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Identifying and profiling structural similarities between Spike of SARS-CoV-2 and other viral or host proteins with Machaon

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, int...

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Autores principales: Kakoulidis, Panos, Vlachos, Ioannis S., Thanos, Dimitris, Blatch, Gregory L., Emiris, Ioannis Z., Anastasiadou, Ema
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10356814/
https://www.ncbi.nlm.nih.gov/pubmed/37468602
http://dx.doi.org/10.1038/s42003-023-05076-7
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author Kakoulidis, Panos
Vlachos, Ioannis S.
Thanos, Dimitris
Blatch, Gregory L.
Emiris, Ioannis Z.
Anastasiadou, Ema
author_facet Kakoulidis, Panos
Vlachos, Ioannis S.
Thanos, Dimitris
Blatch, Gregory L.
Emiris, Ioannis Z.
Anastasiadou, Ema
author_sort Kakoulidis, Panos
collection PubMed
description 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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spelling pubmed-103568142023-07-21 Identifying and profiling structural similarities between Spike of SARS-CoV-2 and other viral or host proteins with Machaon Kakoulidis, Panos Vlachos, Ioannis S. Thanos, Dimitris Blatch, Gregory L. Emiris, Ioannis Z. Anastasiadou, Ema Commun Biol Article 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. Nature Publishing Group UK 2023-07-19 /pmc/articles/PMC10356814/ /pubmed/37468602 http://dx.doi.org/10.1038/s42003-023-05076-7 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Kakoulidis, Panos
Vlachos, Ioannis S.
Thanos, Dimitris
Blatch, Gregory L.
Emiris, Ioannis Z.
Anastasiadou, Ema
Identifying and profiling structural similarities between Spike of SARS-CoV-2 and other viral or host proteins with Machaon
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
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10356814/
https://www.ncbi.nlm.nih.gov/pubmed/37468602
http://dx.doi.org/10.1038/s42003-023-05076-7
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