In Silico and In Vitro Evaluation of the Molecular Mimicry of the SARS-CoV-2 Spike Protein by Common Short Constituent Sequences (cSCSs) in the Human Proteome: Toward Safer Epitope Design for Vaccine Development
Abstract
:1. Introduction
2. Materials and Methods
2.1. Basic Bioinformatics
2.2. Functional Classification of cSCS-Containing Human Proteins
2.3. cSCSs in Human Proteins
2.4. Peptide Synthesis and Conjugation
2.5. Antibodies
2.6. ELISA (Enzyme-Linked Immunosorbent Assay)
2.7. Western Blot Analysis
3. Results
3.1. Rationales and Strategies
3.2. Informatical Characterization of Human Proteins Containing cSCSs
3.3. Molecular Characterization of the Human Proteins Containing cSCSs In Silico
3.4. ELISA for Anti-cSCS Antibodies
3.5. Western Blot Analysis
4. Discussion
4.1. High Occurrence of cSCSs Is Likely a Coincidence
4.2. Anti-Peptide 2 Antibody Is an Autoantibody
4.3. The Human Unc-80 Protein Is a Potential Target of an Autoantibody
4.4. Implications for Vaccine Development, Long COVID, Tolerance, and Memory
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Human Protein | cSCS(S1/S2) | Accessibility (Method I) * | Accessibility (Method II) * | ||
---|---|---|---|---|---|
Spike | Human Protein | Spike | Human Protein | ||
Ryanodine receptor 1 Ryanodine receptor 2 Ryanodine receptor 3 | TLLAL (S1) | 003XX | 00243 | 10110 | 10130 |
Protein unc-80 homolog | EPLVD (S1) | 20633 | XXXXX | 21102 | 44435 |
PLVDL (S1) | 06330 | XXXXX | 11020 | 44354 | |
LPDPS (S2) | 02388 | XXXXX | 02435 | 14544 | |
Teneurin-4 | GTTLD (S1) | 02513 | 30547 | 12214 | 12435 |
Neural adhesion molecule L1-like protein | PSKPS (S2) | 885X5 | 29543 | 35545 | 35312 |
IL-7 | KLNDL (S1) | 20250 | 74563 | 31242 | 45542 |
LNDLC (S1) | 02501 | 45630 | 12421 | 55420 | |
NDLCF (S1) | 25010 | 56303 | 24211 | 54202 | |
LVLLP (S1) | XXXXX | 31550 | 00001 | 00001 |
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Mizuno, Y.; Nakasone, W.; Nakamura, M.; Otaki, J.M. In Silico and In Vitro Evaluation of the Molecular Mimicry of the SARS-CoV-2 Spike Protein by Common Short Constituent Sequences (cSCSs) in the Human Proteome: Toward Safer Epitope Design for Vaccine Development. Vaccines 2024, 12, 539. https://doi.org/10.3390/vaccines12050539
Mizuno Y, Nakasone W, Nakamura M, Otaki JM. In Silico and In Vitro Evaluation of the Molecular Mimicry of the SARS-CoV-2 Spike Protein by Common Short Constituent Sequences (cSCSs) in the Human Proteome: Toward Safer Epitope Design for Vaccine Development. Vaccines. 2024; 12(5):539. https://doi.org/10.3390/vaccines12050539
Chicago/Turabian StyleMizuno, Yuya, Wataru Nakasone, Morikazu Nakamura, and Joji M. Otaki. 2024. "In Silico and In Vitro Evaluation of the Molecular Mimicry of the SARS-CoV-2 Spike Protein by Common Short Constituent Sequences (cSCSs) in the Human Proteome: Toward Safer Epitope Design for Vaccine Development" Vaccines 12, no. 5: 539. https://doi.org/10.3390/vaccines12050539