Hydrophobic zippers and hook-and-eye: evolutionarily conserved protein sequence motifs in eukaryotic acidic ribosomal proteins which are assumed to be involved in the association of the protein family.

The acidic ribosomal protein family of eukaryotic cells is thought to form a complex on ribosomes mainly by hydrophobic forces. To investigate the structural basis of how they associate with one another, the primary sequences of the related proteins accumulated from various organisms were analyzed searching for evolutionarily conserved hydrophobic motifs. Initially it is shown that all the P1-type 13-kDa proteins contain a bilateral hydrophobic zipper on a putative alpha-helix, which consists of two periodic arrays of hydrophobic amino acid residues arranged on the opposite sides of an alpha-helix. The P2-type 13-kDa proteins, except for those from the yeast Saccharomyces cerevisiae, are shown to contain two kinds of hydrophobic areas on putative alpha-helices, which can sterically bind to each other in a hook-and-eye fashion. On the other hand, the 38-kDa proteins contain a hydrophobic zipper and a hydrophobic hook in different helical regions. Thus, it is proposed that the 13-kDa proteins associate with the 38-kDa proteins via the hydrophobic zipper or hydrophobic hook-and-eye, and associate with one another with these hydrophobic elements.