A bottom-up coarse-grained model for nucleosome–nucleosome interactions with explicit ions

The nucleosome core particle (NCP) is a large complex of 145-147 base pairs of DNA and eight histone proteins and is the basic building block of chromatin that forms the chromosomes. Here, we develop a coarse-grained (CG) model of the NCP derived through a systematic bottom-up approach based on unde...

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Bibliographic Details
Main Authors: Sun, Tiedong, Minhas, Vishal, Mirzoev, Alexander, Korolev, Nikolay, Lyubartsev, Alexander P., Nordenskiöld, Lars
Other Authors: School of Biological Sciences
Format: Article
Language:English
Published: 2022
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Online Access:https://hdl.handle.net/10356/161452
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Institution: Nanyang Technological University
Language: English
Description
Summary:The nucleosome core particle (NCP) is a large complex of 145-147 base pairs of DNA and eight histone proteins and is the basic building block of chromatin that forms the chromosomes. Here, we develop a coarse-grained (CG) model of the NCP derived through a systematic bottom-up approach based on underlying all-atom MD simulations to compute the necessary CG interactions. The model produces excellent agreement with known structural features of the NCP and gives a realistic description of the nucleosome-nucleosome attraction in the presence of multivalent cations (Mg(H2O)62+ or Co(NH3)63+) for systems comprising 20 NCPs. The results of the simulations reveal structural details of the NCP-NCP interactions unavailable from experimental approaches, and this model opens the prospect for the rigorous modeling of chromatin fibers.