The alpha 1/2 helical backbone of the prodomains defines the intrinsic inhibitory specificity in the cathepsin L-like cysteine protease subfamily

Proregions of papain-like cysteine proteases are potent and often highly se lective inhibitors of their parental enzymes. The molecular basis of their selectivity is poorly understood. For two closely related members of the ca thepsin L-like subfamily we established strong selectivity differences. The propeptide of cathepsin S was observed to inhibit cathepsin L with a K-i o f 0.08 nM, yet cathepsin L propeptide inhibited cathepsin S only poorly. To identify the respective structural correlates we engineered chimeric prope ptides and compared their inhibitory specificity with the wild-types. Speci ficity resided in the N-terminal part, strongly suggesting that the backbon e of the prodomain was the underlying structure. (C) 2000 Federation of Eur opean Biochemical Societies.