Revealing Topological Barriers against Knot Untying in Thermal and Mechanical Protein Unfolding by Molecular Dynamics Simulations
Abstract
:1. Introduction
2. Materials and Methods
2.1. Models
2.2. Molecular Dynamics Simulation
2.3. Thermal Denaturation
2.4. Mechanical Denaturation
2.5. Knot Detection Algorithm
3. Results
3.1. Knot Untying under Enhanced Thermal Fluctuations
3.2. Knot Maintenance in Thermal Protein Unfolding
3.3. Steered Translocation of YbeA through SWCNT
3.4. Four Aspects of Barriers Jointly against Knot Untying in Protein Unfolding
3.5. Site Mutations Manifesting Barriers against Knot Untying
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Xu, Y.; Kang, R.; Ren, L.; Yang, L.; Yue, T. Revealing Topological Barriers against Knot Untying in Thermal and Mechanical Protein Unfolding by Molecular Dynamics Simulations. Biomolecules 2021, 11, 1688. https://doi.org/10.3390/biom11111688
Xu Y, Kang R, Ren L, Yang L, Yue T. Revealing Topological Barriers against Knot Untying in Thermal and Mechanical Protein Unfolding by Molecular Dynamics Simulations. Biomolecules. 2021; 11(11):1688. https://doi.org/10.3390/biom11111688
Chicago/Turabian StyleXu, Yan, Runshan Kang, Luyao Ren, Lin Yang, and Tongtao Yue. 2021. "Revealing Topological Barriers against Knot Untying in Thermal and Mechanical Protein Unfolding by Molecular Dynamics Simulations" Biomolecules 11, no. 11: 1688. https://doi.org/10.3390/biom11111688