Human cysteine protease cathepsin L was inactivated at acid pH by a first-o
rder process. The inactivation rate decreased with increasing concentration
s of a small synthetic substrate, suggesting that substrates stabilize the
active conformation. The subs;rate-independent inactivation rate constant i
ncreased with organic solvent content of the buffer, consistent with intern
al hydrophobic interactions, disrupted by the organic solvent, also stabili
zing the enzyme. Circular dichroism showed that the inactivation is accompa
nied by large structural changes, a decrease in alpha-helix content being e
specially pronounced. The high activation energy of the reaction at pH 3.0
(200 kJ.mol(-1)) supported such a major conformational change occurring. Th
e acid inactivation of cathepsin L was irreversible, consistent with the pr
opeptide being needed for proper folding of the enzyme. Aspartic protease c
athepsin D was shown to cleave denatured, but not active cathepsin L, sugge
sting a potential mechanism for in vivo regulation and turnover of cathepsi
n L inside lysosomes.