Visual and archaeal rhodopsins: similarities, differences and controversy.

Rhodopsins are currently known to belong to two distinct protein families. The visual rhodopsins, found in eyes throughout the animal kingdom, are photosensory pigments. Archaeal rhodopsins, found in extreme halophiles, function as light-driven proton pumps (bacteriorhodopsins), chloride ion pumps (halorhodopsins), or photosensory receptors (sensory rhodopsins). Light absorption by rhodopsins triggers their characteristic photoconversion extending into the (milli)second time range. There are three main paradigms of rhodopsins photoconversion. (1) Initiation of the trans-cis isomerization is the very primary consequence of light absorption. (2) Rhodopsins store light energy via the charge-separation mechanism (the charge of Schiff base is separated from its counterion). (3) Full trans-cis isomerization of the chromophore is a prerequisite for the full biological activity of rhodopsins. These paradigms will be questioned.