Structural Prediction of Membrane‐Bound Proteins

A prediction algorithm based on physical characteristis of the twenty amino acids and refined by comparison to the proposed bacteriorhodopsin structure was devised to delineate likely membrane‐buried regions in the primary sequences of proteins known to interact with the lipid bilayer. Application of the method to the sequence of the carboxyl terminal one‐third of bovine rhodopsin predicted a membrane‐buried helical hairpin structure. With the use of lipid‐buried segments in bacteriorhodopsin as well as regions predicted by the algorithm in other membrane‐bound proteins, a hierarchical ranking of the twenty amino acids in their preferences to be in lipid contact was calculated. A helical wheel analysis of the predicted regions suggests which helical faces are within the protein interior and which are in contact with the lipid bilayer.