Extreme disorder in an ultrahigh-affinity protein complex

Abstract

Molecular communication in biology is mediated by protein interactions. According to the current paradigm, the specificity and affinity required for these interactions are encoded in the precise complementarity of binding interfaces. Even proteins that are disordered under physiological conditions or that contain large unstructured regions commonly interact with well-structured binding sites on other biomolecules. Here we demonstrate the existence of an unexpected interaction mechanism: the two intrinsically disordered human proteins histone H1 and its nuclear chaperone prothymosin-α associate in a complex with picomolar affinity, but fully retain their structural disorder, long-range flexibility and highly dynamic character. On the basis of closely integrated experiments and molecular simulations, we show that the interaction can be explained by the large opposite net charge of the two proteins, without requiring defined binding sites or interactions between specific individual residues. Proteome-wide sequence analysis suggests that this interaction mechanism may be abundant in eukaryotes.

Intrinsically disordered domains: Sequence ➔ disorder ➔ function relationships

“…Such complexes are called fuzzy . Some fuzzy complexes remain entirely disordered yet bind with high affinity . Structure‐to‐disorder transitions upon binding have also been observed for some proteins, with at least one protein showing simultaneous structural changes in both directions for different regions …”

Ratiometric Single‐Molecule FRET Measurements to Probe Conformational Subpopulations of Intrinsically Disordered Proteins

“…Because of this plasticity, IDPs can bind to multiple partners with tunable affinities, and often function as hubs in cellular signaling processes (Wright & Dyson, 2015). As a result of these interactions, they may either maintain their unstructured state or undergo disorder‐to‐order transitions (Borgia et al., 2018; Sugase, Dyson, & Wright, 2007).…”

Perspective: Chain dynamics of unfolded and intrinsically disordered proteins from nanosecond fluorescence correlation spectroscopy combined with single-molecule FRET

“…While some IDPs fold upon binding, 3 many of them remain partially, largely, or even completely unstructured in the bound state. 131 In the extreme case, highly oppositely charged IDPs can interact with very high affinity and yet remain entirely unstructured in the complex 78 (Fig. 5).…”

“…47,60,69 By placing the fluorophores into different positions within the chain, these properties can be mapped across different parts of the molecule to test for the consistency with simple polymer models or deviations that might be caused by heterogeneity in intrachain interactions. 47,53,54,[77][78][79] In summary, single-molecule FRET in combination with rapid correlation analysis [nanosecond-FCS (nsFCS)] enables us to quantify both equilibrium distance distributions and chain dynamics in unfolded and intrinsically disordered proteins. These quantities provide a direct link to the concepts of polymer physics as a way of describing and understanding the behavior of unfolded proteins.…”