School of Biological Sciences, Nanyang Technological University, Singapore 639798.
Department of Materials and Environmental Chemistry, Stockholm University, Stockholm 10691, Sweden.
J Chem Theory Comput. 2022 Jun 14;18(6):3948-3960. doi: 10.1021/acs.jctc.2c00083. Epub 2022 May 17.
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(HO) or Co(NH)) 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.
核小体核心颗粒（NCP）是由 145-147 对 DNA 和 8 个组蛋白组成的大型复合物，是形成染色体的染色质的基本构建块。在这里，我们通过基于底层全原子 MD 模拟的系统自下而上方法开发了 NCP 的粗粒度（CG）模型，以计算必要的 CG 相互作用。该模型与 NCP 的已知结构特征非常吻合，并在存在多价阳离子（Mg(HO) 或 Co(NH)）的情况下对包含 20 个 NCP 的系统进行了核小体-核小体吸引力的真实描述。模拟结果揭示了实验方法无法获得的 NCP-NCP 相互作用的结构细节，该模型为严格的染色质纤维建模开辟了前景。
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