Topographical organization of cytochrome b in the yeast mitochondrial membrane determined by fluorescence studies with N-cyclohexyl-N'-[4-(dimethylamino)naphthyl]carbodiimide.

In previous studies, we reported that dicyclohexylcarbodiimide (DCCD) inhibited proton translocation in the cytochrome bc1 complex from yeast mitochondria and was bound selectively to cytochrome b. Extensive trypsin digestion of [14C]DCCD-labeled cytochrome b isolated from a cytochrome bc1 complex treated with DCCD yielded a single radiolabeled 7.0 kDa peptide with the N-terminus VTLWNVG, indicating that trypsin cleavage had occurred at arginines-110 and -178. This segment of cytochrome b contains one acidic residue, aspartate-160, localized in amphiphilic, non-membrane-spanning, helix cd. To explore the environment of amphiphilic helix cd, we employed a fluorescent derivative of DCCD, N-cyclohexyl-N'-[4-(dimethylamino)naphthyl]carbodiimide (NCD-4). After incubation of NCD-4 with a cytochrome bc1 complex isolated from yeast mitochondria, a fluorescent compound was formed with a 340 nm excitation peak and a 441 nm emission peak. NCD-4 was selectively bound to cytochrome b and inhibited proton translocation with only a minimal inhibitory effect on electron transfer in the cytochrome bc1 complex reconstituted into proteoliposomes. Competition experiments and trypsin digestion of NCD-4-labeled cytochrome b indicated that NCD-4 and DCCD were bound to the same site on cytochrome b. The fluorescence of NCD-4 bound to the cytochrome bc1 complex was quenched equally by CAT-16, an amphiphilic spin-label that intercalates at the membrane surface, and 5-doxylstearic acid, a nitroxide derivative of stearic acid, and to a lesser extent by 7-doxylstearic and 12-doxylstearic acids.(ABSTRACT TRUNCATED AT 250 WORDS)