核小体是染色质的基本结构, 是真核生物基因存储的最小单元. 它由组蛋白八聚体以及缠绕在表面的 DNA 共同构成. 核小体结构是动态的, 可通过隐藏或者暴露 DNA 上核小体结合蛋白的相互作用位点, 调控 DNA 与结合蛋白的相互作用, 从而调控基因表达. 已有的实验方法可以在分子层面研究核小体与结合蛋白的相互作用, 但无法充分提供原子层面的机理解释. 分子动力学模拟为核小体的研究提供了原子层面的高分辨率方法, 实现了核小体行为可视化, 是实验方法的有力补充. 回顾了分子动力学模拟在核小体结构、组蛋白尾部调控核小体功能, 以及核小体间相互作用的研究进展, 并探讨了 3 种分子动力学加速算法在核小体研究中的应用.

Nucleosomes are the fundamental units of the chromatin structure and the smallest units of gene storage in eukaryotes. They consist of a histone octamer and DNA wrapped around it. The dynamic nucleosome structure can regulate interactions between DNA and binding proteins by hiding or exposing the binding sites on DNA, eventually governing gene expression. Experimental methods can be used to study the interactions between nucleosomes and binding proteins at the molecular level but cannot provide mechanistic explanations at the atomic level. Molecular dynamics simulations provide a highresolution method at the atomic level for studying nucleosomes, enabling the visualization of nucleosome behavior and serving as a powerful complement to experimental methods. Herein, the study reviewed the progress in molecular dynamics simulations of the nucleosome structure, regulation of nucleosome function by histone tails, and interactions between nucleosomes. Additionally, the applications of the three acceleration algorithms of molecular dynamics simulations in nucleosome research were discussed.