Large-scale analysis of secondary structure changes in proteins suggests a role for disorder-to-order transitions in nucleotide binding proteins

Conformational changes in proteins often involve secondary structure transitions. Such transitions can be divided into two types: disorder-to-order changes, in which a disordered segment acquires an ordered secondary structure (e.g., disorder to α-helix, disorder to β-strand), and order-to-order changes, where a segment switches from one ordered secondary structure to another (e.g., α-helix to β-strand, α-helix to turn). In this study, we explore the distribution of these transitions in the proteome. Using a comprehensive, yet highly conservative method, we compared solved three-dimensional structures of identical protein sequences, looking for differences in the secondary structures with which they were assigned. Protein chains in which such secondary structure transitions were detected, were classified into two sets according to the type of transition that is involved (disorder-to-order or order-to-order), allowing us to characterize each set by examining enrichment of gene ontology terms. The results reveal that the disorder-to-order set is significantly enriched with nucleotide binding proteins, whereas the order-to-order set is more diverse. Remarkably, further examination reveals that >22% of the purine nucleotide binding proteins include segments which undergo disorder-to-order transitions, suggesting that such transitions play an important role in this process. Proteins 2010. © 2009 Wiley-Liss, Inc.