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In depth look at rhodopsin

Before we continue with the analysis of the mutations, we first learn more about the function of rhodopsin.

Rhodopsin is a small protein situated in the membrane of the light sensitive part of a rod cell in the eye.

Exercise 6

A. Where in the picture below are the rod cells situated in the eye?

Schematische weergave van een oog

B. Where in the picture below of a rod cell are the rhodopsin proteins located. Schematische weergave van een staafje

The programme Yasara can show 3D structures nicely. If Yasara is not yet installed on the computer, you can ask your teacher.

Proceed via the next steps.

1. Start Yasara.

2. Load rhodopsin via the menu in the left top of the window: File > Load > PDB file. Choose the rhodopsin.pdb file and click OK.

3. When you move the mouse pointer to the bottom part of the Yasara screen, a so called sequence bar pops up. This shows the amino acid order of the protein. With the button in left top corner of the bar (looks like a blue drawing-pin) you can permanently visualize this bar.

4. If you click on an amino acid in the sequence bar, the central C-atom of the amino acid starts flashing. If you keep the Ctrl-key pressed while you click on the amino acid in the bar you are automatically transferred to the right location in the protein.

5. By holding the mouse key pressed the protein can be moved:

Left: rotate
Middle: move the protein
Right: zoom

Exercise 7

A. Which elements from the periodic table are the depicted by the colored spheres(green, blue, red etc.)?

Press F6. The protein is now visualized in a different manner. The helices (helix is the shape of a spiral staircase) you now see are special proteinstructures. In this proteins they ensure attachment to the membrane.
Between the helices a small molecule is situated: retinal.

Retinal bevindt zich tussen de helices van rhodopsine

Retinal changes shape under influence of light. Inactive retinal (bend structure) does not transfer a signal to the brains. Active retinal (straight structure) does proceed a signal towards the brain.

Retinal transformeert onder invloed van licht

B. Is retinal in the 3D-protein active or inactive?

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