Metal ions are essential to the structure and physiological functions of ba
cteriorhodopsin. Experimental evidence suggests the existence of specific c
ation binding to the negatively charged groups of Asp85 and Asp212 via an e
lectrostatic interaction. However, only using electrostatic force is not en
ough to explain the role of the metal cations because the carboxylate of As
p85 is well known to be protonated in the M intermediate. Considering the p
resence of some aromatic amino acid residues in the vicinity of the retinal
pocket, the existence of cation-pi interactions between the metal cation a
nd aromatic amino acid residues is suggested. Obviously, introduction of th
is kind of interaction is conducive to understanding the effects of the met
al cations and aromatic amino acid residues inside the protein on the struc
tural stability and proton pumping of bacteriorhodopsin.