Predicting Membrane Protein Structure

Abstract

The transmembrane segments of a membrane protein may be predicted from a membrane propensity profile of its amino acid sequence, in which the amino acids are represented by their frequencies of occurrence in a number of putative transmembrane segments. When this sequence has been smoothed by a running average function, the transmembrane segments appear as extended, positive peaks. In an application of this technique to a pool of ten previously studied membrane proteins, the predicted intra- and extra- membrane structures agreed 93.6% on a residue-by-residue basis with the previously suggested structures. This algorithm has been applied to predict the transmembrane segments in subunits I, II, III, IV, V, VIa, VII, VIIIa, and VIIIb of bovine cytochrome c oxidase and has also been used as a tool for studying structural homology between different species cytochrome oxidase subunit I.