Identifying and profiling structural similarities between Spike of SARS-CoV-2 and other viral or host proteins with Machaon
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Abstract
Using protein structure to predict function, interactions, and evolutionary history is still an open challenge, with existing approaches relying extensively on protein homology and families. Here, we present Machaon, a data-driven method combining orientation invariant metrics on phi-psi angles, inter-residue contacts and surface complexity. It can be readily applied on whole structures or segments—such as domains and binding sites. Machaon was applied on SARS-CoV-2 Spike monomers of native, Delta and Omicron variants and identified correlations with a wide range of viral proteins from close to distant taxonomy ranks, as well as host proteins, such as ACE2 receptor. Machaon’s meta-analysis of the results highlights structural, chemical and transcriptional similarities between the Spike monomer and human proteins, indicating a multi-level viral mimicry. This extended analysis also revealed relationships of the Spike protein with biological processes such as ubiquitination and angiogenesis and highlighted different patterns in virus attachment among the studied variants. Available at: https://machaonweb.com .
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Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764 · see citing works
Evolutionary-scale prediction of atomic level protein structure with a language model
Lin, Z., Akin, H., Rao, R., Hie, B., Zhu, Z., Lu, W., Smetanin, N., Verkuil, R., Kabeli, O., Shmueli, Y., et al. (2022) · doi:10.1101/2022.07.20.500902 · Cited by 5,523 · see citing works
Highly accurate protein structure prediction for the human proteome
Tunyasuvunakool, K., Adler, J., Wu, Z., Green, T., Zielinski, M., Žídek, A., Bridgland, A., Cowie, A., Meyer, C., Laydon, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03828-1 · Cited by 3,025 · cited 1× · see citing works
“Our proposed method could be used with predicted data, such as the Human Proteome data from AlphaFold DB 66 or the meta-genomic proteins from ESM Metagenomics Atlas 67 and decipher previously unknown relationships.”
Qi, F., Qian, S., Zhang, S., & Zhang, Z. (2020) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2020.03.044 · Cited by 905 · see citing works
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- Authors
- Kakoulidis, P., Vlachos, I. S., Thanos, D., Blatch, G. L., Emiris, I. Z., & Anastasiadou, E.
- Affiliations
- National and Kapodistrian University of Athens (GR)
- Broad Institute (US)
- Biomedical Research Foundation of the Academy of Athens (GR)
- Higher Colleges of Technology (AE)
- Corresponding author
- Anastasiadou, Ema
- ORCID
- Venue
- Communications Biology
- Published
- 2023-07-19
- Volume
- 6
- Issue
- 1
- Pages
- 752-752
- ISSN
- 2399-3642 (ISSN-L)
- PMC
- PMC10356814
- OpenAlex
- W4384819512
- Cited by
- 4
- References
- 4
- Citations by year
- 2026: 1 · 2025: 1 · 2024: 2
- FWCI
- 0.19
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Communications Biology (publishedVersion, cc-by)
- Research Square (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Victoria University Research Repository (Victoria University) (submittedVersion, cc-by)
- ResearchOnline@ND (The University of Notre Dame) (submittedVersion)
- HAL (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- European Commission (5002780)
- General Secretariat for Research and Technology (5002780)
- European Regional Development Fund (MIS: 5002780)
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Keywords
- SARS-CoV-2 spike protein, structural similarity, viral mimicry, host proteins, ACE2 receptor, Omicron variant, Delta variant, inter-residue contacts, surface complexity, viral attachment, ubiquitination, angiogenesis
- MeSH terms
- COVID-19, SARS-CoV-2, Binding Sites, Humans, Receptors, Virus
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