Identification of Intrinsic Disorder in Complexes from the Protein Data Bank

Abstract

Background: Intrinsically disordered proteins or regions (IDPs or IDRs) lack stable structures in solution, yet often fold upon binding with partners. IDPs or IDRs are highly abundant in all proteomes and represent a significant modification of sequence → structure → function paradigm. The Protein Data Bank (PDB) includes complexes containing disordered segments bound to globular proteins, but the molecular mechanisms of such binding interactions remain largely unknown. Results: In this study, we present the results of various disorder predictions on a nonredundant set of PDB complexes. In contrast to their structural appearances, many PDB proteins were predicted to be disordered when separated from their binding partners. These predicted-to-be-disordered proteins were observed to form structures depending upon various factors, including heterogroup binding, protein/DNA/RNA binding, disulfide bonds, and ion binding. Conclusions: This study collects many examples of disorder-to-order transition in IDP complex formation, thus revealing the unusual structure–function relationships of IDPs and providing an additional support for the newly proposed paradigm of the sequence → IDP/IDR ensemble → function.