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
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...
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Published in | Journal of chemical information and modeling Vol. 64; no. 10; pp. 4134 - 4148 |
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Main Authors | , , , , |
Format | Journal Article |
Language | English |
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American Chemical Society
27.05.2024
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Abstract | 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. |
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AbstractList | 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. |
Author | Velázquez-Libera, José Luis Caballero, Julio Alzate-Morales, Jans Tuñón, Iñaki Ruiz-Pernía, J. Javier |
AuthorAffiliation | Departamento de Bioinformática, Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería Departamento de Química Física |
AuthorAffiliation_xml | – name: Departamento de Bioinformática, Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería – name: Departamento de Química Física |
Author_xml | – sequence: 1 givenname: José Luis orcidid: 0000-0002-4941-6619 surname: Velázquez-Libera fullname: Velázquez-Libera, José Luis email: josevlibera2010@gmail.com organization: Departamento de Bioinformática, Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería – sequence: 2 givenname: Julio orcidid: 0000-0003-0182-1444 surname: Caballero fullname: Caballero, Julio email: jcaballero@utalca.cl organization: Departamento de Bioinformática, Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería – sequence: 3 givenname: Jans orcidid: 0000-0001-9624-7849 surname: Alzate-Morales fullname: Alzate-Morales, Jans organization: Departamento de Bioinformática, Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería – sequence: 4 givenname: J. Javier orcidid: 0000-0002-4640-0419 surname: Ruiz-Pernía fullname: Ruiz-Pernía, J. Javier organization: Departamento de Química Física – sequence: 5 givenname: Iñaki orcidid: 0000-0002-6995-1838 surname: Tuñón fullname: Tuñón, Iñaki email: ignacio.tunon@uv.es organization: Departamento de Química Física |
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SubjectTerms | 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 |
Title | 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 |
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