Effects of the Q80K Polymorphism on the Physicochemical Properties of Hepatitis C Virus Subtype 1a NS3 Protease
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sequence Analysis and Statistical Treatment
2.2. Comparative Modeling
2.3. Molecular Dynamics (MD) Simulations
2.4. Trajectory Analysis
2.5. Correlation Network Analysis
2.6. Phylogenetic Analysis
3. Results
3.1. Sequence Analysis, Statistical Treatment, and Comparative Modeling
3.2. Assessing Dynamic Properties of the Models in Aqueous Solution
3.3. Hydrogen Bonding Interactions
3.4. Correlation Network Analysis and Community Network Comparison
3.5. Phylogenetic Analysis
4. Discussion
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Models | DOPE Score | ERRAT2 | QMean | Ramachandran Plot | ||
---|---|---|---|---|---|---|
R1 | R2 | R3 | ||||
2f9v | −22100 | 94.047 | −0.35 | 95.5 | 4.5 | 0.0 |
c1mutKSN | −21543 | 83.132 | 0.19 | 97.9 | 2.1 | 0.0 |
c1mutKSS | −21453 | 92.261 | 0.21 | 98.5 | 1.5 | 0.0 |
c2mutKAG | −21581 | 91.071 | 0.13 | 98.5 | 1.5 | 0.0 |
c2mutKAS | −21665 | 89.881 | 0.44 | 98.5 | 1.5 | 0.0 |
Atoms | Occupancy (%) | ||||
---|---|---|---|---|---|
Donor | Acceptor | c1mutKSN | c1mutKSS | c2mutKAG | c2mutKAS |
HIS57–ND1 | ASP81–CG | - | 10.34 | - | 48.99 |
HIS57–ND1 | ASP81–OD1 | - | 6.38 | - | 27.41 |
HIS57–ND1 | ASP81–OD2 | - | 7.64 | - | 20.04 |
SER139–OG | LYS136–O | 13.14 | 26.55 | 6.58 | 20.44 |
Atoms | Distance (Å) | ||||
---|---|---|---|---|---|
Donor | Acceptor | c1mutKSN | c1mutKSS | c2mutKAG | c2mutKAS |
HIS57–ND1 | ASP81–CG | 4.97 ± 1.00 | 5.69 ± 1.75 | 5.41 ± 1.34 | 4.95 ± 1.89 |
HIS57–ND1 | ASP81–OD1 | 5.13 ± 0.96 | 5.87 ± 1.89 | 5.76 ± 1.36 | 4.87 ± 2.14 |
HIS57–ND1 | ASP81–OD2 | 5.27 ± 1.00 | 5.83 ± 1.94 | 5.73 ± 1.37 | 5.02 ± 2.10 |
SER139–OG | LYS136–O | 4.35 ± 1.81 | 4.33 ± 1.97 | 5.20 ± 1.99 | 4.88 ± 2.12 |
c1mutKSN | c1mutKSS | c2mutKAG | c2mutKAS | |
---|---|---|---|---|
c1mutKSN | 1 | 0.62 | 0.37 | 0.42 |
c1mutKSS | 1 | 0.57 | 0.47 | |
c2mutKAG | 1 | 0.46 | ||
c2mutKAS | 1 |
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Peres-da-Silva, A.; Antunes, D.; Quintanilha Torres, A.L.; Caffarena, E.R.; Lampe, E. Effects of the Q80K Polymorphism on the Physicochemical Properties of Hepatitis C Virus Subtype 1a NS3 Protease. Viruses 2019, 11, 691. https://doi.org/10.3390/v11080691
Peres-da-Silva A, Antunes D, Quintanilha Torres AL, Caffarena ER, Lampe E. Effects of the Q80K Polymorphism on the Physicochemical Properties of Hepatitis C Virus Subtype 1a NS3 Protease. Viruses. 2019; 11(8):691. https://doi.org/10.3390/v11080691
Chicago/Turabian StylePeres-da-Silva, Allan, Deborah Antunes, André Luiz Quintanilha Torres, Ernesto Raul Caffarena, and Elisabeth Lampe. 2019. "Effects of the Q80K Polymorphism on the Physicochemical Properties of Hepatitis C Virus Subtype 1a NS3 Protease" Viruses 11, no. 8: 691. https://doi.org/10.3390/v11080691