Hinge Region in DNA Packaging Terminase pUL15 of Herpes Simplex Virus: A Potential Allosteric Target for Antiviral Drugs
Abstract
:1. Introduction
2. Materials and Methods
2.1. Estimated Rate of Change
2.2. Phylogenetic Tree
2.3. Protein Structure Modeling
2.4. ATP-Binding Site Prediction
2.5. DNA-Binding Site Prediction
2.6. Cross-Correlation of Residue Fluctuations
3. Results
3.1. Publications on HHV, HIV, and Influenza
3.2. Relative Substitution Rates for HHV-1 Proteins
3.3. Phylogenetic Tree Analysis
3.4. Structure Model of pUL15
3.5. Cross-Correlation between Residue Fluctuations
3.6. Ligand-Binding Site in pUL15
3.7. Model of pUL15 Complexed with ATP
3.8. Model of pUL15 Bound to DNA
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Herpesvirus | Abbreviation | Accession Number | % Identity with HHV-1 |
---|---|---|---|
Human Alphaherpesvirus 1 | HHV-1 | YP 009137089.1 | 100.0% |
Human Alphaherpesvirus 2 | HHV-2 | YP_009137166.1 | 94.8% |
Human Alphaherpesvirus 3 | HHV-3 | NP_040165.1 | 59.0% |
Human Gammaherpesvirus 4 | HHV-4 | YP 401690.1 | 32.2% |
Human Betaherpesvirus Type 5 | HHV-5 | YP_081537.1 | 36.0% |
Human Betaherpesvirus 6B | HHV-6B | NP_050241.1 | 34.5% |
Human Betaherpesvirus 7 | HHV-7 | YP_073802.1 | 33.0% |
Human Gammaherpesvirus 8 | HHV-8 | YP_001129382.1 | 31.6% |
Chimpanzee Herpesvirus Strain 105640 | ChHV-2 | YP_009011001.1 | 95.0% |
Cercopithecine Herpesvirus 2 | CeHV-2 | YP_164457.1 | 87.3% |
Equid Alphaherpesvirus 1 | EHV-1 | YP_053090.1 | 63.9% |
Equid Gammaherpesvirus 2 | EHV-2 | NP_042630.2 | 30.6% |
Equid Alphaherpesvirus 4 | EHV-4 | NP_045262.1 | 63.7% |
Equid Gammaherpesvirus 5 | EHV-5 | YP_009118419.1 | 31.6% |
Equid Alphaherpesvirus 8 | EHV-8 | YP_006273027.1 | 29.6% |
Equid Alphaherpesvirus 9 | EHV-9 | YP_002333526.2 | 64.1% |
Felid Herpesvirus 1 | FHV-1 | YP_003331564.1 | 64.3% |
Fruit bat Alphaherpesvirus 1 | FBAHV-1 | YP_009042077.1 | 82.6% |
Bovine Alphaherpesvirus 1 | BHV-1 | NP 045342.1 | 60.4% |
Bovine Gammaherpesvirus 4 | BHV-4 | NP 076521.1 | 31.3% |
Bovine Alphaherpesvirus 5 | BHV-5 | YP 003662508.1 | 60.6% |
Bovine Gammaherpesvirus 6 | BHV-6 | YP 009042007.1 | 31.0% |
Gallid Alphaherpesvirus 2 | GaHV-2 | AAF66813.1 | 53.9% |
Suid Alphaherpesvirus 1 | SuHV-1 | YP 068358.1 | 55.2% |
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Thaljeh, L.F.; Rothschild, J.A.; Naderi, M.; Coghill, L.M.; Brown, J.M.; Brylinski, M. Hinge Region in DNA Packaging Terminase pUL15 of Herpes Simplex Virus: A Potential Allosteric Target for Antiviral Drugs. Biomolecules 2019, 9, 603. https://doi.org/10.3390/biom9100603
Thaljeh LF, Rothschild JA, Naderi M, Coghill LM, Brown JM, Brylinski M. Hinge Region in DNA Packaging Terminase pUL15 of Herpes Simplex Virus: A Potential Allosteric Target for Antiviral Drugs. Biomolecules. 2019; 9(10):603. https://doi.org/10.3390/biom9100603
Chicago/Turabian StyleThaljeh, Lana F., J. Ainsley Rothschild, Misagh Naderi, Lyndon M. Coghill, Jeremy M. Brown, and Michal Brylinski. 2019. "Hinge Region in DNA Packaging Terminase pUL15 of Herpes Simplex Virus: A Potential Allosteric Target for Antiviral Drugs" Biomolecules 9, no. 10: 603. https://doi.org/10.3390/biom9100603