2A.Z in the chromatin dynamics using normal mode analysis. Analysis of the directionality of the global dynamics of the oligonucleosome reveals (i) the in-planar stretching as well as out-of-planar bending motions as the relaxation mechanisms of the oligonucleosome and (ii) the freedom of the individual nucleosome in expressing the combination of the above-mentioned motions as the global mode of dynamics. The highly dynamic N-termini of H3 and (H2A.Z-H2B) dimer evidence their participation in the transcriptionally active state. The key role of variant H2A.Z histone as a major source of vibrant motions via weaker intra- and intermolecular correlations is emphasized in this chapter.
authors.affiliation: Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Pondicherry, India. amutha_ramu@yahoo.com
authors.forename: Amutha
authors.initials: A
authors.lastname: Ramaswamy
authors.forename: Ilya
authors.initials: I
authors.lastname: Ioshikhes
mesh_terms: D000818:Animals; D042002:Chromatin Assembly and Disassembly; D019281:Dimerization; D006657:Histones / Q000032:analysis / Q000378:metabolism*; D009707:Nucleosomes / Q000737:chemistry* / Q000378:metabolism*; D011499:Protein Processing, Post-Translational
chemical_list: D006657:Histones; D009707:Nucleosomes