The orientation of the thirteen polypeptides of rat-liver cytochrome c oxidase in the inner mitochondrial membrane was studied by proteolytic digestion of mitoplasts and sonicated particles. After separation by sodium dodecylsulfate gel electrophoresis proteins were transferred on nitrocellulose, and individual polypeptides were identified by incubation with polypeptide-specific antisera, followed by fluorescein-isothiocyanate-conjugated protein A.The three catalytic polypeptides 1-111 and seven nuclear coded polypeptides (IV, Vb, VIa, VIc, VIIa, VIIb and VIII) were found accessible to proteases from the cytoplasmic phase. Polypeptides 11, IV, Va, Vb and VIa were accessible from the matrix phase, indicating a transmembraneous orientation of polypeptides 11, IV, V b and VIa. Together with data on cross-linking and on cytochrome-c-protected labeling of polypeptides, a model of the cytochrome c oxidase complex was developed. It is suggested that the cytochrome c binding site on polypeptide I1 is surrounded by several nuclear-coded polypeptides, which may modulate the affinity of the enzyme towards cytochrome c.Cytochrome c oxidase represents the terminal electron carrier of the respiratory chain, and the third coupling site of mitochondria. The enzyme from mammalian tissues is composed out of thirteen different polypeptides which occur in stoichiometric (1 : 1) amounts (for review see [l, 21). The two heme a and the two copper ions were found associated with subunits I and I1 and the proton channel with subunit 111 [l -41. Therefore these polypeptides are denoted 'catalytic' subunits. They are encoded on mitochondrial DNA, whereas the other ten polypeptides are of nuclear origin. Since a definite function of nuclear-coded polypeptides is still lacking, they are suggested to have a regulatory role [I, 21. For an understanding of the mechanism and the regulation of electron transfer from cytochrome c to oxygen and of proton translocation through the membrane, the knowledge of the topological orientation of the various polypeptides is required. Previous results on the sidedness of polypeptides in yeast cytochrome c oxidase [S -71 can only be compared with the mammalian enzyme complex concerning the catalytic subunits, since this enzyme contains six (instead of ten) nuclearcoded polypeptides [8 -101.Topological studies on beef-heart cytochrome c oxidase were performed using an immunological [I 1,121 or a chemical labeling [13]. In these studies a complete separation of the ten nuclear-coded polypeptides, however, was not obtained.In the present study the orientation of the polypeptides of cytochrome c oxidase in the inner mitochondrial membrane towards the cytoplasm or the matrix was investigated by proteolytic digestion of mitoplasts and submitochondrial particles and subsequent analysis by immunoblotting with subunit-specific antisera. A complete separation of all thirteen polypeptides was obtained by application of a high resolution SDS-gel electrophoretic system [14]. It was found that in addition to the catalyti...