Retinal binding site

Reduction of bacteriorhodopsin during illumination in the presence of borohydride produces a fluorescent species which absorbs at 360 nm [195,196]. The fine structure of the absorption band of this form is like that of retro-retinal, but the participation of such an isomer in the photocycle of bacteriorhodopsin [215,216] is unlikely. Rather, planarization of the chromophore by constraints of the retinal binding site might be responsible for the fine structure [110]. 

Sullivan JM, Scott KM, Falls HF et al (1993) A novel rhodopsin mutation at the retinal binding-site (Lys-296-Met) in Adrp. Invest Ophthalmol Vis Sci 34 1149... 

The all-fran retinal does not fit into the 11-cm retinal binding site on opsin therefore, npon isomerization the trans isomer separates from the protein. At this point an electrical impulse is generated and transmitted to the brain. In the absence of light, enzymes mediate the isomerization of all-fran retinal back to 11-cm retinal, and rhodopsin is regenerated by the binding of the cis isomer to opsin, as described above. With the completion of this step, the vision cycle can begin again. 

The effect of the protein matrix on the bR chromophore can be described in terms of the existence of an effective electric field at the retinal binding site originated by the charges and location of the amino acid residues that form the pocket surrounding the chromophore. The effective electric field acting along the molecular... 

Rafferty, C.N. and Shichi, H., Xhe involvement of water at the retinal binding site in rhodopsin and early Hght-induced intramolecular proton transfer, Photochem. Photobiol, 33, 229,1981. 

Binding of these ligands does not occur in a concave groove located on the surface of the receptor protein as otherwise often imagined. As described in Section 2.2.1, the x-ray structure of rhodopsin showed that retinal is bound deep in the seven-helical structure with major interaction points in TM-III and TM-VI, as well as the covalent attachment point in TM-VII. In fact, rhodopsin interacts with basically all transmembrane segments. Importantly, side-chains from the transmembrane helices cover the retinal molecule on all sides, and its binding site is found deep in the middle of... 

The dynamics of proton binding to the extra cellular and the cytoplasmic surfaces of the purple membranes were measured by the pH jump methods [125], The purple membranes selectively labeled by fluorescein Lys-129 of bacteri-orhodopsin were pulsed by protons released in the aqueous bulk from excited pyranine and the reaction of the protons with the indicators was measured. Kinetic analysis of the data implied that the two faces of the membrane differ in then-buffer capacities and in their rates of interaction with bulk protons. The extracellular surfaces of the purple membrane contains one anionic proton binding site per protein molecule with pA" 5.1. This site is within a Coulomb cage radius from Lys-129. The cytoplasmic surface of the purple membrane bears four to five pro-tonable moieties that, due to close proximity, function as a common proton binding site. The reaction of the proton with this cluster is at a very fast rate (3 X 1010 M-1 sec ). The proximity between the elements is sufficiently high that even in 100 mM NaCl, they still function as a cluster. Extraction of the chromophore retinal from the protein has a marked effect on the carboxylates of the cytoplasmic surface, and two to three of them assume positions that almost bar their reaction with bulk protons. Quantitative evaluation of the dynamics of proton transfer from photoactivated bacteriorhodopsin to the bulk has been done by using numerical... 

Three distinct G-proteins have been fully characterized. These are transducin (T), which allows rhodopsin to stimulate a high-affinity cyclic GMP phosphodiesterase upon photoactivation in retinal rods Gs, which allows receptors to stimulate the activity of adenylate cyclase and Gh which allows receptors to inhibit adenylate cyclase activity. These three G-proteins contain three non-identical subunits (a, /3 and y). It is their a subunits which provide the binding site for GTP as well as distinct sites for interaction with specific receptor and effector systems and for Mg2+. The /3 subunits associated with all three regulatory proteins are apparently identical although T has a different y subunit. 

Visual pigments display characteristic absorption spectra which result from the very specific interactions between protein and chromophore in the binding site, i.e., the absorbance spectrum of retinal at ca. 380 nm is red-shifted to ca. 500 nm in bovine rhodopsin. However, depending on species, rhodopsins absorb from 440 to ca. 600 nm. Porphyropsins show a similar spread in their absorption maxima, absorb at longer wavelengths than the corresponding rhodopsins, and have lower extinction coefficients (ca. 75%) than rhodopsins (e.g., bovine rhodopsin e, ca. 40500) [17] as shown in Fig. 2. 

Fig. 8. A nonisomerizing procedure for the extraction of retinals from their binding sites in visual pigments [90],...

Fig. 9. Procedure for ascertaining that a retinal analog occupies the natural binding site [92],...

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