Mapping the transition state for a binding reaction between ancient intrinsically disordered proteins

Abstract

Intrinsically disordered protein domains often have multiple binding partners. It is plausible that the strength of pairing with specific partners evolves from an initial low affinity to a higher affinity. However, little is known about the molecular changes in the binding mechanism that would facilitate such a transition. We previously showed that the interaction between two intrinsically disordered domains, NCBD and CID, likely emerged in an ancestral deuterostome organism as a low-affinity interaction that subsequently evolved into a higher-affinity interaction before the radiation of modern vertebrate groups. Here we map native contacts in the transition states of the low-affinity ancestral and high-affinity human NCBD/CID interactions. We show that the coupled binding and folding mechanism is overall similar but with a higher degree of native hydrophobic contact formation in the transition state of the ancestral complex and more heterogeneous transient interactions, including electrostatic pairings, and an increased disorder for the human complex. Adaptation to new binding partners may be facilitated by this ability to exploit multiple alternative transient interactions while retaining the overall binding and folding pathway. Intrinsically disordered protein domains often have multiple binding partners. It is plausible that the strength of pairing with specific partners evolves from an initial low affinity to a higher affinity. However, little is known about the molecular changes in the binding mechanism that would facilitate such a transition. We previously showed that the interaction between two intrinsically disordered domains, NCBD and CID, likely emerged in an ancestral deuterostome organism as a low-affinity interaction that subsequently evolved into a higher-affinity interaction before the radiation of modern vertebrate groups. Here we map native contacts in the transition states of the low-affinity ancestral and high-affinity human NCBD/CID interactions. We show that the coupled binding and folding mechanism is overall similar but with a higher degree of native hydrophobic contact formation in the transition state of the ancestral complex and more heterogeneous transient interactions, including electrostatic pairings, and an increased disorder for the human complex. Adaptation to new binding partners may be facilitated by this ability to exploit multiple alternative transient interactions while retaining the overall binding and folding pathway. Intrinsically disordered proteins (IDPs) are abundant in the human proteome (1Oates M.E. Romero P. Ishida T. Ghalwash M. Mizianty M.J. Xue B. Dosztányi Z. Uversky V.N. Obradovic Z. Kurgan L. Dunker A.K. Gough J. D2P2: database of disordered protein predictions.Nucleic Acids Res. 2013; 41 (23203878): D508-D51610.1093/nar/gks1226Crossref PubMed Scopus (336) Google Scholar) and are frequently involved in mediating protein-protein interactions in the cell. The functional advantages of disordered proteins include exposure of linear motifs for association with other proteins, accessibility for post-translational modifications, formation of large binding interfaces, and the ability to interact specifically with multiple partners. 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