DETECTION OF NONTOPOLOGICAL MOTIFS IN PROTEIN STRUCTURES

We present an efficient technique for the comparison of protein struct ures, The algorithm uses a vector representation of the secondary stru cture elements and searches for spatial configurations of secondary st ructure elements in proteins, In such recurring protein folds, the ord er of the secondary structure elements in the protein chains is disreg arded, The method is based on the geometric hashing paradigm and imple ments approaches originating in computer vision. It represents and mat ches the secondary structure element vectors in a 3-D translation and rotation invariant manner, The matching of a pair of proteins takes on average under 3 s on a Silicon Graphics Indigo2 workstation, allowing extensive all-against-all comparisons of the data set of non-redundan t protein structures, Here we have carried out such a comparison for a data set of over 500 protein molecules, The detection of recurring to pological and non-topological, secondary structure element order-indep endent protein folds may provide further insight into evolution, Moreo ver, as these recurring folding units are likely to be conformationall y favourable, the availability of a data set of such topological moths can serve as a rich input for threading routines. Below, we describe this rapid technique and the results it has obtained, While some of th e obtained matches conserve the order of the secondary structure eleme nts, others are entirely order independent, As an example, we focus on the results obtained for Che Y, a signal transduction protein, and on the profilin-beta-actin complex, The Che Y molecule is composed of a five-stranded, parallel beta-sheet flanked by five helices. Here we sh ow its similarity with the Escherichia call elongation factor, with L- arabinose binding protein, with haloalkane dehalogenase and with adeny late kinase, The profilin-beta-actin contains an antiparallel beta-ple ated sheet with alpha-helical termini, Its similarities to lipase, fru ctose disphosphatase and beta-lactamase are displayed.