Cleavage Site Prediction for Activation of Avian Cathelicidin Peptides

Abstract

The innate immune systems of multicellular organisms contain host defense peptides that, through varied mechanisms, help defend against viruses. Cathelicidins, a class of host defense peptides, have a signal, a cathelin, and a C-terminal active domain. The cathelin domain is highly conserved, while the active domain varies greatly. We anticipate that better understanding how animals’ innate immune systems fight viruses will provide insights into new therapeutics. Birds, in particular, are associated with potential viral pathogens. As the number of sequenced avian cathelicidin peptides increases, we hypothesized that through bioinformatics we can predict the active peptide domain of sequenced avian cathelicidin precursor proteins. We compiled 61 avian cathelicidin candidate sequences from the NCBI database and an additional 18 from Uniprot, and we used multiple sequence alignment to establish a consensus sequence. The middle region of the sequences displayed high levels of consensus, while near the C-terminal region displayed much greater sequence variation. The sequences were submitted for analysis by the DRAMP antimicrobial peptide database, which identified likely active regions in 6 of 79 sequences submitted. The alignment of 5 of the 6 sequences suggests a conserved cleavage site in their precursor proteins. This predicted cleavage site was applied to the remaining 73 precursor candidates to identify their mature cathelicidin sequences. Analysis of these sequences with CAMP R3 predicted the majority to be antimicrobial.