A systematic analysis of nucleosome core particle and nucleosome-nucleosome stacking structure

Chromatin condensation is driven by the energetically favourable interaction between nucleosome core particles (NCPs). The close NCP-NCP contact, stacking, is a primary structural element of all condensed states of chromatin in vitro and in vivo. However, the molecular structure of stacked nucleosom...

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Main Authors: Korolev, Nikolay, Lyubartsev, Alexander P., Nordenskiöld, Lars
Other Authors: School of Biological Sciences
Format: Article
Language:English
Published: 2018
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Online Access:https://hdl.handle.net/10356/87537
http://hdl.handle.net/10220/45421
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Institution: Nanyang Technological University
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spelling sg-ntu-dr.10356-875372023-02-28T17:01:59Z A systematic analysis of nucleosome core particle and nucleosome-nucleosome stacking structure Korolev, Nikolay Lyubartsev, Alexander P. Nordenskiöld, Lars School of Biological Sciences Nucleosome Core Particles (NCPs) Stacked Nucleosomes Chromatin condensation is driven by the energetically favourable interaction between nucleosome core particles (NCPs). The close NCP-NCP contact, stacking, is a primary structural element of all condensed states of chromatin in vitro and in vivo. However, the molecular structure of stacked nucleosomes as well as the nature of the interactions involved in its formation have not yet been systematically studied. Here we undertake an investigation of both the structural and physico-chemical features of NCP structure and the NCP-NCP stacking. We introduce an “NCP-centred” set of parameters (NCP-NCP distance, shift, rise, tilt, and others) that allows numerical characterisation of the mutual positions of the NCPs in the stacking and in any other structures formed by the NCP. NCP stacking in more than 140 published NCP crystal structures were analysed. In addition, coarse grained (CG) MD simulations modelling NCP condensation was carried out. The CG model takes into account details of the nucleosome structure and adequately describes the long range electrostatic forces as well as excluded volume effects acting in chromatin. The CG simulations showed good agreement with experimental data and revealed the importance of the H2A and H4 N-terminal tail bridging and screening as well as tail-tail correlations in the stacked nucleosomes. MOE (Min. of Education, S’pore) Published version 2018-07-31T08:05:03Z 2019-12-06T16:44:02Z 2018-07-31T08:05:03Z 2019-12-06T16:44:02Z 2018 Journal Article Korolev, N., Lyubartsev, A. P., & Nordenskiöld, L. (2018). A systematic analysis of nucleosome core particle and nucleosome-nucleosome stacking structure. Scientific Reports, 8(1), 1543-. 2045-2322 https://hdl.handle.net/10356/87537 http://hdl.handle.net/10220/45421 10.1038/s41598-018-19875-0 en Scientific Reports © 2018 The Author(s) (Nature Publishing Group). This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. 14 p. application/pdf
institution Nanyang Technological University
building NTU Library
continent Asia
country Singapore
Singapore
content_provider NTU Library
collection DR-NTU
language English
topic Nucleosome Core Particles (NCPs)
Stacked Nucleosomes
spellingShingle Nucleosome Core Particles (NCPs)
Stacked Nucleosomes
Korolev, Nikolay
Lyubartsev, Alexander P.
Nordenskiöld, Lars
A systematic analysis of nucleosome core particle and nucleosome-nucleosome stacking structure
description Chromatin condensation is driven by the energetically favourable interaction between nucleosome core particles (NCPs). The close NCP-NCP contact, stacking, is a primary structural element of all condensed states of chromatin in vitro and in vivo. However, the molecular structure of stacked nucleosomes as well as the nature of the interactions involved in its formation have not yet been systematically studied. Here we undertake an investigation of both the structural and physico-chemical features of NCP structure and the NCP-NCP stacking. We introduce an “NCP-centred” set of parameters (NCP-NCP distance, shift, rise, tilt, and others) that allows numerical characterisation of the mutual positions of the NCPs in the stacking and in any other structures formed by the NCP. NCP stacking in more than 140 published NCP crystal structures were analysed. In addition, coarse grained (CG) MD simulations modelling NCP condensation was carried out. The CG model takes into account details of the nucleosome structure and adequately describes the long range electrostatic forces as well as excluded volume effects acting in chromatin. The CG simulations showed good agreement with experimental data and revealed the importance of the H2A and H4 N-terminal tail bridging and screening as well as tail-tail correlations in the stacked nucleosomes.
author2 School of Biological Sciences
author_facet School of Biological Sciences
Korolev, Nikolay
Lyubartsev, Alexander P.
Nordenskiöld, Lars
format Article
author Korolev, Nikolay
Lyubartsev, Alexander P.
Nordenskiöld, Lars
author_sort Korolev, Nikolay
title A systematic analysis of nucleosome core particle and nucleosome-nucleosome stacking structure
title_short A systematic analysis of nucleosome core particle and nucleosome-nucleosome stacking structure
title_full A systematic analysis of nucleosome core particle and nucleosome-nucleosome stacking structure
title_fullStr A systematic analysis of nucleosome core particle and nucleosome-nucleosome stacking structure
title_full_unstemmed A systematic analysis of nucleosome core particle and nucleosome-nucleosome stacking structure
title_sort systematic analysis of nucleosome core particle and nucleosome-nucleosome stacking structure
publishDate 2018
url https://hdl.handle.net/10356/87537
http://hdl.handle.net/10220/45421
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