A statistical technique for predicting membrane protein structure

Abstract

A statistical technique has been developed for predicting the transmembrane segments of membrane proteins from their amino acid sequences. A protein's amino acid sequence is represented by a sequence of membrane propensity values derived from the frequency of occurrence of the amino acids in a number of putative transmembrane segments. A running average over this numeric sequence yields a membrane propensity profile from which transmembrane segments may be chosen. When this method is applied to a pool of ten putative membrane proteins, the predicted intra- and extramembrane regions agree 93.6% on a residue-by-residue basis with previously suggested structures. Predictions of transmembrane segments in cytochrome c oxidase subunits I, II and III and cytochrome b from several species are given, and structural homology between species is examined using membrane propensity profiles. Conclusions are then made about the functionality of several regions in these proteins.