Insights into Conformational Dynamics and Allostery in DNMT1-H3Ub/USP7 Interactions
Abstract
:1. Introduction
2. Results
2.1. Structural Data of DNMT1 Complexes
2.2. Modulation of Global Motions of DNMT1 upon Complex Binding
2.3. MD Simulations Reveal More Dynamic Plasticity in DNMT1 Complexes
2.4. DNMT1–H3Ub/USP7 Are High-Potential Signaling Complexes
2.5. Allosteric Communication Pathways in DNMT1-H3Ub/USP7
2.6. Allosteric Pockets Regulate DNMT1 Complexes through Protein–Protein Interactions
3. Discussion
4. Materials and Methods
4.1. Structural Models and MD Simulation
4.2. Residue Fluctuations and Correlations Analysis
4.3. Elastic Network Models
4.4. Perturbation Response Scanning
4.5. Dynamic Network Analysis and Allosteric Pocket Identification
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Sample Availability
References
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Zhu, Y.; Ye, F.; Zhou, Z.; Liu, W.; Liang, Z.; Hu, G. Insights into Conformational Dynamics and Allostery in DNMT1-H3Ub/USP7 Interactions. Molecules 2021, 26, 5153. https://doi.org/10.3390/molecules26175153
Zhu Y, Ye F, Zhou Z, Liu W, Liang Z, Hu G. Insights into Conformational Dynamics and Allostery in DNMT1-H3Ub/USP7 Interactions. Molecules. 2021; 26(17):5153. https://doi.org/10.3390/molecules26175153
Chicago/Turabian StyleZhu, Yu, Fei Ye, Ziyun Zhou, Wanlin Liu, Zhongjie Liang, and Guang Hu. 2021. "Insights into Conformational Dynamics and Allostery in DNMT1-H3Ub/USP7 Interactions" Molecules 26, no. 17: 5153. https://doi.org/10.3390/molecules26175153