AlphaFold2 Reveals Structural Patterns of Seasonal Haplotype Diversification in SARS-CoV-2 Nucleocapsid Protein Variants
Abstract
:1. Introduction
2. Materials and Methods
3. Results
3.1. Full-Length Analysis of the N-Protein Using Backbone Root Mean Square Deviations (RMSD)
3.2. Regional Analysis with TM Scores Using US-Align
3.3. Protein Disorder and pLDDT Scores
3.4. Protein Disorder and Binding Capacity Across the Pandemic
3.5. Normal Mode Analysis of Haplotypes and VOCs
3.6. Exploring Electrostatic Potential Surface Fingerprints
3.7. Benchmarking Alphafold2 Reference Structures against Experimental Cryo-EM Models
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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State-Chain | GDT-TS (AS2S) | TM Score/L (US-Align Server) | Superimposed RMSD < 5 Å (AS2S) |
---|---|---|---|
NTD-A (7CDZ) | 91.99 × (128/131) = 89.88 | *L1: 0.93398, L2: 0.91375 | 1.293/128 |
NTD-B (7CDZ) | 90.35 × (127/131) = 87.59 | 0.92756, 0.90091 | 1.366/127 |
NTD-C (7CDZ) | 95.24 × (126/131) = 91.60 | 0.95983, 0.92447 | 0.941/126 |
NTD-D (7CDZ) | 94.26 × (122/131) = 87.78 | 0.93300, 0.90592 | 1.1108/122 |
CTD-A (7CE0) | 69.73 × (109/110) = 69.10 | 0.74156 | 2.508/109 |
CTD-B (7CE0) | 69.50 × (109/110) = 68.87 | 0.73968 | 2.519/109 |
CTD-C (7CE0) | 69.39 × (107/110) = 67.50 | 0.73391 | 2.476/107 |
CTD-D (7CE0) | 68.93 × (107/110) = 67.05 | 0.73302 | 2.490/107 |
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Ali, M.A.; Caetano-Anollés, G. AlphaFold2 Reveals Structural Patterns of Seasonal Haplotype Diversification in SARS-CoV-2 Nucleocapsid Protein Variants. Viruses 2024, 16, 1358. https://doi.org/10.3390/v16091358
Ali MA, Caetano-Anollés G. AlphaFold2 Reveals Structural Patterns of Seasonal Haplotype Diversification in SARS-CoV-2 Nucleocapsid Protein Variants. Viruses. 2024; 16(9):1358. https://doi.org/10.3390/v16091358
Chicago/Turabian StyleAli, Muhammad Asif, and Gustavo Caetano-Anollés. 2024. "AlphaFold2 Reveals Structural Patterns of Seasonal Haplotype Diversification in SARS-CoV-2 Nucleocapsid Protein Variants" Viruses 16, no. 9: 1358. https://doi.org/10.3390/v16091358