Features of transmembrane helices useful for membrane protein prediction

For the development of a high-performance software system of membrane protein prediction, we analyzed the distribution of hydrophobicity and the amphiphilicity around transmembrane helices, using dataset of membrane proteins whose 3D structures or topologies are known. The moving average of 7 residues showed that there are a hydrophobicity peak in the center of a transmembrane helix and two amphiphilicity peaks at both ends of the hydrophobicity peak. The shapes of the peaks were asymmetric with respect to the center of the hydrophobicity peak. The membrane protein prediction system SOSUI (Hirokawa and Mitaku, Bioinformatics, 1998) was improved on the basis of the asymmetric profiles of hydrophobicity and amphiphilicity, resulting in the accuracy of 98% for positive dataset and 96% for negative one of prokaryotes, and the comparable accuracy was obtained also for eukaryotes.