Exploring the Desumoylation Process of SENP1: A Study Combined MD Simulations with QM/MM Calculations on SENP1-SUMO1-RanGAP1
Exploring the Desumoylation Process of SENP1: A Study Combined MD Simulations with QM/MM Calculations on SENP1-SUMO1-RanGAP1
复制标题
DOI：
10.1021/ci4002487
复制
发表时间：
2013-08
影响因子：
5.6
通讯作者：
Ting Shi;Yuhui Han;Weihua Li;Yanlong Zhao;Yaqin Liu;Zhimin Huang;Shaoyong Lu;Jian Zhang
中科院分区：
文献类型：
--
作者：
Ting Shi;Yuhui Han;Weihua Li;Yanlong Zhao;Yaqin Liu;Zhimin Huang;Shaoyong Lu;Jian Zhang
小的泛素相关修饰物（SUMO）特异性蛋白酶（SENP）将SUMO加工成成熟的形式，并将其从各种修饰的底物中解配。由异常SENP1催化的去氧基化导致的平衡丧失与癌症和转录因子活性有关。尽管SENP1具有重要作用，但其去苏酰化的分子基础尚不清楚。本文将MD模拟和QM/MM方法相结合来研究脱硫化的催化机制。结果表明，底物SUMO1-RanGAP1通过内部疏水相互作用的断裂和异肽从反式到顺式的异构化，进入了SENP1的催化口袋。随后，SENP1中的亲核硫阴离子Cys603攻击SUMO1中Gly97的羰基碳触发反应，依次生成四面体中间体和酰基酶中间体，最终释放SENP1酶和游离SUMO1和RanGAP1两种产物。在此过程中，亲核攻击被确定为速率决定步骤，势能势垒为20.2 kcal/mol。这些结果与诱变和其他实验的实验数据一致。我们的研究结果阐明了SENP1及其底物的催化机制，并可能为更好地理解SENP去氧基化提供帮助。特别是，我们已经确定了SENP1中去苏酰化所需的关键残基，这可能有助于设计新的SENP1相关疾病抑制剂。
The small ubiquitin-related modifier (SUMO)-specific protease (SENP) processes SUMOs to mature forms and deconjugates them from various modified substrates. Loss of the equilibrium from desumoylation catalyzed by abnormal SENP1 is associated with cancers and transcription factor activity. In spite of the significant role of SENP1, the molecular basis of its desumoylation remains unclear. Here, MD simulations and QM/MM methods are combined to investigate the catalytic mechanism of desumoylation. The results showed that substrate SUMO1-RanGAP1 fitted into the catalytic pocket of SENP1 by the break of internal hydrophobic interactions and the isomerization of isopeptide from trans to cis. After that, the nucleophilic sulfur anion of Cys603 in SENP1 attacked the carbonyl carbon of Gly97 of SUMO1 to trigger the reaction, and then a tetrahedral intermediate and an acyl-enzyme intermediate were generated in turn, leading to the final release of enzyme SENP1 and two products, free SUMO1 and RanGAP1. In the process, nucleophilic attack was identified as the rate-determining step with a potential energy barrier of 20.2 kcal/mol. These results are in agreement with experimental data from mutagenesis and other experiments. Our findings elucidate the catalytic mechanism of SENP1 with its substrate and may provide a better understanding of SENP desumoylation. In particular, we have identified key residues in SENP1 needed for desumoylation that might be beneficial for the design of novel inhibitors of SENP1-related diseases.