Rhodopsin description

Rhodopsin is an interesting and complex molecule. It was defined conceptually in the 1930 s. It has been defined technically since the mid 1950 s. In recent times, it has been elucidated in detail via the genetic code. Except for detailing the two sugars shown in the box on the right, Crouch Ma 16 have provided a detailed description of the... 

Of special interest is the marked dependence of < >iSq for both 11-cis and all-trans molecules, on Aexc (176). As in the case of retinal (174,178), no quantitative rationalization of this wavelength dependence is available. However, as we shall subsequently see, the strikingly different photochemical behavior of the biopigments in this respect has provided the basis for a quantitative description of the primary photochemical event in rhodopsins. 

Since LR-TDDFT breaks down for the description of the photodynamics of PSB5 and P-TDDFT is computationally too demanding for the description of the full RPSB, we employ ROKS for the QM/MM description of the photoreaction in rhodopsin (see Section 7.5). 

Our rhodopsin model system is based on the crystal structures of bovine rhodopsin [10] embedded in a membrane mimetic environment (Fig. 7.3) [3], The BLYP [76,77] functional is used for the QM subsystem, which is evolved according to the Car-Parrinello algorithm [20]. For the description of the electronically excited Sj state, ROKS [24,25] is employed. 

AMI and PM3 for the description of the secondary structure in peptides and proteins has been performed recently [116], and it was shown that the description of the peptide conformers is considerably improved by OM1 and OM2 compared with AMI and PM3, although in some cases, there still were discrepancies with available ab initio data. MNDO-PSDCI molecular orbital theory has recently been used to calculate the spectroscopic properties of sensory rhodopsin from Natronobacterium pharaonis [117], demonstrating that MNDO is also a reliable tool for the calculation of optical spectra. 

It is noted, however, that the experimental CW fluorescence spectrum exhibits a still larger Stokes shift of a 4500cm. This finding indicates that an appropriate theoretical description of the femtosecond isomerization in rhodopsin needs to account for the interaction of retinal... 

Infrared spectroscopic studies of macromolecules became increasingly powerful with the development of Fourier transform techniques [44, 47, 48, 59-67]. (See Chap. 1 for a description of an FTIR spectrometer.) FTIR measurements can be used to probe changes in the bonding or interactions of individual amino acid side chains in proteins. Bacteriorhodopsin provides an illustration. When bacterio-rhodopsin is illuminated, its protonated retinylidine Schiff base chromophore isomerizes and then transfers a proton to a group in the protein. FTIR measurements showed the formation of an absorption band at 1,763 cm in addition to a set of absorption changes attributable to the chromophore [63, 68]. In bacteriorhodopsin that was enriched in [4- C]-aspartic acid the band appeared at 1,720 cm and an additional shift to 1,712 cm was obtained when the sovent was replaced by D2O. These observations indicated that the band reflected C=0 stretching of a protonated aspartic acid, leading to identification of a particular aspartic acid residue as the H" acceptor for deprotonation of the chromophore. 

Since the crystal structure of the rhodopsin protein became available in 2000, a more accurate description of the protein environment was available for computational investigation and for the interpretation of the experimental data. In 2003 Ferre and co-workers performed the... 

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