Center for Systems Biology, Soochow University, Jiangsu, China.
PLoS One. 2012;7(5):e36660. doi: 10.1371/journal.pone.0036660. Epub 2012 May 4.
The histone acetylation of post-translational modification can be highly dynamic and play a crucial role in regulating cellular proliferation, survival, differentiation and motility. Of the enzymes that mediate post-translation modifications, the GCN5 of the histone acetyltransferase (HAT) proteins family that add acetyl groups to target lysine residues within histones, has been most extensively studied. According to the mechanism studies of GCN5 related proteins, two key processes, deprotonation and acetylation, must be involved. However, as a fundamental issue, the structure of hGCN5/AcCoA/pH3 remains elusive. Although biological experiments have proved that GCN5 mediates the acetylation process through the sequential mechanism pathway, a dynamic view of the catalytic process and the molecular basis for hGCN5/AcCoA/pH3 are still not available and none of theoretical studies has been reported to other related enzymes in HAT family. To explore the molecular basis for the catalytic mechanism, computational approaches including molecular modeling, molecular dynamic (MD) simulation and quantum mechanics/molecular mechanics (QM/MM) simulation were carried out. The initial hGCN5/AcCoA/pH3 complex structure was modeled and a reasonable snapshot was extracted from the trajectory of a 20 ns MD simulation, with considering post-MD analysis and reported experimental results. Those residues playing crucial roles in binding affinity and acetylation reaction were comprehensively investigated. It demonstrated Glu80 acted as the general base for deprotonation of Lys171 from H3. Furthermore, the two-dimensional QM/MM potential energy surface was employed to study the sequential pathway acetylation mechanism. Energy barriers of addition-elimination reaction in acetylation obtained from QM/MM calculation indicated the point of the intermediate ternary complex. Our study may provide insights into the detailed mechanism for acetylation reaction of GCN5, and has important implications for the discovery of regulators against GCN5 enzymes and related HAT family enzymes.
组蛋白乙酰化的翻译后修饰是高度动态的，在调节细胞增殖、存活、分化和迁移中起着关键作用。在介导翻译后修饰的酶中，组蛋白乙酰转移酶（HAT）蛋白家族中的 GCN5 酶将乙酰基添加到组蛋白中的靶赖氨酸残基上，这一酶得到了最广泛的研究。根据 GCN5 相关蛋白的机制研究，必须涉及两个关键过程，去质子化和乙酰化。然而，作为一个基本问题，hGCN5/AcCoA/pH3 的结构仍然难以捉摸。尽管生物实验已经证明 GCN5 通过顺序机制途径介导乙酰化过程，但催化过程的动态视图和 hGCN5/AcCoA/pH3 的分子基础仍然不可用，也没有理论研究报告其他 HAT 家族相关酶。为了探索催化机制的分子基础，进行了包括分子建模、分子动力学（MD）模拟和量子力学/分子力学（QM/MM）模拟在内的计算方法。构建了初始 hGCN5/AcCoA/pH3 复合物结构，并从 20 ns MD 模拟轨迹中提取了一个合理的快照，同时考虑了 MD 后分析和报道的实验结果。综合研究了对结合亲和力和乙酰化反应起关键作用的残基。结果表明，Glu80 作为 H3 中 Lys171 去质子化的广义碱。此外，还采用二维 QM/MM 势能面研究了顺序乙酰化机制。QM/MM 计算得到的乙酰化加成-消除反应的能垒表明了中间三元复合物的位置。我们的研究可能为 GCN5 的乙酰化反应的详细机制提供了一些见解，并对发现针对 GCN5 酶和相关 HAT 家族酶的调节剂具有重要意义。
