Atomistic Analysis of ToxN and ToxI Complex Unbinding Mechanism
Abstract
:1. Introduction
2. Results and Discussion
2.1. Stability of the Systems
2.2. The Interaction between ToxI and ToxN
2.3. The Function of G5
2.4. Induced-Fit Mechanism
2.5. The Dissociation of ToxN(A) from the ToxIN Complex
2.6. The Dissociation of ToxI(c) from ToxN(A)
3. Modelling and Simulation
3.1. Molecular Dynamics Simulations
3.2. Residue-Inhibitor Interaction Decomposition
3.3. SMD and PMF in 3nD
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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System | Methods | Total Number of Atoms | MD Length (ns) |
---|---|---|---|
ToxIN | Equilibrated MD | 93,408 | 1000 × 3 = 3000 |
ToxI | Equilibrated MD | 26,478 | 1000 × 3 = 3000 |
ToxN | Equilibrated MD | 19,351 | 1000 × 3 = 3000 |
G5A | Equilibrated MD | 17,016 | 1000 |
G5H | Equilibrated MD | 16,349 | 1000 |
ToxIN | SMD | 115,152 | 338.8 × 2 = 677.6 |
ToxN(A)-ToxI(c) | SMD | 50,534 | 338.8 × 2 = 677.6 |
ToxN(A)-3′ terminus of ToxI(c) | SMD | 43,306 | 338.8 |
ToxI(c) | SMD | 38,519 | 338.8 |
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Hu, G.; Yu, X.; Bian, Y.; Cao, Z.; Xu, S.; Zhao, L.; Ji, B.; Wang, W.; Wang, J. Atomistic Analysis of ToxN and ToxI Complex Unbinding Mechanism. Int. J. Mol. Sci. 2018, 19, 3524. https://doi.org/10.3390/ijms19113524
Hu G, Yu X, Bian Y, Cao Z, Xu S, Zhao L, Ji B, Wang W, Wang J. Atomistic Analysis of ToxN and ToxI Complex Unbinding Mechanism. International Journal of Molecular Sciences. 2018; 19(11):3524. https://doi.org/10.3390/ijms19113524
Chicago/Turabian StyleHu, Guodong, Xiu Yu, Yunqiang Bian, Zanxia Cao, Shicai Xu, Liling Zhao, Baohua Ji, Wei Wang, and Jihua Wang. 2018. "Atomistic Analysis of ToxN and ToxI Complex Unbinding Mechanism" International Journal of Molecular Sciences 19, no. 11: 3524. https://doi.org/10.3390/ijms19113524