Topology of membrane proteins

Integral membrane proteins play important roles in living cells. Due to difficulties of experimental techniques, theoretical approaches, i.e., topology prediction methods, are important for structure determination of this class of proteins. Here we show a detailed comparison of transmembrane topology prediction methods. According to this comparison, we conclude that the topology of integral membrane proteins is determined by the maximum divergence of the amino acid composition of sequence segments. These segments are located in different areas of the cell, which can be characterized by different physicochemical properties. The results of these prediction methods compared to the X-ray diffraction data of several transmembrane proteins will also be discussed.