Two mutants of the cysteine proteinase inhibitor, stefin B, were prepared by ligating the aminoterminal region from cystatin C and kininogen, members of two other families of cystatin superfamily. The mutant proteins were expressed in Escherichia coli and purified to homogeneity. Inhibition and kinetic constants were determined for authentic and mutated stefins against the four different cysteine proteinases, papain and human cathepsins B, L and H. Inhibition of both amino-terminal elongated stefin B mutants was decreased particularly for cathepsin H.A model of the tertiary structure of cathepsin H and its complex with stefin B was constructed. The framework for the model of cathepsin H consisted of structurally conserved regions from tertiary structures of three cysteine proteinases. Variable regions were selected from fragments of other proteins from the protein data base. We suggest that reduced binding of stefins with elongated amino termini is caused by the mini chain of cathepsin H which is probably in close proximity to the amino termini in the complexes. This mini chain is bridged to Cys214 and has already been proposed to be responsible for the aminopeptidase activity of cathepsin H. We conclude that the amino-terminal region of stefin B plays an important role in determining the strength of inhibition of cathepsin H.Cells of animals and plants contain a variety of cysteine proteinases (CP) similar to papain [I]. Mammalian cysteine proteinases include the lysosomal enzymes cathepsins B, H, L, S and C. These enzymes differ from each other in many respects, such as their pH optima or substrate specificity [2]. Some of them are true endopeptidases, while others display exclusively or additional aminopeptidase (cathepsin H) 13, 41 or carboxypeptidase activity (cathepsin B) [2]. The involvement of CPs in different physiological processes is variable as well. Some cathepsins degrade primarily proteins of the cells themselves in the process of aulophagy, while others take part in the degradation of foreign proteins in processes such as antigen processing and presentation [S -71.The inhibition of cysteine proteinases by protein inhibitors is an important mechanism for regulation of their activity [8]. The number of different cystatins (protein inhibitors which inhibit cysteine proteinases) exceeds the number of target enzymes [9]. The superfamily of cystatins of mammalian origin is usually divided into three families ; stefins, cystatins and kininogens [9, 101. In other organisms, there are more inhibitors which can be classified into those three families or form new families with intermediate properties [11]. Up to now, several cystatins have been isolated from human Knowledge on the mechanism of inhibition of cystatins is based on the crystallographic studies, where the tertiary structures of chicken cystatin [21] and human stefin B [22] were determined as representatives of two families. The mode of interaction with cysteine proteinases was first predicted from computer docking 1211 which was later confirme...