The nature of the chromophore binding site of light-adapted bacteriorhodopsin is analyzed by using modified neglect of differential overlap with partial single and double configuration interaction (MNDO- PSDCI) molecular orbital theory to interpret previously reported linear and nonlinear optical spectroscopic measurements. We conclude that in the absence of divalent metal cations in close interaction with Asp85 and Asp212, a positively charged amino acid must be present in the same vicinity. We find that models in which Arg82 is pointed upward into the chromophore binding site and directly stabilizes Asp85 and Asp212 are successful in rationalizing the observed one-photon and two-photon properties. We conclude further that a water molecule is strongly hydrogen bonded to the chromophore imine proton. The chromophore '1B(u)*+' and '1A(g)*-' states, despite extensive mixing, exhibit significantly different configurational character. The lowest-lying '1B(u)(*+' state is dominated by single excitations, whereas the second-excited '1A(g)*-' state is dominated by double excitations. We can rule out the possibility of a negatively charged binding site, because such a site would produce a lowest-lying 1A(g)*-' state, which is contrary to experimental observation. The possibility that Arg82 migrates toward the extracellular surface during the photocycle is examined.
Kusnetzow, A., Singh, D. L., Martin, C. H., Barani, I. J., & Birge, R. R. (1999). Nature of the chromophore binding site of bacteriorhodopsin: The potential role of Arg82 as a principal counterion. Biophysical Journal, 76(5), 2370–2389. https://doi.org/10.1016/S0006-3495(99)77394-7