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A method for assessing the environmental properties of membrane-spanning alpha-helical peptides in proteins has been proposed. The algorithm employs a set of environmental preference parameters derived for amino acid residues based on the analysis of the 3-D structures of membrane domains in bacteriorhodopsin and photoreaction centers Rhodopseudomonas viridis and Rhodobacter sphaeroides. The resulting 3-D-1-D scores for transmembrane segments are significantly different from those derived for alpha-helices in globular proteins. The parameters obtained have been used to construct environmental profiles for membrane alpha-helices in bacteriorhodopsin and photoreaction centers. The profiles successfully recognize their own sequences in several specially designed large databases. The method has been applied to several membrane proteins with unknown spatial structures. Most of their membrane-spanning peptides were efficiently recognized by the profiles. The predicted environment of the residues in the membrane segments fits the experimental data well. The approach is independent of any homology data and can be employed to delineate the membrane segments of a protein with environmental characteristics close to those of bacteriorhodopsin and photoreaction centers. The alignment of these segments with the reference profiles provides a considerable amount of data about their lipid and protein exposure.

Recognition of transmembrane α-helical segments with environmental profiles