Simulations of a protein fold switch reveal crowding-induced population shifts driven by disordered regions

Macromolecular crowding effects on globular proteins, which usually adopt a single stable fold, have been widely studied. However, little is known about crowding effects on fold-switching proteins, which reversibly switch between distinct folds. Here we study the mutationally driven switch between the folds of G(A) and G(B), the two 56-amino acid binding domains of protein G, using a structure-based dual-basin model. We show that, in the absence of crowders, the fold populations P(A) and P(B) can be controlled by the strengths of contacts in the two folds, κ(A) and κ(B). A population balance, P(A) ≈ P(B), is obtained for κ(B)/κ(A) = 0.92. The resulting model protein is subject to crowding at different packing fractions, ϕ(c). We find that crowding increases the G(B) population and reduces the G(A) population, reaching P(B)/P(A) ≈ 4 at ϕ(c) = 0.44. We analyze the ϕ(c)-dependence of the crowding-induced G(A)-to-G(B) switch using scaled particle theory, which provides a qualitative, but not quantitative, fit of our data, suggesting effects beyond a spherical description of the folds. We show that the terminal regions of the protein chain, which are intrinsically disordered only in G(A), play a dominant role in the response of the fold switch to crowding effects.