Wang Xuebin, Liu Ning, Li Nuan, Lu Shaoyong, Chai Zongtao
Department of Pharmacy, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China.
Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area, Ministry of Education, Peptide & Protein Drug Research Center, School of Pharmacy, Ningxia Medical University, Yinchuan 750004, China.
Biomolecules. 2025 May 22;15(6):749. doi: 10.3390/biom15060749.
Ubiquitin-specific protease 7 (USP7), a deubiquitinase enzyme responsible for removing ubiquitin (Ub) from target proteins, plays a crucial role in oncogenic pathways and has been implicated in various human diseases. X-ray crystallography has revealed distinct conformations of USP7, including apo (ligand-free), allosteric inhibitor-, and Ub-bound states. However, the dynamic mechanisms underlying the allosteric inhibition of USP7 remain unclear. This study investigates the effect of allosteric inhibitor binding on the dynamics of USP7 through multiple replica molecular dynamics simulations. Our results demonstrate that Ub binding stabilizes the USP7 conformation, while allosteric inhibitor binding increases flexibility and variability in the fingers and palm domains of USP7. Furthermore, our analysis of USP7 local regions reveals that allosteric inhibitor binding not only restrains the dynamics of the C-terminal Ub binding site, thereby impeding the accessibility of Ub to USP7, but also disrupts the proper alignment of the catalytic triad (Cys223-His464-Asp481) in USP7. Additionally, community network analysis indicates that intra-domain communications within the fingers domain in USP7 are significantly enhanced upon allosteric inhibitor binding. This study reveals that the binding of an allosteric inhibitor induces a dynamic shift in enzyme's conformational equilibrium, effectively disrupting its catalytic activity through allosteric modulation.
泛素特异性蛋白酶7（USP7）是一种负责从靶蛋白上移除泛素（Ub）的去泛素化酶，在致癌途径中起关键作用，并与多种人类疾病有关。X射线晶体学揭示了USP7的不同构象，包括无配体（apo）、变构抑制剂结合和Ub结合状态。然而，USP7变构抑制的动态机制仍不清楚。本研究通过多个重复分子动力学模拟研究变构抑制剂结合对USP7动力学的影响。我们的结果表明，Ub结合稳定了USP7的构象，而变构抑制剂结合增加了USP7手指和手掌结构域的灵活性和变异性。此外，我们对USP7局部区域的分析表明，变构抑制剂结合不仅限制了C末端Ub结合位点的动力学，从而阻碍Ub与USP7的结合，还破坏了USP7中催化三联体（Cys223-His464-Asp481）的正确排列。此外，群落网络分析表明，变构抑制剂结合后，USP7手指结构域内的域内通讯显著增强。本研究表明，变构抑制剂的结合诱导了酶构象平衡的动态变化，通过变构调节有效地破坏了其催化活性。
