Rhodopsin, retinal molecules

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 light-absorbing part of a rod cell contains the pigment rhodopsin, which consists of the opsin attached to the 11-cis-retinal molecule (1) (Figure 12.3). Free 11-cis-retinal absorbs in the ultraviolet, but when attached to opsin the absorption is in the visible region. 

There are several different rhodopsins in the cones. All of them contain retinal molecules as light-sensitive components, the absorption properties of which are modulated by the different proportions of opsin they... 

Fig. 15.1. A universal biological sensor based on rhodopsin (a protein), a schematic view, (a) The sensor consists of seven a-helices (shown here as ribbons) connected in a sequential way by some oligopeptide links. The molecule is anchored in the cell wall (Upid bilayer), due to the hydrophobic effect the rhodopsin s hpophilic amino acid residues are distributed on the rhodopsin surface, (b) The o —helices (this time shown for simphcity as cyhnders) fmn a cavity. Some of the cylindars have been cut out to display a cis-retinal molecule bound (in one of the versions of the sensor) to the amino acid 296 (lysine denoted as K, in heUx 7). (c) The cis-retinal (a chain of alternating single and double bonds) is able to absorb a photon and change its conformation to trans (at position 11). This triggers the cascade of processes responsible for our vision. The protruding protein loops exhibit specific interactions with some drugs. Such a system is at the basis of the interactions with about 70% of drugs.

Vision, our ability to perceive light, is the result of an isomerization reaction. Our eyes contain millions of cells called rods that are packed with rhodopsin, an 11-m-retinal molecule... 

About 57 per cent of the photons that enter the eye reach the retina the rest are scattered or absorbed by the ocular fluid. Here the primary act of vision takes place, in which the chromophore of a rhodopsin molecule absorbs a photon in another n-to-n transition. A rhodopsin molecule consists of an opsin protein molecule to which is attached an 11-ds-retinal molecule (Atlas E3 and 3). The latter resembles half a carotene molecule, showing Nature s economy in its use of available materials. The attachment is by the formation of a proton-ated Schiff s base, utilizing the CHO group of the chromophore and the terminal NHj group of the side chain of a lysine residue from opsin (5). The free 11-ds-retinal molecule absorbs in the ultraviolet, but attachment to the opsin protein molecule shifts the absorption into the visible region. The rhodopsin molecules are situated in the membranes of special cells (the rods and the cones ) that cover the retina. The opsin molecule is anchored into the cell membrane by two hydrophobic groups and largely surrounds the chromophore (Fig. 12.52). 

Classical simulations often lack the crucial insight into the problem, because one cannot simply use the force to characterize all the possible interactions. Fortunately, with decades of development, theoretical calculations have become quite sophisticated for crystals and molecules, although not yet for realistic nanometer-sized materials. For solids, the pseudopotential as well as the full-potential linearized augmented plane-wave (FLAPW) method within the density functional theory are well developed. Modern quantum chemical techniques (Gaussian98 [5] and MOLPRO [6]) are quite efficient to compute the potential surfaces for a given molecule. In order to illustrate those possibilities, we show some of our own results in simulating the reaction path for a segment of the retinal molecule in rhodopsin [7]. 

The distribution of rods and cones is shown in Figure 3b centered about the fovea, the area of the retina that has the highest concentration of cones with essentially no rods and also has the best resolving capabiUty, with a resolution about one minute of arc. The fovea is nominally taken as a 5° zone, with its central 1° zone designated the foveola. There are about 40 R and 20 G cones for each B cone in the eye as a whole, whereas in the fovea there are almost no B cones. A result of this is that color perception depends on the angle of the cone of light received by the eye. The extremely complex chemistry involved in the stimulation of opsin molecules, such as the rhodopsin of the rods, and the neural connections in the retinal pathway are well covered in Reference 21. 

In photoreceptor cells, the rods and cones of the human retina, the retinal is linked to a specific protein termed opsin. The resulting pigment is known as rhodopsin. When a photon of light of the proper wavelength hits a molecule of rhodopsin, two chemical events take place. First, the ll-c -retinal is converted to the all-trans form and, secondly, the all-trani-retinal is released from the rhodopsin ... 

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