Labeling of complex III, with [35S]diazobenzenesulfonate: orientation of this electron transfer segment in the mitochondrial inner membrane

[34S]Diazobenzenesulfonate has been used to tag the surface-exposed polypeptides of isolated complex III. All nine different component polypeptides were labeled, indicating that each is at least partially exposed on the surface of the isolated, detergent-dispersed complex. Labeling studies were also conducted on the membrane-bound complex. Preparations of intact mitochondria and submitochondrial particles were separately labeled with [35S]diazobenzenesulfonate in order to determine the distribution of the polypeptides of complex III between the outer (cytoplasmic) and inner (matrix) surfaces of the mitochondrial inner membrane, respectively. Polypeptides II and III were the only components labeled in a significant amount in submitochondrial particles (i.e., from the matrix side). Polypeptides III, IV, and VI were heavily labeled in mitochondria (i.e., from the cytoplasmic side). Polypeptides I,II, V, and VII were also labeled in mitochondria but to a much lesser extent. Polypeptides VIII and IX were not significantly labeled from either side of the membrane. The labeling data and information obtained from previous crosslinking studies [Smith, R.J. & Capaldi, R.A. (1977) Biochemistry 16, 2629-2633] are used to derive a picture of the arrangement of complex III in the mitochondrial inner membrane.