Mapping protein sequence spaces by recurrence quantification analysis: a case study on chimeric structures

Recurrence quantification analysis (RQA) was used to characterize the foldi ng properties of 22 chimeric sequences derived from two parent proteins of similar length but different three-dimensional arrangement. A non-linear re lation between sequence data and their RQA representation was revealed, whi ch points to new information carried by this method as compared with classi cal best-alignment methods. This new information is significantly correlate d with the folding properties of the hybrid polypeptide chains, as substant iated by careful statistical analysis of the recurrence plots' numerical de scriptors, thus encouraging their systematic use to complement sequence dat a in both proteomics and protein engineering tasks. Even the direct visual screening of the qualitative graphical features of recurrence plots is show n to provide useful hints to discriminate between different recurrence stru ctures of protein sequences.