Labeling of integral proteins with 3-(trifluoromethyl)-3-(m-[125I]iodophenyl)diazirine ([125I]TID) was shown previously [Hoppe, J., Brunner, J., & Jorgensen, B. B. (1984) Biochemistry 23, 5610-5616] to be affected strongly by interactions among membrane-embedded polypeptide segments. This study describes a detailed analysis of the [125I]TID-label distribution pattern among individual amino acids in a membranous segment of bacteriorhodopsin (bR) following itş labeling in purple membrane. The segment analyzed (residues 84-99 in the bR amino acid sequence) is predominantly hydrophobic and has been suggested to be part of the third transmembrane a-helix in the bR polypeptide chain. Within this segment eight residues were identified to be labeled by [125I]TID. Their distribution along the polypeptide chain is consistent with the idea that in the native protein this segment forms a helix whose cylindrical envelope is accessible to the labeling reagent from one face only. Thus, the labeling pattern suggests a possible correlation between lipid contact of individual residues and their labeling by [I25I]TID. The finding that [125I]TID labeling occurred at the less polar half of the helix surface (assuming 3.6 residues per turn of the coil) is further consistent with the view that bR is an "inside-out" protein with the majority of polar and charged residues facing the interior of the molecule and nonpolar residues exposed to the lipid bilayer [Engelman, D. M., & Zaccai, G. (1980) Proc. Natl. Acad. Sci. US.A. 77, 5894-5898].
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