Sekharan, Sivakumar:
Ab intio studies of the origin of spectral tuning mechanisms in Rhodopsin, Barthorhodopsin and Isorhodopsin
Duisburg, Essen, 2007
Dissertation / Fach: Chemie
Fakultät für Chemie
Ab intio studies of the origin of spectral tuning mechanisms in Rhodopsin, Barthorhodopsin and Isorhodopsin
Sekharan, Sivakumar
Betreuer(in), Doktorvater:
Buß, Volker
Gutachter(in), Rezensent(in):
Gärtner, Wolfgang
Duisburg, Essen
129 S.
DuEPublico ID:
Signatur der UB:
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One of the most basic and unresolved puzzle 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; while the artificial retinal analogue isorhodopsin containing the isomeric 9-cis form peaks at 485 nm and the early photo intermediate bathorhodopsin encompassing a distorted all-trans-retinal absorbs at 543 nm. 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. 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 and/or non- polar amino acids lining the binding pocket. Employing the best available structural data we show 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. We have studied the wavelength dependence of 11-cis-, 9-cis- and all-transretinal absorbencies of the chromophore at the multiconfigurational level of theory using second order perturbation theory (CASPT2) within an atomic natural orbital (ANO) basis set on MP2 and SCC-DFTB optimized geometries in vacuo and in protein environments. In addition to the quantum-mechanical description for the chromophore and its counterion we have used three types of atomic charges obtained from a natural population analysis (NPA), Mulliken population analysis (MPA) and from the environment insensitive CHARMM charges, to account for the electrostatic interaction between the chromophore and the polar amino acids. We demonstrate that in vacuo, the sensitivity of the retinal chromophore to its protonation state covers a wavelength range of 610 to 353 nm. In protein, by far the largest effect is exerted by the counterion (Glu-113) on the absorption maximum. Since the protein environment provides and stabilizes the chromophore distortion necessary for the selective and ultrafast transformation to bathorhodopsin, we conclude that this is its primary role and that spectral tuning by the binding pocket is not the goal pursued by evolution.