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Molecular modeling of the chromatosome particle

Bharath, Srinivas MM and Chandra, Nagasuma R and Rao, MRS (2003) Molecular modeling of the chromatosome particle. In: Nucleic-Acids-Research, 31 (14). pp. 4264-4274.

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Abstract

In an effort to understand the role of the linker histone in chromatin folding, its structure and location in the nucleosome has been studied by molecular modeling methods. The structure of the globular domain of the rat histone H1d, a highly conserved part of the linker histone, built by homology modeling methods, revealed a three-helical bundle fold that could be described as a helix–turn–helix variant with its characteristic properties of binding to DNA at the major groove. Using the information of its preferential binding to four-way Holliday junction (HJ) DNA, a model of the domain complexed to HJ was built, which was subsequently used to position the globular domain onto the nucleosome. The model revealed that the primary binding site of the domain interacts with the extra 20 bp of DNA of the entering duplex at the major groove while the secondary binding site interacts with the minor groove of the central gyre of the DNA superhelix of the nucleosomal core. The positioning of the globular domain served as an anchor to locate the C-terminal domain onto the nucleosome to obtain the structure of the chromatosome particle. The resulting structure had a stem-like appearance, resembling that observed by electron microscopic studies. The C-terminal domain which adopts a high mobility group (HMG)-box-like fold, has the ability to bend DNA, causing DNA condensation or compaction. It was observed that the three S/TPKK motifs in the C-terminal domain interact with the exiting duplex, thus defining the path of linker DNA in the chromatin fiber. This study has provided an insight into the probable individual roles of globular and the C-terminal domains of histone H1 in chromatin organization.

Item Type: Journal Article
Additional Information: Copyright of this article belongs to Oxford University Press
Keywords: histone;chromatosome;molecular modeling methods
Department/Centre: Division of Biological Sciences > Biochemistry
Date Deposited: 01 Oct 2007
Last Modified: 19 Sep 2010 04:39
URI: http://eprints.iisc.ernet.in/id/eprint/11975

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