Structural determinants of spectral tuning in retinal proteins-bacteriorhodopsin vs sensory rhodopsin II

The mechanism of spectral tuning in the rhodopsin family of proteins, that act as light-driven proton (ion) pumps and light detectors, has been investigated by a combined ab initio quantum mechanical/molecular mechanical technique. Calculations are performed on two members of the family, bacteriorhodopsin (bR) and sensory rhodopsin II (sRII), for which crystal structures of high resolution are available, to explore the physical mechanisms of spectral tuning. Despite a high degree of similarity in the three-dimensional structure, electrostatic environments in bR and sRII differ sufficiently to shift absorption maxima of their common chromophore, a retinal bound to a lysine via a protonated Schiff base, from 568 nm in bR to 497 nm in sRII. This spectral shift, involving the electronical ground state (SO) and first excited state (S-1) of retinal, is predicted correctly within 10 nm. The spectral shift can be attributed predominantly to a change in polarization of the S, state, and is induced predominantly by a shift of the G helix that renders the distance between the Schiff base nitrogen of retinal and the Asp201 counterion shorter in sRII than in bR. A second, weakly allowed excited state, S-2, is predicted to lie energetically close to S-1, at 474 nm. Its energetic proximity to the S, state suggests strong vibronic coupling and explains a shoulder observed at 457 nm in the sRII spectrum.