Sequence Analysis of Complex Membrane Proteins (Cytochrome c Oxidase)

In recent years, aminoacid sequence analysis has been extended to hydrophobic proteins, especially those which are constituents of biological membranes and are known as integral or intrinsic membrane proteins. Both expressions refer to the fact that parts of the structures of such proteins extend into and more often penetrate the lipid bilayer of biomembranes, giving rise to a firm association between the hydrocarbon chains of the fatty acids or cholesterol and protein domains made up from about 12 mostly hydrophobic amino acids out of the 20 known to build the protein structure. Integration of these residues into the membrane — most often in ~20-membered helical conformation — is governed by the free energy (-ΔG) of their transfer from a random coil configuration in the aqueous phase into an ordered (helical) conformation in the lipid phase [1].