In Silico Analysis of the Effects of Omicron Spike Amino Acid Changes on the Interactions with Human Proteins
Abstract
:1. Introduction
2. Results
2.1. Predicted Impact of Omicron Variant on Spike–Antibodies Interfaces
2.2. Predicted Impact of Omicron Variant on Spike-ACE2 Interface
3. Discussion
4. Materials and Methods
4.1. Definition of the Set of Omicron Amino Acid Changes
4.2. Datasets Used for Structural Analyses
4.3. Modeling and Analysis of the Effects of Mutations Associated with the Spike Protein in the Omicron Variant
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Sample Availability
References
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Residue Position in the Spike Sequence | Number of Complexes with Loss of Interactions Involving the Residue | Number of Complexes with Gain of Interactions Involving the Residue | Number of Spike Chains Including the Residue in the Starting Dataset (Total Number of Spike Chains in the Dataset: 342) |
---|---|---|---|
145 | 6 | 2 | 69 |
212 | 1 | 1 | 204 |
339 | 0 | 8 | 321 |
371 | 3 | 14 | 318 |
373 | 4 | 4 | 319 |
375 | 2 | 11 | 321 |
417 | 44 | 24 | 322 |
440 | 5 | 15 | 321 |
446 | 3 | 13 | 258 |
477 | 0 | 28 | 270 |
478 | 17 | 6 | 270 |
484 | 42 | 5 | 279 |
493 | 42 | 46 | 321 |
496 | 1 | 38 | 321 |
498 | 22 | 18 | 310 |
501 | 6 | 45 | 307 |
505 | 48 | 27 | 323 |
Residues Involved in H-Bonds in the Spike-ACE2 Interface | Reference Spike-ACE2 Complex | Omicron Spike-ACE2 Complex | |||
---|---|---|---|---|---|
Spike Residue (in Parenthesis, the Replacement in Omicron Variant) | ACE2 Residue | 6LZG | 6M0J | 6LZG mut | 6M0J mut |
LYS 417 (ASN) | ASP 30 | + | + | ||
GLY 446 (SER) | GLN 42 | + | + (SER 446) | ||
TYR 449 | ASP 38 | + | + | + | |
TYR 449 | GLN 42 | + | + | + | |
ALA 475 | SER 19 | + | |||
ASN 487 | GLN 24 | + | + | ||
ASN 487 | TYR 83 | + | + | + | + |
GLN 493 (ARG) | GLU 35 | + | |||
GLY 496 (SER) | LYS 353 | + | + | ||
GLN 498 (ARG) | GLN 42 | + | |||
THR 500 | TYR 41 | + | + | + | + |
THR 500 | ASP 355 | + | |||
THR 500 | ARG 358 | + | |||
ASN 501 (TYR) | LYS 353 | + (TYR 500) | |||
GLY 502 | LYS 353 | + | + | + | + |
Total number of H-bonds | 10 | 10 | 3 | 9 |
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D’Arminio, N.; Giordano, D.; Scafuri, B.; Biancaniello, C.; Petrillo, M.; Facchiano, A.; Marabotti, A. In Silico Analysis of the Effects of Omicron Spike Amino Acid Changes on the Interactions with Human Proteins. Molecules 2022, 27, 4827. https://doi.org/10.3390/molecules27154827
D’Arminio N, Giordano D, Scafuri B, Biancaniello C, Petrillo M, Facchiano A, Marabotti A. In Silico Analysis of the Effects of Omicron Spike Amino Acid Changes on the Interactions with Human Proteins. Molecules. 2022; 27(15):4827. https://doi.org/10.3390/molecules27154827
Chicago/Turabian StyleD’Arminio, Nancy, Deborah Giordano, Bernardina Scafuri, Carmen Biancaniello, Mauro Petrillo, Angelo Facchiano, and Anna Marabotti. 2022. "In Silico Analysis of the Effects of Omicron Spike Amino Acid Changes on the Interactions with Human Proteins" Molecules 27, no. 15: 4827. https://doi.org/10.3390/molecules27154827