Patterns of Dynamics Comprise a Conserved Evolutionary Trait

Abstract

The importance of protein dynamics in function may suggest an evolutionary selection on large-scale protein motions. Here we systematically studied the dynamic characteristics in 2221 protein domains (58477 sequences) of the Pfam database. We defined the patterns of dynamics (PODs) based on the estimated NMR order parameters and the predicted degree of disorder, and found a significant correlation between them in families of both structured and disordered protein domains. We demonstrate that conservation of dynamic patterns frequently exceeds conservation of sequence and is comparable to the patterns of hydropathy and nonspecific interaction potential. Similarity of dynamic patterns is weakly correlated to structure similarity and to the degree of disorder. We illustrate that POD alignments could be applied to sequentially divergent or intrinsically disordered regions. We propose that patterns of dynamics comprise a conserved evolutionary trait, which could be used to infer evolutionary relationships as an alternative to sequence and structure.

Keywords: Divergent sequences; Evolutionary relationship; Intrinsically disordered proteins; Protein dynamics; Structure conservation.