Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

Short Linear Motifs in the Spike Protein of Sars-Cov-2 Variants Provide Clues Into Immune Hijack and Evasion Mechanisms of Omicron Variant

Anjana Soorajkumar
,
Ebrahim Alakraf
,
Mohammed Uddin
ORCID logo ,
Stefan S Du Plessis
ORCID logo ,
Alawi Alsheikh-Ali
ORCID logo ,
Richard K. Kandasamy
* ORCID logo
Version 1 : Received: 16 June 2022 / Approved: 17 June 2022 / Online: 17 June 2022 (13:49:02 CEST)

A peer-reviewed article of this Preprint also exists.

Soorajkumar, A.; Alakraf, E.; Uddin, M.; Du Plessis, S.S.; Alsheikh-Ali, A.; Kandasamy, R.K. Computational Analysis of Short Linear Motifs in the Spike Protein of SARS-CoV-2 Variants Provides Possible Clues into the Immune Hijack and Evasion Mechanisms of Omicron Variant. Int. J. Mol. Sci. 2022, 23, 8822. Soorajkumar, A.; Alakraf, E.; Uddin, M.; Du Plessis, S.S.; Alsheikh-Ali, A.; Kandasamy, R.K. Computational Analysis of Short Linear Motifs in the Spike Protein of SARS-CoV-2 Variants Provides Possible Clues into the Immune Hijack and Evasion Mechanisms of Omicron Variant. Int. J. Mol. Sci. 2022, 23, 8822.

DOI: 10.3390/ijms23158822

Abstract

Short Linear Motifs (SLiMs) are short linear sequences that can mediate protein-protein interaction. Mimicking eukaryotic SLiMs to compete with extra or intracellular binding partners or to sequester host proteins is the crucial strategy of viruses to pervert the host system. The evolved proteins in viruses facilitate minimal protein-protein interactions that significantly affect intracellular signaling networks. Unfortunately, very little information about the SARS-CoV-2 SLiMs is known, especially across the SARS-CoV-2 variants. Through ELM database-based sequence analysis of spike protein from all the major SARS-CoV-2 variants, we identified four overriding SLiMs in the SARS-CoV-2 Omicron variant including LIG_TRFH_1, LIG_REV1ctd_RIR_1, LIG_CaM_NSCaTE_8, and MOD_LATS_1. These SLiMs are highly likely to interfere with various immune functions, interact with host intracellular proteins, regulate cellular pathways, and lubricate viral infection and transmission. These cellular interactions possibly serve as potential therapeutic targets for these variants, and this approach can be further exploited to combat emerging SARS-CoV-2 variants.

Keywords

coronaviruses; SARS-CoV-2; variant; Omicron; SLiMs; spike protein; motifs; covid-19

Subject

LIFE SCIENCES, Immunology

Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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