The Spike Protein of SARS-CoV-2 Is Adapting Because of Selective Pressures
Abstract
:1. Introduction
2. Data Sources
3. Materials and Methods
3.1. Neutral Evolution Test
3.2. Structural Analysis
4. Results
5. Discussion
6. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Reference | Alpha | Beta | Gamma | Delta | Omicron | ||||||
---|---|---|---|---|---|---|---|---|---|---|---|
339 | G | D | + | ||||||||
371 | S | L | - | ||||||||
373 | S | P | - | ||||||||
375 | S | F | + | ||||||||
417 | K | N | + | T | + | N | + | ||||
440 | N | K | + | ||||||||
446 | G | S | - | ||||||||
452 | L | R | - | ||||||||
477 | S | N | + | ||||||||
478 | T | K | + | K | + | ||||||
484 | E | K | + | K | + | A | / | ||||
490 | F | ||||||||||
493 | Q | R | - | ||||||||
496 | G | S | - | ||||||||
498 | Q | R | - | ||||||||
501 | N | Y | + | Y | + | Y | + | Y | + | ||
505 | T | Y | + | Y | + | Y | + | H | - | ||
547 | T | K | + | ||||||||
570 | A | D | + | ||||||||
614 | D | G | - | G | - | G | - | G | - | G | - |
655 | H | Y | + | Y | + | ||||||
677 | Q | ||||||||||
679 | N | K | + | ||||||||
681 | P | H | - | R | - | H | - |
Reference | Alpha | Beta | Gamma | Delta | Omicron | |||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
417 | K | 4 | K | 1 | K | 3 | ||||||
446 | G | 1 | ||||||||||
449 | Y | 6 | Y | 5 | Y | 2 | ||||||
453 | Y | 1 | Y | 3 | Y | 1 | Y | 3 | Y | 3 | ||
455 | L | 2 | L | 3 | L | 4 | L | 2 | ||||
456 | F | 5 | F | 4 | F | 8 | F | 5 | F | 2 | F | 3 |
473 | Y | Y | 1 | Y | 1 | |||||||
475 | A | 2 | A | 2 | A | 1 | A | 1 | A | 1 | A | 2 |
476 | G | G | 1 | G | 1 | |||||||
486 | F | 9 | F | 5 | F | 8 | F | 6 | F | 5 | F | 7 |
487 | N | 3 | N | 7 | N | 5 | N | 2 | N | 6 | N | 4 |
489 | Y | 4 | Y | 4 | Y | 5 | Y | 5 | Y | 4 | Y | 6 |
493 | Q | 2 | Q | 13 | Q | 6 | Q | 2 | Q | 3 | R | 7 |
494 | S | S | 2 | S | 2 | S | 2 | |||||
496 | G | 1 | G | 2 | S | 2 | ||||||
498 | Q | 7 | Q | 3 | Q | 3 | Q | 4 | Q | 2 | R | 4 |
500 | T | 9 | T | 8 | T | 8 | T | 10 | T | 7 | T | 6 |
501 | N | 1 | Y | 12 | N | 5 | Y | 14 | N | 9 | Y | 14 |
502 | G | 5 | G | 5 | G | 1 | G | 2 | G | 4 | G | 6 |
503 | V | V | 1 | |||||||||
505 | Y | 12 | Y | 10 | T | 13 | Y | 16 | Y | 20 | H | 13 |
SARS-CoV-2 | Alpha | Beta | Gamma | Delta | Omicron | |
---|---|---|---|---|---|---|
Hydrogen bonds | 10 | 8 | 2 | 6 | 12 | 13 |
Hydrophobic contacts | 18 | 11 | 21 | 16 | 10 | 12 |
Contacts | 74 | 77 | 72 | 72 | 80 | 82 |
Mean distance (Å) | 3.563 | 3.572 | 3.414 | 3.569 | 3.492 | 3.557 |
Number of residues | 17 | 14 | 16 | 13 | 17 | 16 |
RMSD (Ǻ) | TM Score | |
---|---|---|
Alpha | 0.55 | 0.99 |
Beta | 0.74 | 0.98 |
Gamma | 0.54 | 0.99 |
Delta | 0.55 | 0.99 |
Omicron | 1.11 | 0.97 |
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López-Cortés, G.I.; Palacios-Pérez, M.; Veledíaz, H.F.; Hernández-Aguilar, M.; López-Hernández, G.R.; Zamudio, G.S.; José, M.V. The Spike Protein of SARS-CoV-2 Is Adapting Because of Selective Pressures. Vaccines 2022, 10, 864. https://doi.org/10.3390/vaccines10060864
López-Cortés GI, Palacios-Pérez M, Veledíaz HF, Hernández-Aguilar M, López-Hernández GR, Zamudio GS, José MV. The Spike Protein of SARS-CoV-2 Is Adapting Because of Selective Pressures. Vaccines. 2022; 10(6):864. https://doi.org/10.3390/vaccines10060864
Chicago/Turabian StyleLópez-Cortés, Georgina I., Miryam Palacios-Pérez, Hannya F. Veledíaz, Margarita Hernández-Aguilar, Gerardo R. López-Hernández, Gabriel S. Zamudio, and Marco V. José. 2022. "The Spike Protein of SARS-CoV-2 Is Adapting Because of Selective Pressures" Vaccines 10, no. 6: 864. https://doi.org/10.3390/vaccines10060864