Structural prediction of membrane-bound proteins.
A prediction algorithm based on physical characteristics 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.
D000595:Amino Acid Sequence; D000596:Amino Acids; D000818:Animals; D001436:Bacteriorhodopsins; D002338:Carotenoids; D002417:Cattle; D008051:Lipid Bilayers; D008565:Membrane Proteins; D011487:Protein Conformation; D012243:Rhodopsin; D013329:Structure-Activity Relationship
D000596:Amino Acids; D008051:Lipid Bilayers; D008565:Membrane Proteins; D002338:Carotenoids; D001436:Bacteriorhodopsins; D012243:Rhodopsin