Recognition of protein structure: determining the relative energetic contributions of beta-strands, alpha-helices and...

We examine the role of residues of secondary structure in recognition of the native structure of proteins. The accuracy of recognition was estimated by computing the Z-score values for fragments of protein chains in threading tests. By testing different combinations of secondary structure fragments of 240 non-homologous proteins we show that the overwhelming majority of proteins can be successfully recognized by the energies of interaction between residues of secondary structure. We also found that beta-structures contribute more significantly to fold recognition than alpha-helices or loops. To validate the Z-score calculations in measuring the accuracy of recognition we evaluated the deviation of the energy distribution from the normal law. The normal law satisfactory approximates the shape of the energy distribution for the majority of proteins and chain fragments; however, deviations are often observed for short fragments and for fragments with relatively high Z-score values. The results of the study justify recognition of remote homologs by threading methods based on a backbone of secondary structure rather than of a whole chain because loops of homologs differ more significantly than strands and helices, and the contribution of loops in structure recognition is relatively small.