The Structural and Dynamical Properties of the Hydration of SNase Based on a Molecular Dynamics Simulation
Abstract
:1. Introduction
2. Results and Discussion
2.1. Structural Fluctuations
2.2. Radial Distributions Function
2.3. Mean Square Displacement of SNase and Hydration Water
2.4. Hydration Dynamics Based on Mutation
2.5. Hydrogen Bonding Dynamics
3. Materials and Methods
3.1. Molecule Dynamics Simulation
3.2. Analysis Methods
3.2.1. Root Mean Square Fluctuation
3.2.2. Root Mean Square Deviation
3.2.3. Mean Square Displacement
3.2.4. Radial Distributions Function
3.2.5. Hydration Dynamics Analysis Based on Mutation
3.2.6. Hydration Bonding
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Sample Availability
References
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Mutation | SN0 | SN1 | SN2 | SN3 |
---|---|---|---|---|
Coil(%) | 17 | 19 | 18 | 20 |
β-Sheet(%) | 28 | 27 | 28 | 26 |
β-Bridge(%) | 2 | 3 | 2 | 2 |
Bend(%) | 14 | 11 | 12 | 12 |
Turn(%) | 12 | 14 | 13 | 14 |
α-Helix(%) | 25 | 24 | 25 | 25 |
3-Helix(%) | 2 | 2 | 1 | 1 |
Temperature (K) | 150 | 180 | 210 | 240 | 270 | 300 |
---|---|---|---|---|---|---|
SASA (nm2) | 80.2 ± 0.6 | 81.5 ± 1.1 | 82.9 ± 0.8 | 83.9 ± 1.3 | 84.4 ± 1.2 | 85.6 ± 1.6 |
Mutation | SN0 | SN1 | SN2 | SN3 | |||||
---|---|---|---|---|---|---|---|---|---|
Temperature (K) | 150 | 180 | 210 | 240 | 270 | 300 | 300 | 300 | 300 |
Position (nm) | 0.276 | 0.274 | 0.274 | 0.272 | 0.27 | 0.272 | 0.272 | 0.276 | 0.276 |
Height | 1.794 | 1.719 | 1.667 | 1.554 | 1.513 | 1.503 | 1.491 | 1.415 | 1.381 |
Mutation | SN0 | SN1 | SN2 | SN3 |
---|---|---|---|---|
τs (ps) | 58.9 ± 0.35 | 57.8 ± 0.30 | 49.4 ± 0.40 | 46.3 ± 0.36 |
τ1 (ps) | 4.8 ± 0.05 | 4.7 ± 0.05 | 4.3 ± 0.05 | 3.1 ± 0.13 |
Mutation | SN0 | SN1 | SN2 | SN3 |
---|---|---|---|---|
tμ (ps) | 4.8 ± 0.01 | 4.3 ± 0.01 | 4.2 ± 0.01 | 3.8 ± 0.00 |
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Liu, H.; Xiang, S.; Zhu, H.; Li, L. The Structural and Dynamical Properties of the Hydration of SNase Based on a Molecular Dynamics Simulation. Molecules 2021, 26, 5403. https://doi.org/10.3390/molecules26175403
Liu H, Xiang S, Zhu H, Li L. The Structural and Dynamical Properties of the Hydration of SNase Based on a Molecular Dynamics Simulation. Molecules. 2021; 26(17):5403. https://doi.org/10.3390/molecules26175403
Chicago/Turabian StyleLiu, Hangxin, Shuqing Xiang, Haomiao Zhu, and Li Li. 2021. "The Structural and Dynamical Properties of the Hydration of SNase Based on a Molecular Dynamics Simulation" Molecules 26, no. 17: 5403. https://doi.org/10.3390/molecules26175403