Insights into protease sequence similarities by comparing substrate sequences and phylogenetic dynamics.

Based on substrate sequences, we proposed a novel method for comparing sequence similarities among 68 proteases compiled from the MEROPS online database. The rank vector was defined based on the frequencies of amino acids at each site of the substrate, aiming to eliminate the different order variances of magnitude between proteases. Without any assumption on homology, a protease specificity tree is constructed with a striking clustering of proteases from different evolutionary origins and catalytic types. Compared with other methods, almost all the homologous proteases are clustered in small branches in our phylogenetic tree, and the proteases belonging to the same catalytic type are also clustered together, which may reflect the genetic relationship among the proteases. Meanwhile, certain proteases clustered together may play a similar role in key pathways categorized using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Consequently, this method can provide new insights into the shared similarities among proteases. This may inspire the design and development of targeted drugs that can specifically regulate protease activity.