Identification of surface exposed amino acids of isolated and membrane-bound CF1 by protease accessibility

In order to compare surface-exposed amino acids in isolated and membrane-bound CF1 the technique of limited proteolysis was employed. The cleavage sites of several proteases were identified by sequence analysis of the resulting peptides after isolation by SDS-PAGE. In isolated CF1 the N-terminal region of the α subunit was found to be highy sensitive to proteases; the accessible peptide bonds included αE17-G18, αR21-E22, αE22-V23, and αK24-V25. Additional protease-attacked bonds in α subunit were αS86-S87, xαE125-S126. and αR127-L128. In the β subunit of isolated CF1 the bonds βL14-E15 and βV76-A77 were identified as being accessible. All identified protease accessible amino acids are located at the protein surface according to a molecular model of CF1 computed after the crystal structure of mitochondrial F1 by S. Engelbrecht (1997). In membrane bound CF1 the primarily accessible peptide bond of the N-terminal domain of α is αR21-E22. After this bond is cleaved by trypsin, the αK24-V25 becomes accessible to further trypsin attack. Moreover, the peptide bonds αR14O-S141 and αG16O-R161 are cleaved. According to the Engelbrecht model αG16O is almost completely shielded and actually this amino acid was hardly accessible to protease in isolated CF1. The β subunit in general is much more sensitive to proteolysis in membrane-bound than in solubilized CF1. In the β subunit of membrane-bound CF1 a papain-sensitive bond βG102-G103 was identified. The results indicate major structural alterations when CF1 is extracted from the CF0CF1 complex. Thiol modulation, i.e. reduction of the regulatory disulfide bond between γC199 and γC205 of y subunit, enhances the accesibility of a number of peptide bonds, in particular ααG160-R161, to proteolytic attack by papain. In contrast, thylakoid membrane energization results in masking of this peptide bond.