Immunological probes for bacteriorhodopsin. Identification of three distinct antigenic sites on the cytoplasmic...

We have prepared site-specific immunological reagents to study the orientation and surface topography of the integral membrane protein bacteriorhodopsin. Monoclonal and polyclonal antibodies with strong affinity for antigenic determinants on proteolytic and cyanogen bromide fragments of bacteriorhodopsin have been isolated and characterized. Three distinct antibody binding sites have been identified on the cytoplasmic surface of bacteriorhodopsin. The first due is readily accessible in native bacteriorhodopsin and lies close to the COOH terminus. This binding site is lost when only three amino acid residues are removed from the COOH terminus. The second site, which is also near the COOH terminus, is located approximately within the 17 COOH terminal amino acid residues. The third site is in the fragment that comprises Tyr-83 to Met-118 and is probably contained in the short loop connecting the third and fourth helices. The use of COOH terminus-specific antibodies in determination of the orientation of bacteriorhodopsin molecules in the Halobacterium halobium membrane confirms the earlier conclusion that the COOH terminus is on the cytoplasmic side.