Department of Chemistry, New York University, New York, New York 10003, USA.
J Am Chem Soc. 2010 Jul 14;132(27):9471-9. doi: 10.1021/ja103932d.
Zinc-dependent histone deacetylase 8 (HDAC8) catalyzes the removal of acetyl moieties from histone tails, and is critically involved in regulating chromatin structure and gene expression. The detailed knowledge of its catalytic process is of high importance since it has been established as a most promising target for the development of new antitumor drugs. By employing Born-Oppenheimer ab initio QM/MM molecular dynamics simulations and umbrella sampling, a state-of-the-art approach to simulate enzyme reactions, we have provided further evidence against the originally proposed general acid-base catalytic pair mechanism for Zinc-dependent histone deacetylases. Instead, our results indicated that HDAC8 employs a proton-shuttle catalytic mechanism, in which a neutral His143 first serves as the general base to accept a proton from the zinc-bound water molecule in the initial rate-determining nucleophilic attack step, and then shuttles it to the amide nitrogen atom to facilitate the cleavage of the amide bond. During the deacetylation process, the Zn(2+) ion changes its coordination mode and plays multiple catalytic roles. For the K(+) ion, which is located about 7 A from the catalytic Zn(2+) ion and conserved in class I and II HDACs, our simulations indicated that its removal would lead to the different transition state structure and a higher free energy reaction barrier for the rate-determining step. It is found that the existence of this conserved K(+) ion would enhance the substrate binding, increase the basicity of His143, strengthen the catalytic role of zinc ion, and improve the transition state stabilization by the enzyme environment.
锌依赖的组蛋白去乙酰化酶 8（HDAC8）催化组蛋白尾部乙酰基的去除，对于调节染色质结构和基因表达至关重要。由于其已被确立为开发新型抗肿瘤药物的最有前途的靶标，因此了解其催化过程的详细信息非常重要。通过使用 Born-Oppenheimer 从头算 QM/MM 分子动力学模拟和伞状采样（一种模拟酶反应的最先进方法），我们提供了进一步的证据，证明锌依赖性组蛋白去乙酰化酶最初提出的通用酸碱催化对机制是不正确的。相反，我们的结果表明，HDAC8 采用质子转移催化机制，其中中性 His143 首先作为通用碱从锌结合的水分子中接受质子，然后将质子转移到酰胺氮原子上，以促进酰胺键的断裂。在去乙酰化过程中，Zn（2+）离子改变其配位模式并发挥多种催化作用。对于位于催化 Zn（2+）离子约 7Å处且在 I 类和 II 类 HDAC 中保守的 K（+）离子，我们的模拟表明，其去除会导致不同的过渡态结构和更高的自由能反应势垒对于速率决定步骤。研究发现，这种保守的 K（+）离子的存在可以增强底物结合，提高 His143 的碱性，增强锌离子的催化作用，并通过酶环境改善过渡态的稳定性。
