Previous studies with site-specific mutants of bacteriorhodopsin have demonstrated that replacement of Asp-85 or Arg-82 affects the absorption spectrum. Between pH 5.5 and 7, the Asp-85 --Glu and Arg-82 -* Ala mutants exist in a pH-dependent equilibrium between purple (A..-550/540 nm) and blue (A..=x= 600/590 nm) forms of the pigment.Measurement of proton transport as a function of wavelength in reconstituted vesicles shows that proton-pumping activities for the above mutants reside exclusively in their respective purple species. For both mutants, formation of the blue form with decreasing pH is accompanied by loss of proton transport activity. The Asp-85 -* Asn mutant displays a blue chromophore (A.,. = 588 nm), is inactive in proton translocation from pH 5 to 7.5, and shows no transition to the purple form.In contrast, the Asp-212 -+ Asn mutant is purple (A.. 1 555 nm) and shows no transition to a blue chromophore with decreasing pH. The experiments suggest that (a) the pKa of the purple-to-blue transition is directly influenced by the pKa of the carboxylate at residue 85 and (it) the relative strengths of interaction between the protonated Schiff base, Asp-85, and Arg-82 make a major contribution to the regulation of color and function of bacteriorhodopsin.Structure-function studies with bacteriorhodopsin (bR) have shown that replacement of the membrane-buried residues has profound effects on steady-state proton pumping in reconstituted vesicles (1). Further insights into the specific role of the above aspartic residues in proton translocation have come from studies of the photocycles of bR mutants with the techniques of low-temperature and time-resolved spectroscopy (2-4). Measurements of lightinduced conductivity changes in mixed micelles have demonstrated that the Asp-96 -> Asn (D96N) mutation slows down the kinetics of proton uptake by about two orders of magnitude, without a significant effect on either the kinetics or the quantum yield of proton release (3). Optical spectroscopic experiments and photovoltage measurements with this mutant show that the rate of decay of the M intermediate of the photocycle and the associated charge movement are greatly slowed down (4, 5). These results show clearly that Asp-96 plays a key role in the proton uptake step of the photocycle. Similar studies with the mutants D85E and D85N have indicated a role for Asp-85 in proton release. Thus, replacement of Asp-85 with Asn results in complete loss of proton transport activity (1), and optical spectroscopic measurements detect no significant formation of an M-like intermediate except at high pH (6, 7). The D85E mutant was shown to be partially active in proton translocation, with increased formation of an M-like photointermediate at higher pH values (7). Fourier-transform IR spectroscopy experiments suggest that Asp-85 serves as a proton acceptor in the early phase of the photocycle (2). In related studies, slower photocycles and lower quantum yields have been observed for mutants in which Asp-115 and Asp-212 are ...