Origin of Spectral Tuning in Rhodopsin—It Is Not the Binding Pocket

Abstract

One of the most basic and unresolved puzzles in the chemistry of vision is the mechanism regulating the absorbance of the visual photoreceptors. Rhodopsin, the rod pigment that mediates black/white vision in the human eye, absorbs at 498 nm; the three cone pigments responsible for trichromatic (color) vision absorb at 425, 530, and 560 nm, respectively. Since the chromophore in these receptors is the same protonated Schiff base of 11-cis-retinal (pSb11), the spectra of these pigments are clearly a function of the protein environment the chromophore "sees"; in other words, the spectra are tuned by the protein. [1] Three mechanisms are generally agreed to be involved in spectral tuning: 1) distortion of the chromophore as a result of steric interactions with the protein binding pocket; 2) interaction of the chromophore with the counterion balancing its positive charge; and 3) interaction of the chromophore with the remaining polar residues of the amino acids lining the binding pocket. However, the importance of these contributions could not be assessed quantitatively as long as realistic structures of the visual pigments were not available. This changed with the first X-ray crystal structure of rhodopsin, [2] now solved down to 2.2-resolution, [3] which made it possible to study the chromophore including its environment with high-quality quantum-mechanical methods. [4][5][6][7] Despite considerable insights gained from these studies, fundamental questions remain, in particular to what extent the amino acid residues of the binding pocket affect the spectrum of the chromophore.Very recently the absorption cross section of pSb11 in the gas phase was determined by analyzing fragments of photochemically excited ions.[8] Devoid of the restraining forces and charges of the protein environment, the chromophore in the gas phase or vacuum appears tailor-made for high-level quantum-mechanical calculations. It also presents a welldefined point of reference for the analysis of spectral tuning in rhodopsin. Using multiconfigurational perturbation theory we have been able to reproduce the experimental absorption maximum of the bare rhodopsin chromophore (610 nm) with high accuracy.[9] Employing the same theoretical platform we show in the following that the three contributions discussed above add up quantitatively to the experimentally observed spectral shift of the chromophore on going from the vacuum to the rhodopsin molecule. By far the largest contributor to the shift is the counterion, while the role of the polar amino acid residues of the protein pocket, contrary to general consensus, is limited to modulating the spectrum.The calculations were performed on three pSb11 model systems derived from the SCC-DFTB-refined [10] geometry of the rhodopsin binding pocket with 2.2-resolution shown in Figure 1, and they increasingly reflect the influence of the protein. Starting with the optimized vacuum structure pSb11 vac described earlier, [9] changes in the geometry corresponding to the calculated rhodopsin structure were added whic...

Mechanism of a proton pump analyzed with computer simulations

“…If the calculated gas phase value is too high, the underestimation of the blue shift due to the protein environment can lead to an artefactual error compensation as, e.g., in the case of TD-DFT. The experimental value of 2.03 eV is reasonably reproduced by CASPT2 [91] and Spectroscopy Oriented Configuration Interaction (SORCI, [92,93]) [42], but overestimated by TD-DFT [42]. The absorption spectrum of SRII is blue shifted by 70 nm relative to bacteriorhodopsin [94,95].…”

The Tautomeric Half-reaction of BphD, a C-C Bond Hydrolase

“…Similarly, the spectrum of a substituted stilbene derivative was red-shifted 102 nm upon binding to an antibody (21). Recent theoretical calculations suggest that the spectrum of rhodopsin is primarily determined by the interaction of the positively charged chromophore with Glu-113, which may account for a shift as large as 157 nm (22). For BphD, it is possible that Arg-190, which interacts with the carboxylate of HOPDA, may similarly perturb the spectrum of the keto tautomer.…”

Assessment of semiempirical methods for the photoisomerisation of a protonated Schiff base

“…Single-point CASPT2 calculations can also be used to study the retinal chromophore, including interactions with the protein binding pocket, with geometries provided by lower level methods [9][10][11]. CASPT2//CASSCF has further been used to calculate the excitation energies [12] and absorption spectra [13,14] of retinal in the full protein environment using a combined quantum mechanical/ molecular mechanical (QM/MM) description.…”