Mining the Common Peptide Sequences between Virus and Host

Peptides are short chains of amino acids linked by peptide bonds. One important application for synthesized peptides is to serve as antibodies to react to the protein of interest, which are broadly utilized in detecting viral pathogens in clinical laboratories. Recently scientists are aware of common peptides between proteins (called molecular mimicry in recent literatures) causing unexpected molecular interactions. Not only common peptides (as short as 6-aa long) found between two viral proteins could be responsible for false-positive result in clinical diagnosis, such molecular mimicry could also be responsible for cross-reactivity in molecular interactions that are totally unexpected. In particular, some bacteria or viruses are reported to have short common peptides with respect to their host proteins. Such common peptides could show impacts on various molecular interactions such as therapeutic vaccination, etc. In this project, we will develop a sequence analysis platform to reveal common peptides and share the findings with our laboratory collaborators through a web-based database application. We begin with emerging viruses that are commonly seen in Taiwan – the influenza viruses and enteroviruses, attempting to document common peptides for each of the two viruses versus human proteome. Not only we have been fully investigating these two viruses for past decades so we know much better their molecular and epidemiological characteristics, we have long-term collaboration with the Clinical Virology Laboratory at Chang Gung Memorial Hospital, which offers us opportunity to experimentally justify any found common peptides for clinical relevance. Inclusion of other pathogenic organisms or hosts could easily follow after we prototyped the system with at least the two mentioned emerging viruses. The platform will include an efficient search engine we term Common Peptide Explorer (CPE) to catalog common peptides between two pairs of organisms – influenza virus vs human, and enterovirus vs human. A database system Common Peptide DataBase (CPDB) will also be developed to host the found common peptides and allows users to query them. We expect the findings will provide insights into basic molecular virology, especially the interactions between virus and host at the peptide level.

Project ID:PB10703-1491
External Project ID:MOST106-2221-E182-066