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A Bottom-Up Coarse-Grained Model for Nucleosome–Nucleosome Interactions with Explicit Ions
[Image: see text] 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 appr...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical Society
2022
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9202350/ https://www.ncbi.nlm.nih.gov/pubmed/35580041 http://dx.doi.org/10.1021/acs.jctc.2c00083 |
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author | Sun, Tiedong Minhas, Vishal Mirzoev, Alexander Korolev, Nikolay Lyubartsev, Alexander P. Nordenskiöld, Lars |
author_facet | Sun, Tiedong Minhas, Vishal Mirzoev, Alexander Korolev, Nikolay Lyubartsev, Alexander P. Nordenskiöld, Lars |
author_sort | Sun, Tiedong |
collection | PubMed |
description | [Image: see text] 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(H(2)O)(6)(2+) or Co(NH(3))(6)(3+)) 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. |
format | Online Article Text |
id | pubmed-9202350 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-92023502022-06-17 A Bottom-Up Coarse-Grained Model for Nucleosome–Nucleosome Interactions with Explicit Ions Sun, Tiedong Minhas, Vishal Mirzoev, Alexander Korolev, Nikolay Lyubartsev, Alexander P. Nordenskiöld, Lars J Chem Theory Comput [Image: see text] 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(H(2)O)(6)(2+) or Co(NH(3))(6)(3+)) 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. American Chemical Society 2022-05-17 2022-06-14 /pmc/articles/PMC9202350/ /pubmed/35580041 http://dx.doi.org/10.1021/acs.jctc.2c00083 Text en © 2022 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by/4.0/Permits the broadest form of re-use including for commercial purposes, provided that author attribution and integrity are maintained (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Sun, Tiedong Minhas, Vishal Mirzoev, Alexander Korolev, Nikolay Lyubartsev, Alexander P. Nordenskiöld, Lars A Bottom-Up Coarse-Grained Model for Nucleosome–Nucleosome Interactions with Explicit Ions |
title | A Bottom-Up Coarse-Grained Model for Nucleosome–Nucleosome
Interactions with Explicit Ions |
title_full | A Bottom-Up Coarse-Grained Model for Nucleosome–Nucleosome
Interactions with Explicit Ions |
title_fullStr | A Bottom-Up Coarse-Grained Model for Nucleosome–Nucleosome
Interactions with Explicit Ions |
title_full_unstemmed | A Bottom-Up Coarse-Grained Model for Nucleosome–Nucleosome
Interactions with Explicit Ions |
title_short | A Bottom-Up Coarse-Grained Model for Nucleosome–Nucleosome
Interactions with Explicit Ions |
title_sort | bottom-up coarse-grained model for nucleosome–nucleosome
interactions with explicit ions |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9202350/ https://www.ncbi.nlm.nih.gov/pubmed/35580041 http://dx.doi.org/10.1021/acs.jctc.2c00083 |
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