Sequence Analysis of Less Hydrophobic Transmembrane Segments in Polytopic Membrane Proteins

To understand the function of membrane proteins, the knowledge of their structure, especially the knowledge of the position of transmembrane segments (TMSs) and of their membrane topology (i.e., orientation of TMSs across the membrane), is crucial. Since most TMSs of α-type polytopic (i.e., having multiple TMSs) membrane proteins are composed of hydrophobic amino acids, they are usually detected as peaks in the hydropathy plot [1]. However, there are a certain amount of TMSs that are relatively hydrophobic and so it is hard to distinguish them with relatively hydrophobic loop segments. Although how such less hydrophobic segments span the membrane has been a mystery, Ota et al. found an important clue on its mechanism [4]; according their result, each TMS has its own topogenic tendency like membrane proteins with a single TMS. Their topogenic tendency is determined by the distribution of neighboring positively-charged residues like the positive-inside rule [3]. Namely, if a TMS has more positive charges on its nearby N-terminal side, it tends to have the Nin/Cout orientation; otherwise, a TMS tends to be in the Nout/Cin orientation. Thus, if two neighboring TMSs have the same topogenic tendency, a loop segment between them may become a TMS to resolve this contradiction. To confirm this idea, we systematically analyzed the sequence features of both less-hydrophobic TMSs and relatively-hydrophobic loops. Our result not only supports Ota et al.’s conclusion but also implies a more general model of membrane topogenesis.