Depletion interactions modulate coupled folding and binding in crowded environments

TL;DR

This study investigates how macromolecular crowding influences the folding, binding, and stability of intrinsically disordered proteins (IDPs), revealing that depletion interactions and crowder size significantly modulate these processes.

Contribution

It introduces a quantitative framework combining depletion interactions and polymer physics to explain IDP behavior in crowded cellular environments.

Findings

IDP complex stability increases with crowder size and concentration

Depletion interactions explain the effects better than scaled-particle theory

Crowder size and polymer properties critically influence IDP interactions

Abstract

Intrinsically disordered proteins (IDPs) abound in cellular regulation. Their interactions are often transitory and highly sensitive to salt concentration and posttranslational modifications. However, little is known about the effect of macromolecular crowding on the kinetics and stability of the interactions of IDPs with their cellular targets. Here, we investigate the influence of crowding on the coupled folding and binding between two IDPs, using polyethylene glycol as a crowding agent across a broad size range. Single-molecule F\"orster resonance energy transfer allows us to quantify several key parameters simultaneously: equilibrium dissociation constants, kinetic association and dissociation rates, and translational diffusion coefficients resulting from changes in microviscosity. We find that the stability of the IDP complex increases not only with the concentration but also with the size of the crowders, in contradiction to scaled-particle theory. However, both the equilibrium and the kinetic results can be explained quantitatively by depletion interactions if the polymeric properties of proteins and crowders are taken into account. This approach thus provides an integrated framework for addressing the complex interplay between depletion effects and polymer physics on IDP interactions in a crowded environment.