Archaerhodopsins are active transporters, using the energy from sunlight to pump H ions out of the cell to generate a proton motive force that is used for ATP synthesis. Removal of the retinal cofactor (e.g. by treatment with hydroxylamine) abolishes the transporter function and dramatically alters the absorption spectra of the proteins. The proton pumping ability of AR3 has been demonstrated in recombinant E. coli cells and of AR4 in liposomes.
In the resting or ground state of archaerhodopsin, the bound retinal is in the all-trans form, but on absorption of a photon of light, it isomerizes to 13-cis. The protein surrounding the chromophore reacts to the change of shape and undergoes an ordered sequence of conformational changes, which are collectively known as the photocycle. These changes alter the polarity of the local environment surrounding titratable amino acid side chains inside the protein, enabling H to be pumped from the cytoplasm to the extracellular side of the membrane. The intermediate states of the photocycle may be identified by their absorption maxima.