Myelin basic protein, purified from bovine spinal cord, is cleaved by a purified bovine brain acid proteinase to yield three peptide fragments which were purified by gel filtration procedures combined with preparative gel electrophoresis. The purity of the fragments was established by end group analysis, amino acid analysis, polyacrylamide disc gel electrophoresis, and by their encephalitogenic activity. Chemical and biological characterization shows that one'peptide, (peptide 11), originates from the N-terminal end of the basic protein and contains residues 1-43; a second peptide, (peptide I), contains residues 44-89 and a third peptide (peptide III), originates from the C-terminal region with an N-terminal phenylalanine, residue 90, through arginine, residue 170, of the basic protein. The combined amino acid composition of the three fragments account for the amino acid content of the basic protein. The structure of the three peptides demonstrates that the purified brain acid proteinase selectively cleaves the two phenylalanine-phenylalanine linkages formed between residues 43-44 and 89-90 of the basic protein molecule. This study shows that cathepsin D could be the endogenous enzyme responsible for the breakdown of basic protein to form smaller encephalitogenic fragments, some of which are known to be present in crude tissue extracts.It was established in previous studies that most myelin protein components are subject to turnover [l]. Basic protein of myelin is of particular interest because it is known to induce an autoimmune disease associated with demyelination, experimental allergic encephalomyelitis. Previously, Einstein et af. [2] showed that basic protein can be cleaved by acid proteinase to form smaller encephalitogenic fragments, but the composition of these, and the nature of the susceptible bonds cleaved, have never been established. Indeed, early studies on the isolation and structure of basic protein were accompanied by autolysis during extraction, leading to the fortuitous isolation of polypeptide fragments, some of which were encephalitogenic in a particular species [3-51. Therefore, it is of some interest to establish the exact mechanism of basic protein breakdown using a known intracellular enzyme, since this may have some bearing on demyelinating processes in experimental disease and, in addition, provide some insight into the general mechanism of protein turnover in brain. A limited and specific degradation of basic protein could lead to the production of smaller (diffusible) peptides capable of interaction at the immunological sites related to autoimmune phenomena. The present work was designed to determine the nature of the peptide bonds split by the action of brain cathepsin D, as well as the structure and biological activity of the resultant peptides based on the known structure of bovine basic protein [6]. In other tissues, Coffey and de Duve [7] showed that catheptic activity of lysosomes appear to play a rate-limiting role in the pathways of protein breakdown. Thus, studies on the...