Figure 10–31 The three-dimensional structure of a bacteriorhodopsin molecule. (Movie 10.5) (A) the polypeptide chain crosses the lipid bilayer seven times as α helices. the location of the retinal chromophore (purple) and the probable pathway taken by h+ during the light-activated pumping cycle are shown. the first and key step is the passing of an h+ from the chromophore to the side chain of aspartic acid 85 (red, located next to the chromophore) that occurs upon absorption of a photon by the chromophore. Subsequently, other h+ transfers—in the numerical order indicated and utilizing the hydrophilic amino acid side chains that line a path through the membrane—complete the pumping cycle and return the enzyme to its starting state. color code: glutamic acid (orange), aspartic acid (red), arginine (blue). (B) the high-resolution crystal structure of bacteriorhodopsin shows many lipid molecules (yellow with red head groups) that are tightly bound to specific places on the surface of the protein.  (A, adapted from h. luecke et al., Science 286:255–261, 1999. With permission from AAAS; B, from h. luecke et al., J. Mol. Biol. 291:899–911, 1999. With permission from Academic press.)
Interactions with specific lipids are thought to help stabilize many membrane proteins, which work best and sometimes crystallize more readily if some of the lipids remain bound during detergent extraction, or if specific lipids are added back to the proteins in detergent solutions. The specificity of these lipid–protein interactions helps explain why eukaryotic membranes contain such a variety of lipids, with head groups that differ in size, shape, and charge. We can think of the membrane lipids as constituting a two-dimensional solvent for the proteins in the membrane, just as water constitutes a three-dimensional solvent for proteins in an aqueous solution: some membrane proteins can function only in the presence of specific lipid head groups, just as many enzymes in aqueous solution require a particular ion for activity.
Bacteriorhodopsin is a member of a large superfamily of membrane proteins with similar structures but different functions. For example, rhodopsin in rod cells of the vertebrate retina and many cell-surface receptor proteins that bind extracellular signal molecules are also built from seven transmembrane α helices. These proteins function as signal transducers rather than as transporters: each responds to an extracellular signal by activating a GTP-binding protein (G protein) inside the cell and they are therefore called G-protein-coupled receptors (GPCRs), as we discuss in Chapter 15 (see Figure 15–6B). Although the structures of bacteriorhodopsins and GPCRs are strikingly similar, they show no sequence similarity and thus probably belong to two evolutionarily distant branches of an ancient protein family. A related class of membrane proteins, the channelrhodopsins that green algae use to detect light, form ion channels when they absorb a photon. When engineered so that they are expressed in animal brains, these proteins have become invaluable tools in neurobiology because they allow specific neurons to be stimulated experimentally by shining light on them, as we discuss in Chapter 11 (Figure 11–32).
Membrane proteins Often Function as large complexes