We have previously studied the unfolding equilibrium of bacterio-opsin in a single phase solvent, using Förster mechanism fluorescence resonance energy transfer (FRET) as a probe, from tryptophan donors to a dansyl acceptor. We observed an apparent unfolding transition in bacterio-opsin perturbed by increasing ethanol concentrations [Nannepaga et al.(2004) Biochemistry 43, 50-59]. We have further investigated this transition and find the unfolding is pH-dependent. We have now measured the apparent pK of acid-induced unfolding of bacterio-opsin in 90% ethanol. When the acceptor is on helix B (Lys 41), the apparent pK for unfolding is 4.75; on the EF connecting loop (Cys 163), 5.15; and on helix G (Cys 222), 5.75. Five-helix proteolytic fragments are less stable. The apparent unfolding pKs are, for residues 72-248 (Cys 163), 5.46; and 1-166 (Lys 41), 7.36. When interpreted in terms of a simple equilibrium model for unfolding, the apparent pKs give relative free energies of unfolding, in the range of −0.54 to −3.5 kcal/mol. The results suggest that the C-terminal helix of bacterio-opsin is less stably folded than the N-terminal helices. We analyzed the pair-wise helixhelix interaction surfaces of bacteriorhodopsin and three other 7-transmembrane helix proteins, based on crystal structures. The results show that the interaction surfaces are smoother and the helix axis separations are closer in the amino-terminal two-thirds of the proteins compared with the carboxyl terminal one-third. However, the F helix is important in stabilizing the folded structure, as shown by the instability of the 1-166 fragment. Considering the high resolution crystal structure of bacteriorhodopsin, there are no obvious helix-helix interactions involving protein side chains which would be destabilized by protonation at the estimated pH of the unfolding transitions. However, a number of helix-bridging water molecules could become protonated, thereby weakening the helixhelix interactions.In comparison with water-soluble proteins, integral membrane protein folding mechanisms are poorly understood. Results of several folding studies, both in vivo (1) and in vitro (2-6), have been published on membrane proteins containing transmembrane helices. In some in vitro experiments, the membrane proteins were solubilized in detergent micelles, and unfolding was induced by an anionic amphiphile perturbant, docecyl sulfate. In order to obtain free energies of unfolding, it is necessary to assume that the free energy changes are linear with perturbant concentration (7). Due to non-ideal mixing when charged amphiphiles are added to neutral micelles, the assumption of linearity does not necessarily hold (8). An alternative approach would be to examine unfolding in a single phase solvent system. We have been studying the † Supported by a grant from the National Institutes of Health (GM 08194) *To whom to address correspondence at Dept. unfolding equilibrium of bacterio-opsin (BO) 1 in ethanol/water mixtures. We found an apparent unfolding transition in...