Identifying and profiling structural similarities between Spike of SARS-CoV-2 and other viral or host proteins with Machaon
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 an...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-07-01
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| Series: | Communications Biology |
| Online Access: | https://doi.org/10.1038/s42003-023-05076-7 |
| _version_ | 1797774048604717056 |
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| author | Panos Kakoulidis Ioannis S. Vlachos Dimitris Thanos Gregory L. Blatch Ioannis Z. Emiris Ema Anastasiadou |
| author_facet | Panos Kakoulidis Ioannis S. Vlachos Dimitris Thanos Gregory L. Blatch Ioannis Z. Emiris Ema Anastasiadou |
| author_sort | Panos Kakoulidis |
| collection | DOAJ |
| description | 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 . |
| first_indexed | 2024-03-12T22:15:16Z |
| format | Article |
| id | doaj.art-c13aa487e0dc4fb587ab2f65165d66ba |
| institution | Directory Open Access Journal |
| issn | 2399-3642 |
| language | English |
| last_indexed | 2024-03-12T22:15:16Z |
| publishDate | 2023-07-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Communications Biology |
| spelling | doaj.art-c13aa487e0dc4fb587ab2f65165d66ba2023-07-23T11:22:47ZengNature PortfolioCommunications Biology2399-36422023-07-016111610.1038/s42003-023-05076-7Identifying and profiling structural similarities between Spike of SARS-CoV-2 and other viral or host proteins with MachaonPanos Kakoulidis0Ioannis S. Vlachos1Dimitris Thanos2Gregory L. Blatch3Ioannis Z. Emiris4Ema Anastasiadou5Department of Informatics and Telecommunications, National and Kapodistrian University of AthensBroad Institute of MIT and HarvardBiomedical Research Foundation of the Academy of AthensBiomedical Biotechnology Research Unit, Department of Biochemistry and Microbiology, Rhodes UniversityDepartment of Informatics and Telecommunications, National and Kapodistrian University of AthensBiomedical Research Foundation of the Academy of AthensAbstract 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 .https://doi.org/10.1038/s42003-023-05076-7 |
| spellingShingle | Panos Kakoulidis Ioannis S. Vlachos Dimitris Thanos Gregory L. Blatch Ioannis Z. Emiris Ema Anastasiadou Identifying and profiling structural similarities between Spike of SARS-CoV-2 and other viral or host proteins with Machaon Communications Biology |
| title | Identifying and profiling structural similarities between Spike of SARS-CoV-2 and other viral or host proteins with Machaon |
| title_full | Identifying and profiling structural similarities between Spike of SARS-CoV-2 and other viral or host proteins with Machaon |
| title_fullStr | Identifying and profiling structural similarities between Spike of SARS-CoV-2 and other viral or host proteins with Machaon |
| title_full_unstemmed | Identifying and profiling structural similarities between Spike of SARS-CoV-2 and other viral or host proteins with Machaon |
| title_short | Identifying and profiling structural similarities between Spike of SARS-CoV-2 and other viral or host proteins with Machaon |
| title_sort | identifying and profiling structural similarities between spike of sars cov 2 and other viral or host proteins with machaon |
| url | https://doi.org/10.1038/s42003-023-05076-7 |
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