An Approach to Systematic Detection of Protein Structural Motifs

Abstract

A procedure to detect similar local structures of proteins from Ca coodinates ispresented. First, the conformations of peptide segments of seven residues long are approximated by a limited number of representatives, each of which is assigned a symbol. Thus, the entire conformation of a protein is represented by a symbol string. Then, the comparison of these symbol strings using sequence alignment technique 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 inculded several well-known structural motifs such as nucleotide-binding βαβ motif and 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.