Predicting protein functional sites with phylogenetic motifs

In this report, we demonstrate that phylogenetic motifs, sequence regions conserving the overall familial phylogeny, represent a promising approach to protein functional site prediction. Across our structurally and functionally heterogeneous data set, phylogenetic motifs consistently correspond to functional sites defined by both surface loops and active site clefts. Additionally, the partially buried prosthetic group regions of cytochrome P450 and succinate dehydrogenase are identified as phylogenetic motifs. In nearly all instances, phylogenetic motifs are structurally clustered, despite little overall sequence proximity, around key functional site features. Based on calculated false-positive expectations and standard motif identification methods, we show that phylogenetic motifs are generally conserved in sequence. This result implies that they can be considered motifs in the traditional sense as well. However, there are instances where phylogenetic motifs are not (overall) well conserved in sequence. This point is enticing, because it implies that phylogenetic motifs are able to identify key sequence regions that traditional motif-based approaches would not. Further, phylogenetic motif results are also shown to be consistent with evolutionary trace results, and bootstrapping is used to demonstrate tree significance.