Predicting Motif-Mediated Interactions Based on Viral Genomic Composition

Viruses manipulate host cellular machinery to propagate their life cycle, with one key strategy being the mimicry of short linear motifs (SLiMs) found in host proteins. While databases continue to expand with virus–host protein–protein interaction (vhPPI) data, accurately predicting viral mimicry re...

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Bibliographic Details
Published in:International journal of molecular sciences Vol. 26; no. 8; p. 3674
Main Authors: Idrees, Sobia, Paudel, Keshav Raj, Banik, Mithila, Suwal, Newton, Thapa, Rajan, Bashyal, Saroj
Format: Journal Article
Language:English
Published: Switzerland MDPI AG 13.04.2025
MDPI
Subjects:
Adaptation
Amino Acid Motifs
Antiviral agents
Cell cycle
Computational Biology - methods
Datasets
DNA Viruses - genetics
Genome, Viral
Genomes
Host-Pathogen Interactions - genetics
Human papillomavirus
Humans
Influenza
Mutation
Pathogenesis
Protein Interaction Domains and Motifs
Proteins
RNA Viruses - genetics
Viral Proteins - genetics
Viral Proteins - metabolism
Viruses
Viruses - genetics
Australia
viral mimicry
short linear motifs
virus–host interactions
bioinformatics
ISSN:1422-0067, 1661-6596, 1422-0067
Online Access:Get full text
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Summary:Viruses manipulate host cellular machinery to propagate their life cycle, with one key strategy being the mimicry of short linear motifs (SLiMs) found in host proteins. While databases continue to expand with virus–host protein–protein interaction (vhPPI) data, accurately predicting viral mimicry remains challenging due to the inherent degeneracy of SLiMs. In this study, we investigate how viral genomic composition influences motif mimicry and the mechanisms through which viruses hijack host cellular functions. We assessed domain–motif interaction (DMI) enrichment differences, and also predicted new DMIs based on known viral motifs with varying stringency levels, using SLiMEnrich v.1.5.1. Our findings reveal that dsDNA viruses capture significantly more known DMIs compared to other viral groups, with dsRNA viruses also exhibiting higher DMI enrichment than ssRNA viruses. Additionally, we identified new vhPPIs mediated via SLiMs, particularly within different viral genomic contexts. Understanding these interactions is vital for elucidating viral strategies to hijack host functions, which could inform the development of targeted antiviral therapies.
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ISSN:1422-0067
1661-6596
1422-0067
DOI:10.3390/ijms26083674