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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Vydáno v:	International journal of molecular sciences Ročník 26; číslo 8; s. 3674
Hlavní autoři:	Idrees, Sobia, Paudel, Keshav Raj, Banik, Mithila, Suwal, Newton, Thapa, Rajan, Bashyal, Saroj
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	Switzerland MDPI AG 13.04.2025 MDPI
Témata:	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
On-line přístup:	Získat plný text
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Shrnutí:	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.
Bibliografie:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23
ISSN:	1422-0067 1661-6596 1422-0067
DOI:	10.3390/ijms26083674