A Deep Dive into VDAC1 Conformational Diversity Using All-Atom Simulations Provides New Insights into the Structural Origin of the Closed States
Abstract
:1. Introduction
2. Results
2.1. aMD Simulations
2.2. Investigating Subconducting States of mVDAC1
2.3. Refolding of the N-Terminus
3. Discussion
4. Materials and Methods
4.1. System Preparation
4.2. MD Software and Force Field
4.3. aMD Simulations
4.4. PB/PNP and GCMC/BD
4.5. Unbiased MD
4.6. Clustering Analysis
4.7. Molecular Visualization
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Trajectory | Conductance (nS) | |
---|---|---|
3EMN | 3.71 | 2.21 |
A | 2.18 | 4.33 |
B | 1.93 | 3.09 |
C | 2.34 | 2.80 |
D (t ≤ 270 ns) | 1.57 | 3.20 |
D (t > 270 ns) | 3.66 | 2.25 |
D (t ≤ 316 ns) | 1.75 | 3.27 |
E (t > 316 ns) | 3.90 | 2.36 |
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Preto, J.; Gorny, H.; Krimm, I. A Deep Dive into VDAC1 Conformational Diversity Using All-Atom Simulations Provides New Insights into the Structural Origin of the Closed States. Int. J. Mol. Sci. 2022, 23, 1175. https://doi.org/10.3390/ijms23031175
Preto J, Gorny H, Krimm I. A Deep Dive into VDAC1 Conformational Diversity Using All-Atom Simulations Provides New Insights into the Structural Origin of the Closed States. International Journal of Molecular Sciences. 2022; 23(3):1175. https://doi.org/10.3390/ijms23031175
Chicago/Turabian StylePreto, Jordane, Hubert Gorny, and Isabelle Krimm. 2022. "A Deep Dive into VDAC1 Conformational Diversity Using All-Atom Simulations Provides New Insights into the Structural Origin of the Closed States" International Journal of Molecular Sciences 23, no. 3: 1175. https://doi.org/10.3390/ijms23031175