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.