Division Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, D-69120, Germany.
Key laboratory of medicinal chemistry for natural resources, Ministry of Education, Yunnan University, Kunming, Yunnan, 650091, China.
Sci Rep. 2017 Oct 16;7(1):13303. doi: 10.1038/s41598-017-13416-x.
Nucleosomes are important for chromatin compaction and gene regulation; their integrity depends crucially on the structural properties of the histone tails. Recent all-atom molecular dynamics simulations revealed that removal of the N-terminal tails of histone H3, known to destabilize nucleosomes, causes a rearrangement of two arginines of histone H2A, namely R81 and R88 by altering the electrostatic environment of the H2A α3 domain. Whether this rearrangement is the cause or the effect of decreased stability, is unclear. Here, we emulate the altered electrostatic environment that was found after H3 tail clipping through charge-modifying mutations to decouple its impact on intranucleosomal interactions from that of the histone tails. Förster resonance energy transfer experiments on recombinant nucleosomes and all-atom molecular dynamics simulations reveal a compensatory role of those amino acids in nucleosome stability. The simulations indicate a weakened interface between H2A-H2B dimers and the (H3-H4) tetramer, as well as between dimers and DNA. These findings agree with the experimental observations of position and charge dependent decreased nucleosome stability induced by the introduced mutations. This work highlights the importance of the H2A α3 domain and suggests allosteric effects between this domain and the outer DNA gyre as well as the H3 N-terminal tail.
核小体对于染色质的紧缩和基因调控非常重要；其完整性取决于组蛋白尾部的结构特性。最近的全原子分子动力学模拟揭示，已知会破坏核小体稳定性的组蛋白 H3 的 N 端尾部的缺失会导致组蛋白 H2A 的两个精氨酸（即 R81 和 R88）发生重排，通过改变 H2Aα3 结构域的静电环境来实现。这种重排是稳定性降低的原因还是结果尚不清楚。在这里，我们通过电荷修饰突变模拟了在 H3 尾部剪断后发现的改变的静电环境，以将其对核小体内相互作用的影响与组蛋白尾部的影响分离开来。对重组核小体的Förster 共振能量转移实验和全原子分子动力学模拟表明，这些氨基酸在核小体稳定性中起着补偿作用。模拟表明，H2A-H2B 二聚体与（H3-H4）四聚体之间以及二聚体与 DNA 之间的界面减弱。这些发现与实验观察到的引入突变后引起的位置和电荷依赖性核小体稳定性降低的结果一致。这项工作强调了 H2Aα3 结构域的重要性，并表明该结构域与外部 DNA 旋圈以及 H3 N 端尾部之间存在变构效应。
