Two deletion variants of chicken cystatin were produced after cassette mutagenesis of the recombinant Arg-Glu-Phe-[Metl, Ile29, Leu891-chicken egg white cystatin gene in Escherichia coli. The variant des-Serl -Proll-[Alal2, Glu13, Phel4, Metl5, Ile29, Leu891-chicken cystatin (N-del 2) and the variant Arg-Glu-Phe-[Metl, Ile291-des-Cys71 -Met89-chicken cystatin (del-helix 11) were purified and characterized by inibition kinetics, far-ultraviolet-CD and fluorescence spectroscopy, and their folding in guanidine hydrochloride (Gdn/HCl) was studied. The del-helix I1 variant, shortened by 19 amino acids, is a basic, stefin-like mini-cystatin with one disulfide bridge. Its inhibitory properties are identical to chicken cystatin and its stability against Gdn/HCl is similar. The folding of the del-helix I1 variant corresponds best to a single step process. In contrast to this, the reversible folding of natural and recombinant chicken cystatin is more complex when recorded by either tryptophan fluorescence or far-ultraviolet-CD. With increasing GddHC1 concentration, a stabilization of secondary-structural elements is initially observed, followed by unfolding with minor but distinct intermediate states. The N-del 2 variant has a neutral PI and shows folding behaviour very similar to natural and recombinant chicken cystatin. However its inhibition constants with papain, actinidin and cathepsin B and L are 1000-100000-fold higher than those obtained with natural and recombinant chicken cystatin.Chicken cystatin is a small protein inhibitor (116 amino acids) of cysteine proteinases [l, 21 and the best studied member of the cystatin superfamily [3,4]. It has been shown that this molecule is a reversible, tight-binding inhibitor of papain-like enzymes [5-81. A model for the interaction of papain with chicken cystatin was derived from X-ray crystallography of a N-terminally truncated chicken cystatin [91 and from kinetic studies [6, 71. Recently, the solution structures of natural phosphorylated chicken cystatin and of a recombinant variant, Arg-GluPhe-[Metl, Ile29, Leu891-chicken cystatin, were solved by