Quantitative profiling of protease specificity
Fig 5
Comparative analysis of selectomes reveals divergent and conserved features in substrate recognition between MMP-2 and 9.
A. Venn diagram of substrate specificity overlap and distinction between the selectomes of MMP-2 and 9 shows significant selectivity between the two enzymes. Tetramer clusters comprising the selectomes of MMP-2 and 9 were grouped based on their occurrence in the individual and overlapping substrate sets and the corresponding numbers are shown in the Venn diagram. For making Venn diagram we used on-line service at: http://bioinformatics.psb.ugent.be/webtools/Venn/. B. Aggregate specificity profiles based on the unique and overlapping tetramer clusters of MMP-2 and 9 reveal the distribution of selectivity across the catalytic cleft. Hexamer peptides belonging to the tetramer clusters constituting the selective and common substrate sets of MMP-2 and 9 were aligned along P5-P3՛ positions based on the P3-P1՛ matches and the relative abundances of residues at each position were plotted as logos. MMP-2&9/2 denotes residue frequencies based on MMP-2 RP values, while MMP-2&9/9 denotes residue frequencies based on MMP-9 RP values.