Bioinformatics Pipeline for Identification of Binding Motifs of Flexible Protein Tethers

Proteins use conserved binding motifs associated with relatively unconserved flexible amino acid sequences as mobile tethers for interacting molecules, as exemplified by C-terminal tether sequences of bacterial chemotaxis receptors. We describe here a bioinformatics pipeline to discover new instances of flexible tethers and their binding motifs. C-terminal regions of all proteins in subsets of bacteria and archaea were analyzed for flexibility with DisEMBL hotloops, grouped with BLASTCLUST, aligned with ClustalW, analyzed for conserved 5-mers, and then putative tethers were identified as sequences with highly conserved (>80%) 5-mers that were at least 20% more conserved than the rest of the flexible region. The algorithm identified previously known flexible binding domains, as well as >100 other putative flexible tether sequences that should be further investigated for binding targets and flexibility.