In Silico Prediction of the Phosphorylation of NS3 as an Essential Mechanism for Dengue Virus Replication and the Antiviral Activity of Quercetin
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Predicting Phosphorylation
2.2. System Preparation for Molecular Simulation
2.2.1. Initial Structure
2.2.2. Phosphorylated Structure
2.2.3. Solvation
2.2.4. Simulations Steps
2.2.5. Minimization
2.2.6. Heating
2.2.7. Equilibration
2.2.8. MD Simulation
2.2.9. Trajectories Analysis
2.2.10. Docking
2.2.11. Binding Pocket Calculation
3. Results
3.1. Phosphorylation Sites Prediction
3.2. Effects of NS3 Phosphorylation and Conformational Change in Protein Structure
3.3. Protein Movement Changes with Phosphorylation
3.4. Hydrophobicity of the NS3–NS5 Contact Site Increases with Phosphorylation
3.5. Solvent Accessibility in the NS3-NS2B Interaction and the Catalytic Domain
3.6. Phosphorylation Induced Site-Specific Structural Changes
3.7. Docking Analysis of NS3–NS5 Interaction
3.8. Interactions of NS3 with Quercetin
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Appendix A
GPS | Netphos | ScanSite | ||||||
---|---|---|---|---|---|---|---|---|
Kinase | Position | Score | Kinase | Position | Score | Kinase | Position | Score |
MAPK | 9 | 23.1 | cdk5 | 9 | 0.59 | CDK5 | 9 | 0.64 |
SRC | 23 | 10.1 | SRC | 23 | 0.49 | |||
PIKK | 34 | 9.57 | ||||||
PKC | 45 | 9.56 | PRKCZ(PKC) | 45 | 0.52 | |||
PKC | 122 | 0.55 | PRKCE(PKC) | 68 | 0.49 | |||
PIKK | 127 | 9.45 | ||||||
MAPK | 131 | 28 | cdk5 | 131 | 0.68 | GSK3A | 131 | 0.56 |
MAPK | 134 | 11.3 | MAPK3 | 135 | 0.61 | |||
MAPK | 137 | 28.8 | GSK3 | 137 | 0.49 | CDK1 | 137 | 0.6 |
PKC | 163 | 0.53 | ||||||
PKC | 168 | 0.68 | ||||||
PRKDC(PIKK) | 171 | 0.58 | ||||||
AKT | 189 | 10.9 | PKB(AKT) | 189 | 0.73 | CAMK2G | 189 | 0.53 |
PKC | 200 | 0.73 | ||||||
PKC | 218 | 0.71 | ||||||
MAPK | 244 | 25.7 | cdk5 | 244 | 0.65 | CDK1 | 244 | 0.63 |
PKC | 266 | 0.85 | ||||||
MAPK | 271 | 31.4 | cdk5 | 271 | 0.65 | AKT1 | 271 | 0.69 |
PKC | 293 | 0.53 | PRKCD(PKC) | 293 | 0.49 | |||
PKC | 301 | 0.67 | ||||||
MAPK | 317 | 28.3 | cdk5 | 317 | 0.65 | MAPK3 | 317 | 0.63 |
MAPK | 317 | 28.3 | cdk5 | 317 | 0.65 | MAPK3 | 317 | |
PKC | 352 | 0.6 | GSK3A | 321 | ||||
PKC | 358 | 0.63 | CAMK2G | 358 | ||||
PKC | 364 | 9.68 | PRKCA(PKC) | 364 | ||||
PKC | 386 | 0.61 | CAMK2G | 386 | ||||
PKC | 389 | 10.7 | PRKACG(PKC) | 389 | ||||
PKC | 453 | 9.95 | ||||||
SRC | 472 | 11.9 | ||||||
MAPK | 500 | 29.9 | MAPK3 | 500 | ||||
PKC | 507 | 9.59 | ||||||
SRC | 523 | 10.3 | ||||||
AKT1 | 602 | |||||||
MAPK | 317 | 28.3 | cdk5 | 317 | 0.65 | MAPK3 | 317 | |
PKC | 352 | 0.6 | GSK3A | 321 | ||||
PKC | 358 | 0.63 | CAMK2G | 358 | ||||
PKC | 364 | 9.68 | PRKCA(PKC) | 364 | 0.53 | |||
