Identifying and profiling structural similarities between Spike of SARS-CoV-2 and other viral or host proteins with Machaon - Inria - Institut national de recherche en sciences et technologies du numérique Access content directly
Journal Articles Communications Biology Year : 2023

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 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 .

Keywords

Dates and versions

hal-04324248 , version 1 (05-12-2023)

Licence

Attribution

Identifiers

Cite

Panos Kakoulidis, Ioannis Vlachos, Dimitris Thanos, Gregory Blatch, Ioannis Emiris, et al.. Identifying and profiling structural similarities between Spike of SARS-CoV-2 and other viral or host proteins with Machaon. Communications Biology, 2023, 6 (1), pp.752. ⟨10.1038/s42003-023-05076-7⟩. ⟨hal-04324248⟩
18 View
0 Download

Altmetric

Share

Gmail Facebook X LinkedIn More