Membrane Proteins–Physics and Evolution

Abstract

Membrane proteins have significant physical characteristics of amino acid sequences: a cluster of hydrophobic residues at the transmembrane region and clusters of amphiphilic residues at its terminal ends. A high performance prediction system of membrane proteins SOSUI could be developed based on those physical characteristics. This system is applicable to unknown sequences from genomes and even to randomized sequences because it is based on only physical characteristics. When all amino acid sequences from various genomes were analysed, the ratio of membrane proteins was almost constant. Furthermore, the ratio was maintained for completely randomized sequences, if the real amino acid composition was used, indicating that the sequence space for real proteins is much smaller than the whole sequence space.