The free energy folding penalty accompanying binding of intrinsically disordered α‐helical motifs

Abstract

Intrinsically disordered proteins (IDPs) are abundant in eukaryotic proteomes and preform critical roles in many cellular processes, most often through the association with globular proteins. Despite lacking a stable three‐dimensional structure by themselves, they may acquire a defined conformation upon binding globular targets. The most common type of secondary structure acquired by these binding motifs entails formation of an α‐helix. It has been hypothesized that such disorder‐to‐order transitions are associated with a significant free energy penalty due to IDP folding, which reduces the overall IDP‐target affinity. However, the exact magnitude of IDP folding penalty in α‐helical binding motifs has not been systematically estimated. Here, we report the folding penalty contributions for 30 IDPs undergoing folding‐upon‐binding and find that the average IDP folding penalty is +2.0 kcal/mol and ranges from 0.7 to 3.5 kcal/mol. We observe that the folding penalty scales approximately linearly with the change in IDP helicity upon binding, which provides a simple empirical way to estimate folding penalty. We analyze to what extent do pre‐structuring and target‐bound IDP dynamics (fuzziness) reduce the folding penalty and find that these effects combined, on average, reduce the folding cost by around half. Taken together, the presented analysis provides a quantitative basis for understanding the role of folding penalty in IDP‐target interactions and introduces a method estimate this quantity. Estimation and reduction of IDP folding penalty may prove useful in the rational design of helix‐stabilized inhibitors of IDP‐target interactions. Statement The α‐helical binding motifs are ubiquitous among the intrinsically disordered proteins (IDPs). Upon binding their targets, they undergo a disorder‐to‐order transition, which is accompanied by a significant folding penalty whose magnitude is generally not known. Here, we use recently developed statistical‐thermodynamic model to estimate the folding penalties for 30 IDPs and clarify the roles of IDP pre‐folding and bound‐state dynamics in reducing the folding penalty.

Evolutionary fine-tuning of residual helix structure in disordered proteins manifests in complex structure and lifetime

“…The relatively low binding affinity determined for DREB2A(244-272)-R266G was due to decreased binding enthalpy, only partly compensated by entropy. This is in accordance with an analysis by Lah et al 49 , according to which DREB2A(244-272)-R266G would be energetically punished for having less residual structure, but also a higher degree of dynamics in the bound state oppositely reducing the folding penalty. The relation between residual helicity and the amount of formed structure in complex is understudied 21 .…”

Fuzzy recognition by the prokaryotic transcription factor HigA2 from Vibrio cholerae

“…We have previously analyzed the thermodynamics of the HigA2–HigB2 folding-upon-binding interaction and observed that the binding interface is highly optimized in terms of enthalpy, reaching similar levels as in the tightest protein complexes like barnase-barstar 27 . Given that the HigA2–HigB2 binding affinity is in the picomolar range, such strong optimization of interactions is necessary to compensate for the IDR folding free energy penalty, which for folding-upon-binding interactions can be as high as +3.5 kcal/mol 42 . Even though the penalty arising from the restriction of the IDR conformational space, in principle, lowers binding affinity, it is conceivable that it also stimulates the formation of stronger interactions, leading to increased specificity.…”

Extending MeCP2 interactome: canonical nucleosomal histones interact with MeCP2

“…strongly exothermic) accompanied by a large entropic penalty, probably arising from mobility restriction, or even partial refolding, of some disordered regions upon binding, as observed in the circular dichroism spectra of the complexes, which overwhelms the favorable entropic contribution from dehydration of the binding interfaces. Strong enthalpic contributions are common in protein-protein interactions involving IDPs ( 63 , 64 ). In the cases where a considerable reduction of binding affinity was observed (e.g.…”

“…Flexible, highly dynamic regions facilitate structural rearrangements necessary for allosteric interdomain regulation and for exposing different motifs to interact with different biological partners. Interactions in IDPs are often characterized by a moderate-to-low binding affinity and a transient nature, due to the energetic penalty stemming from the conformational change coupled to the binding ( 14 , 15 ).…”