Metallothioneins are unique diamagnetic metal thiolate cluster proteins. Both vertebrate and invertebrate forms contain, besides their large cysteine content (30%), up to 14% lysine plus arginine. In the amino acid sequences, the basic residues are juxtaposed to cysteine residues and have been suggested to play a role in neutralizing the excess negative charge of the metal thiolate complexes [Kojima, Y., Berger, C., Vallee, B. L., & Kägi, J. H. R. (1976) Proc. Natl. Acad. Sci. U.S.A. 73, 3413-3417]. To document such a function, we compared the susceptibility of the lysine residues in cadmium and zinc metallothioneins and in the metal-free S-carboxamidomethyl derivative toward arylation by trinitrobenzenesulfonic acid. The results show an at least 20-fold lower initial rate of reaction with the metal-containing as opposed to that with the metal-free form, indicating a protective effect of metal complex formation on the lysine residues, the degree of protection being dependent on the nature of the metal. The modification of the lysine residues by trinitrobenzenesulfonic acid produces changes in the CD spectral features of the cadmium thiolate cluster structure. The lowered chemical reactivity of the lysine residues in the metal-containing form correlates with an upward displacement of their average pKa's to 10.9 from 10.3 in the metal-free S-carboxamidomethyl derivative. We attribute these effects at least in part to hydrogen bonding of the positively charged epsilon-amino groups to the thiolate ligands of the negatively charged cadmium thiolate units.