Compensatory Adaptations of Structural Dynamics in an Intrinsically Disordered Protein Complex

Abstract

Intrinsically disordered proteins (IDPs) play crucial roles in protein interaction networks and in this context frequently constitute important hubs and interfaces. Here we show by a combination of NMR and EPR spectroscopy that the binding of the cytokine osteopontin (OPN) to its natural ligand, heparin, is accompanied by thermodynamically compensating structural adaptations. The core segment of OPN expands upon binding. This "unfolding-upon-binding" is governed primarily through electrostatic interactions between heparin and charged patches along the protein backbone and compensates for entropic penalties due to heparin-OPN binding. It is shown how structural unfolding compensates for entropic losses through ligand binding in IDPs and elucidates the interplay between structure and thermodynamics of rapid substrate-binding and -release events in IDP interaction networks.

FuzDB: database of fuzzy complexes, a tool to develop stochastic structure-function relationships for protein complexes and higher-order assemblies

“…ID regions may remain dynamic and exhibit a fast exchange of conformations in the complex state [FC0072 (22)]. Fuzzy assemblies can also be generated by ‘unfolding upon binding’ [FC0100 (23)]. Fuzzy regions do not appear in crystal structures of the protein complex, as indicated by missing electron density.…”

Current structural biology of the heparin interactome

“…Paramagnetic relaxation enhancements for spin-labeled cysteine mutants of OPN showed that the heparin-binding site becomes more rigid upon heparin interaction, compensated for elsewhere in the molecule by an increase in the flexibility. The heparin binding site of OPN is a positively charged patch near residue 155, but substantial other stretches of the OPN peptide chain are negatively charged and displaced on heparin binding [24].…”

Investigation of Intrinsically Disordered Proteins through Exchange with Hyperpolarized Water

“…Most importantly,t he glycine residues are not observable in the absence of heparin. [20] This exposure accelerates exchange with hyperpolarized HDO,t hereby rendering them amenable to detection. This leads to distinct effects in the glycine region.…”