An approach to systematic detection of protein structural motifs

A procedure to detect similar local structures of proteins from C alpha coordinates is presented. First, the conformations of seven-residue peptide segments are approximated by a limited number of representatives, each of which is assigned a symbol. Thus, the overall conformation of a protein is represented by a symbol string. The comparison of these symbol strings using a sequence alignment technique then gives pairs of similar local structures. These pairs are considered candidates of structural motifs. The application of the procedure to the analysis of 93 proteins gave 858 pairs of similar local structures, which included several well-known structural motifs such as the nucleotide-binding beta alpha beta-unit and the calcium-binding EF hand. The characterization of amino acid patterns of similar local structures given by the procedure should be useful for the development of protein structure prediction based on the acquisition of empirical rules from a large-scale database.