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...
| Main Authors: | , , , , , |
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| Other Authors: | |
| Format: | Journal Article |
| Language: | English |
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2022
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| Online Access: | https://hdl.handle.net/10356/161452 |
| _version_ | 1826118111664799744 |
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| author | Sun, Tiedong Minhas, Vishal Mirzoev, Alexander Korolev, Nikolay Lyubartsev, Alexander P. Nordenskiöld, Lars |
| author2 | School of Biological Sciences |
| author_facet | School of Biological Sciences Sun, Tiedong Minhas, Vishal Mirzoev, Alexander Korolev, Nikolay Lyubartsev, Alexander P. Nordenskiöld, Lars |
| author_sort | Sun, Tiedong |
| collection | NTU |
| description | 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. |
| first_indexed | 2024-10-01T04:38:03Z |
| format | Journal Article |
| id | ntu-10356/161452 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T04:38:03Z |
| publishDate | 2022 |
| record_format | dspace |
| spelling | ntu-10356/1614522023-02-28T17:11:24Z 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 School of Biological Sciences Science::Biological sciences::Biophysics Science::Chemistry::Physical chemistry::Thermodynamics Nucleosome Core Particle Bottom-Up Coarse-Graining Divide and Conquer Inverse Monte Carlo Cobalt(III)-Hexammine 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 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. Ministry of Education (MOE) Published version The authors thank the National Supercomputing Center (NSCC) of Singapore for its computing resource support. A.P.L. was supported by the Swedish Research Council (Vetenskapsrådet), grant 2017-03950, and computational resources provided by the Swedish National Infrastructure for Computing (SNIC) through National Supercomputer Center (NSC). This work was supported by a Ministry of Education (MOE), Singapore Academic Research Fund Tier 3 Grant (MOE2019-T3-1-012) to L.N. 2022-09-06T01:25:18Z 2022-09-06T01:25:18Z 2022 Journal Article Sun, T., Minhas, V., Mirzoev, A., Korolev, N., Lyubartsev, A. P. & Nordenskiöld, L. (2022). A bottom-up coarse-grained model for nucleosome–nucleosome interactions with explicit ions. Journal of Chemical Theory and Computation, 18(6), 3948-3960. https://dx.doi.org/10.1021/acs.jctc.2c00083 1549-9618 https://hdl.handle.net/10356/161452 10.1021/acs.jctc.2c00083 35580041 2-s2.0-85131601450 6 18 3948 3960 en MOE2019-T3-1-012 Journal of Chemical Theory and Computation 10.5281/zenodo.5833006 © 2022 The Authors. Published by American Chemical Society. This is an open-access article distributed under the terms of the Creative Commons Attribution License. application/pdf application/pdf application/octet-stream |
| spellingShingle | Science::Biological sciences::Biophysics Science::Chemistry::Physical chemistry::Thermodynamics Nucleosome Core Particle Bottom-Up Coarse-Graining Divide and Conquer Inverse Monte Carlo Cobalt(III)-Hexammine Explicit Ions 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 |
| topic | Science::Biological sciences::Biophysics Science::Chemistry::Physical chemistry::Thermodynamics Nucleosome Core Particle Bottom-Up Coarse-Graining Divide and Conquer Inverse Monte Carlo Cobalt(III)-Hexammine Explicit Ions |
| url | https://hdl.handle.net/10356/161452 |
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