Understanding the Interactions of Ubiquitin-Specific Protease 7 with Its Substrates through Molecular Dynamics Simulations: Insights into the Role of Its C‑Terminal Domains in Substrate Recognition

• Published in: Journal of chemical information and modeling Vol. 64; no. 10; pp. 4134 - 4148
• Main Authors: Velázquez-Libera, José Luis, Caballero, Julio, Alzate-Morales, Jans, Ruiz-Pernía, J. Javier, Tuñón, Iñaki
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 27.05.2024
• Subjects: Catalytic activity; Computational Biochemistry; Enzymes; Fluorescence; Humans; Molecular dynamics; Molecular Dynamics Simulation; Protease; Protein Binding; Protein Conformation; Protein Domains; Proteins; Recognition; Rhodamine; Rhodamines - chemistry; Rhodamines - metabolism; Simulation; Stability augmentation; Structural stability; Substrate Specificity; Substrates; Ubiquitin - chemistry; Ubiquitin - metabolism; Ubiquitin-Specific Peptidase 7 - chemistry; Ubiquitin-Specific Peptidase 7 - metabolism
• ISSN: 1549-9596; 1549-960X
• DOI: 10.1021/acs.jcim.3c01971

Ubiquitin-specific protease 7 (USP7) is a deubiquitinase enzyme that plays a critical role in regulating various cellular processes by cleaving ubiquitin molecules from target proteins. The C-terminal loop (CTL) motif is a specific region at the C-terminal end of the USP7 enzyme. Recent experiments suggest that the CTL motif plays a role in USP7’s catalytic activity by contributing to the enzyme’s structural stability, substrate recognition, and catalytic efficiency. The objective of this work is to elucidate these roles through the utilization of computational methods for molecular simulations. For this, we conducted extensive molecular dynamics (MD) simulations to investigate the conformational dynamics and protein–protein interactions within the USP7 enzyme–substrate complex with the substrate consisting of the ubiquitin tagged with the fluorescent label rhodamine 110-gly (Ub-Rho). Our results demonstrate that the CTL motif plays a crucial role in stabilizing the Ubl domains’ conformation and augmenting the stability of active conformations within the enzyme–substrate complex. Conversely, the absence of the CTL motif results in increased flexibility and variability in Ubl domains’ motion, leading to a reduced percentage of active conformations. Furthermore, our analysis of protein–protein interactions highlights the significance of the CTL motif in anchoring the Ubl45 domains to the catalytic domain (CD), thereby facilitating stable interactions with the substrate. Overall, our findings provide valuable insights into the conformational dynamics and protein–protein interactions inherent in the USP7 enzyme–substrate complex. These insights shed light on some mechanistic details of USP7 concerning the substrate’s recognition before its catalytic action.