Introduction - This script shows the structure of bacteriorhodopsin. Bacteriorhodopsin is a typical alpha helical membrane protein. The amphipathic helices in bacteriorhodopsin are also compared to those in a typical water soluble protein. Scroll down until the text corresponding to the view is visible. (Based on 1brd.pdb, R.Henderson et al. J. Mol. Biol. 213 899 (1990) and 1aep.pdb, D.Breiter et al. Biochem. 30 603 (1991)).
This is bacteriorhodopsin from Halobacterium halobium. It is a transmembrane protein containing seven alpha helices.
Bacteriorhodopsin contains amphipathic helices in which the hydrophobic sidechains (GREEN) point outward so they can interact with the fatty acyl chains of the membrane lipids.
The hydrophilic sidechains (YELLOW) point toward the interior of the protein.
Here is water-soluble protein with five alpha helices.
In this case the hydrophobic sidechains (GREEN) point to the interior of the protein.
The hydrophilic residues (YELLOW) point outward toward the solvent.