RECOGNITION OF TRANSMEMBRANE ALPHA-HELICAL SEGMENTS WITH ENVIRONMENTAL PROFILES

A method for assessing the environmental properties of membrane-spanni ng alpha-helical peptides in proteins has been proposed. The algorithm employs a set of environmental preference parameters derived for amin o acid residues based on the analysis of the 3-D structures of membran e domains in bacteriorhodopsin and photoreaction centers Rhodopseudomo nas viridis and Rhodobacter sphaeroides. The resulting 3-D-1-D scores for transmembrane segments are significantly different from those deri ved for alpha-helices in globular proteins, The parameters obtained ha ve been used to construct environmental profiles for membrane alpha-he lices in bacteriorhodopsin and photoreaction centers. The profiles suc cessfully recognize their own sequences in several specially designed large databases. The method has been applied to several membrane prote ins with unknown spatial structures, Most of their membrane-spanning p eptides were efficiently recognized by the profiles, The predicted env ironment of the residues in the membrane segments fits the experimenta l data well, The approach is independent of any homology data and can be employed to delineate the membrane segments of a protein with envir onmental characteristics close to those of bacteriorhodopsin and photo reaction centers. The alignment of these segments with the reference p rofiles provides a considerable amount of data about their lipid and p rotein exposure.