Intersubunit linker cleavage increases conformational flexibility of all substrate-binding loops. Comparative differences in the H/D exchange profiles among cleaved caspase-6 maturation variants [(A) D23A D179A vs. D23A D179CT, (B) D23A D179A vs. ΔN D179CT, and (C) D23A D179CT vs. ΔN D179CT] at the indicated time points of exposure to deuterated solvent. These statistically significant differences in the H/D exchange among cleaved caspase-6 maturation variants [(D) D23A D179A vs. D23A D179CT, (E) D23A D179A vs. ΔN D179CT, and (F) D23A D179CT vs. ΔN D179CT]) after 2 h of incubation were mapped onto the model structure of caspase-6 shown in both ribbon and surface representations. The asterisk designates the D to A substitution at the indicated proteolytic cleavage site, rendering that site uncleavable. For these data, a deuterium uptake difference greater than 0.6 Da is considered significant at the 98% confidence interval. The intensities of the blue and red colors represent the peptides that undergo either a statistically significant decrease (less exchangeable/flexible) or increase (more exchangeable/flexible), respectively, in the H/D exchange along the path of caspase-6 proteolytic activation.