Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
J Phys Chem B. 2010 Sep 16;114(36):11927-33. doi: 10.1021/jp1054183.
Sir2, the histone deacetylase III family, has been subjected to a wide range of studies because of their crucial roles in DNA repair, longevity, transcriptional silencing, genome stability, apoptosis, and fat mobilization. The enzyme binds NAD(+) and acetyllysine as substrates and generates lysine, 2'-O-acetyl-ADP-ribose, and nicotinamide as products. However, the mechanism of the first step in Sir2 deacetylation reaction from various studies is controversial. To characterize this catalytic mechanism of acetyllysine deacetylation by Sir2, we employed a combined computational approach to carry out molecular modeling, molecular dynamics (MD) simulations, quantum mechanics/molecular mechanics (QM/MM) calculations on catalysis by both yeast Hst2 (homologue of SIR two 2) and bacterial Sir2TM (Sir2 homologue from Thermatoga maritima). Our three-dimensional (3D) model of the complex is composed of Sir2 protein, NAD(+), and acetyllysine (ALY) substrate. A 15-ns MD simulation of the complex revealed that Gln115 and His135 play a determining role in deacetylation. These two residues can act as bases to facilitate the deprotonation of 2'-OH from N-ribose. The result is in great agreement with previous mutagenesis analysis data. QM/MM calculations were further performed to study the mechanism of the first step in deacetylation in the two systems. The predicted potential energy barriers for yHst2 and Sir2TM are 12.0 and 15.7 kcal/mol, respectively. The characteristics of the potential energy surface indicated this reaction belongs to a SN2-like mechanism. These results provide insights into the Sir2 mechanism of nicotinamide inhibition and have important implications for the discovery of effectors against Sir2 enzymes.
Sir2 是组蛋白去乙酰化酶 III 家族成员，由于其在 DNA 修复、长寿、转录沉默、基因组稳定性、细胞凋亡和脂肪动员等方面的关键作用，受到了广泛的研究。该酶以 NAD(+)和乙酰化赖氨酸为底物，生成赖氨酸、2'-O-乙酰-ADP-核糖和烟酰胺。然而，从各种研究来看，Sir2 去乙酰化反应第一步的机制存在争议。为了表征 Sir2 乙酰化赖氨酸去乙酰化的催化机制，我们采用了一种组合计算方法，对酵母 Hst2（SIR two 2 的同源物）和细菌 Sir2TM（来自 Thermatoga maritima 的 Sir2 同源物）的催化作用进行了分子建模、分子动力学 (MD) 模拟、量子力学/分子力学 (QM/MM) 计算。我们构建的复合物三维 (3D) 模型由 Sir2 蛋白、NAD(+)和乙酰赖氨酸 (ALY) 底物组成。对复合物的 15-ns MD 模拟表明，Gln115 和 His135 在去乙酰化过程中起决定性作用。这两个残基可以作为碱基，促进 N-核糖 2'-OH 的去质子化。这一结果与之前的突变分析数据非常吻合。进一步进行了 QM/MM 计算，以研究两个系统中去乙酰化第一步的反应机制。预测的 yHst2 和 Sir2TM 的势能垒分别为 12.0 和 15.7 kcal/mol。势能面的特征表明该反应属于 SN2 样机制。这些结果为 Sir2 抑制烟酰胺的机制提供了深入了解，并对发现针对 Sir2 酶的效应物具有重要意义。
