The brain-specific S-100 protein is a mixture of two components, S-100a and S-100b, with a subunit composition of alpha beta or beta 2, respectively. S-100b, isolated by using hydroxylapatite chromatography in its final purification, is homogeneous by the criteria of gel electrophoresis in the absence and presence of sodium dodecyl sulfate (NaDodSO4) and ultracentrifuge studies. Molecular weight studies by both sedimentation equilibrium in 6 M guanidine hydrochloride and 15% NaDodSO4 gels indicated the subunit molecular weight to be 10 500, and since a molecular weight of 21 000 was obtained in native solvents, the protein exists as a dimer in benign medium. The two subunits are held together by noncovalent forces. The S-100b protein undergoes a conformational change upon binding calcium, as revealed by ultraviolet difference spectroscopy and circular dichroism (CD) studies in the aromatic and far-ultraviolet (UV) range. Far-UV CD studies indicated the apparent helical content drops from approximately 58 to 52% in the presence of Ca2+. The effect of K+ on the protein was antagonistic to Ca2+, and the proteins affinity for calcium was lowered by the presence of K+. The conformational state of the protein is very much dependent upon the metal ions (Ca2+, K+) present, suggesting that changing conformation may be the way S-100 responds to local changes in ionic parameters. Fluorescence studies indicate the presence of an abnormal tyrosine in the protein with the emission maximum centered between 327 and 330 nm when the protein is excited at 280 nm.