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Energetics of unwrapping and unstacking of nucleosomes studied by all-atom molecular dynamics simulations

https://repo.qst.go.jp/records/75592
https://repo.qst.go.jp/records/75592
59af7e0e-dd57-4548-b5e3-e94bfefa6fd7
Item type 会議発表用資料 / Presentation(1)
公開日 2019-03-19
タイトル
タイトル Energetics of unwrapping and unstacking of nucleosomes studied by all-atom molecular dynamics simulations
言語
言語 eng
資源タイプ
資源タイプ識別子 http://purl.org/coar/resource_type/c_c94f
資源タイプ conference object
アクセス権
アクセス権 metadata only access
アクセス権URI http://purl.org/coar/access_right/c_14cb
著者 Kono, Hidetoshi

× Kono, Hidetoshi

WEKO 820535

Kono, Hidetoshi

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Sakuraba, Shun

× Sakuraba, Shun

WEKO 820536

Sakuraba, Shun

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Ishida, Hisashi

× Ishida, Hisashi

WEKO 820537

Ishida, Hisashi

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Kono, Hidetoshi

× Kono, Hidetoshi

WEKO 820538

en Kono, Hidetoshi

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Sakuraba, Shun

× Sakuraba, Shun

WEKO 820539

en Sakuraba, Shun

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Ishida, Hisashi

× Ishida, Hisashi

WEKO 820540

en Ishida, Hisashi

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抄録
内容記述タイプ Abstract
内容記述 Nucleosomes create the diverse conformations of chromatin by the intra- and inter-nucleosome interactions. The key factors are the unwrapping of DNA and the unstacking of nucleosomes. We investigated the energetics using all-atom molecular dynamics simulations with an enhanced sampling method on a large scale.
As for the intra-nucleosomal interaction, free energy for unwrapping the outer superhelical turn of the nucleosomal DNA is about 11.5 kcal/mol, which agrees well with values obtained in single molecule experiments. At one end of the DNA, the first five bps unwrap, after which the next five bps unwrap at the same end with little increase in the free energy. The unwrapping then starts at the other end of the DNA, where 10 bps are unwrapped. At this point, further 15 bps unwrap at either end. The unwrapping of the outer superhelical turn is completed when the other end of the DNA unwraps. A detailed analysis of the free energy profile revealed a variety of conformational states, indicating there are many potential paths to outer superhelical turn unwrapping, but the dominant path is likely to be asymmetric.
… 略
会議概要(会議名, 開催地, 会期, 主催者等)
内容記述タイプ Other
内容記述 Biophysical Society Thematic Meeting, Les Houches 2019
発表年月日
日付 2019-04-03
日付タイプ Issued
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