PKC | 386 | 0.61 | CAMK2G | 386 | 0.56 | |||
PKC | 389 | 10.7 | PRKACG(PKC) | 389 | 0.6 | |||
PKC | 453 | 9.95 | ||||||
SRC | 472 | 11.9 | ||||||
MAPK | 500 | 29.9 | MAPK3 | 500 | 0.59 | |||
PKC | 507 | 9.59 | ||||||
SRC | 523 | 10.3 | ||||||
AKT1 | 602 | 0.71 | ||||||
PKC | 364 | 9.68 | PRKCA(PKC) | 364 | 0.53 | |||
PKC | 386 | 0.61 | CAMK2G | 386 | 0.56 | |||
PKC | 389 | 10.7 | PRKACG(PKC) | 389 | 0.6 |
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Effect | DFn | DFd | F | ges | p |
---|---|---|---|---|---|
Time Step | 4795 | 9590 | 4.443 | 0.69 | <0.0001 |
Category | 2 | 9590 | 59671.861 | 0.926 | <0.0001 |
RMSD Emmean Comparisons 1 | ||||||
---|---|---|---|---|---|---|
Category | Emmean | SE | DF | S137 | T189 | WT |
S137 | 7.785 | 0.012 | 14385 | NA | <0.0001 | <0.0001 |
T189 | 3.871 | 0.012 | 14385 | <0.0001 | NA | <0.0001 |
WT | 5.396 | 0.012 | 14385 | <0.0001 | <0.0001 | NA |
Effect | DFn | DFd | F | ges | p |
---|---|---|---|---|---|
Time Step | 4795 | 9590 | 0.843 | 0.297 | 1 |
Category | 2 | 9590 | 1296396.55 | 0.996 | <0.0001 |
ID | N-Lobe Catalytic Domain 120–1168 | Linker 169–179 | NS3 Loop 566–585 | C-Lobe Helicase 180–618 |
---|---|---|---|---|
WT-S137 | 28.97 Å | 8.82 Å | 3.66 Å | 2.82 Å |
WT-T189 | 16.20 Å | 9.78 Å | 3.38 Å | 3.05 Å |
RMSD Emmean Comparisons 1 | ||||||
---|---|---|---|---|---|---|
Category | Emmean | SE | DF | S137 | T189 | WT |
S137 | 11.002 | 0.0045 | 14385 | NA | <0.0001 | <0.0001 |
T189 | 1.908 | 0.0045 | 14385 | <0.0001 | NA | <0.0001 |
WT | 1.733 | 0.0045 | 14385 | <0.0001 | <0.0001 | NA |
ID | Cluster Members | Weighted Score Lowest Energy a |
---|---|---|
WT-NS5 | 29 | −963.8 Kcal/mol |
T189-NS5 | 28 | −949.2 Kcal/mol |
S137-NS5 | 49 | −1141.8 Kcal/mol |
Residue | WT | S137 | T189 |
---|---|---|---|
75 | 54.42 | 35.07 | 52.11 |
177 | 100.35 | 22.45 | 122.17 |
179 | 56.54 | 100.64 | 82.61 |
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Alomair, L.; Almsned, F.; Ullah, A.; Jafri, M.S. In Silico Prediction of the Phosphorylation of NS3 as an Essential Mechanism for Dengue Virus Replication and the Antiviral Activity of Quercetin. Biology 2021, 10, 1067. https://doi.org/10.3390/biology10101067
Alomair L, Almsned F, Ullah A, Jafri MS. In Silico Prediction of the Phosphorylation of NS3 as an Essential Mechanism for Dengue Virus Replication and the Antiviral Activity of Quercetin. Biology. 2021; 10(10):1067. https://doi.org/10.3390/biology10101067
Chicago/Turabian StyleAlomair, Lamya, Fahad Almsned, Aman Ullah, and Mohsin S. Jafri. 2021. "In Silico Prediction of the Phosphorylation of NS3 as an Essential Mechanism for Dengue Virus Replication and the Antiviral Activity of Quercetin" Biology 10, no. 10: 1067. https://doi.org/10.3390/biology10101067