A rapid separation method for bovine brain S100 alpha alpha, S100a, and S100b protein using fast protein liquid chromatography on a Mono Q column and its application in preparation of a large amount of S100 alpha alpha protein are described. The conformation of S100 alpha alpha in the metal-free forms as well as in the presence of calcium were studied by UV absorption, circular dichroism, intrinsic fluorescence, sulfhydryl reactivity, and interaction with a hydrophobic fluorescent probe. The alpha-subunit appears to have nearly identical conformation in S100 alpha alpha and S100a protein dimers. We also confirmed that only the alpha-subunit exposes hydrophobic domains to solvent in the presence of calcium and that cysteine residues exposed upon Ca2+ binding to S100 proteins correspond to Cys 85 alpha and Cys 84 beta. Incubation of S100a with calcium and KCl proved that calcium binding to the putative calcium-binding sites (site I alpha, I beta) triggers a time- and temperature-dependent conformational change in the protein structure which decreases the antagonistic effect of KCl on calcium binding to sites II alpha and II beta and provokes subunit exchanges between protein dimers and the emergence of S100 alpha alpha and S100b (beta beta) proteins. Dynamic fluorescence measurements showed that incubating calcium at high S100a protein concentrations (greater than 10(-5) M) induces an apparent slow dimer-monomer equilibrium which might result in total subunit dissociation at lower protein concentrations. The effect of acidic pH on subunit dissociation in S100a protein (Morero, R. D., and Weber, G. (1982) Biochim. Biophys. Acta 703, 231-240) arises from conformational changes in the protein structure that are similar to those induced by Ca2+ incubation.