Insights into the Protein Functions and Absorption Wavelengths of Microbial Rhodopsins

Using
a quantum mechanical/molecular mechanical approach, the absorption
wavelength of the retinal Schiff base was calculated based on 13 microbial
rhodopsin crystal structures. The results showed that the protein
electrostatic environment decreases the absorption wavelength significantly
in the cation-conducting rhodopsin but only slightly in the sensory
rhodopsin. Among the microbial rhodopsins with different functions,
the differences in the absorption wavelengths are caused by differences
in the arrangement of the charged residues at the retinal Schiff base
binding moiety, namely, one or two counterions at the three common
positions. Among the microbial rhodopsins with similar functions,
the differences in the polar residues at the retinal Schiff base binding
site are responsible for the differences in the absorption wavelengths.
Counterions contribute to an absorption wavelength shift of 50–120
nm, whereas polar groups contribute to a shift of up to ∼10
nm. It seems likely that protein function is directly associated with
the absorption wavelength in microbial rhodopsins.