Crowding Effects on the Mechanical Stability and Unfolding Pathways of Ubiquitin

Abstract

The interiors of cells are crowded, thus making it important to assess the effects of macromolecules on the folding of proteins. Using the self-organized polymer (SOP) model, which is a coarse-grained representation of polypeptide chains, we probe the mechanical stability of ubiquitin (Ub) monomers and trimers ((Ub)₃) in the presence of monodisperse spherical crowding agents. Crowding increases the volume fraction (Φ_c)-dependent average force (⟨f_u(Φ_c)⟩), relative to the value at Φ_c = 0, needed to unfold Ub and the polyprotein. For a given Φ_c, the values of ⟨f_u(Φ_c)⟩ increase as the diameter (σ_c) of the crowding particles decreases. The average unfolding force ⟨f_u(Φ_c)⟩ depends on the ratio D/R_g, where D ≈ σ_c(π/6Φ_c)^1/3, with R_g being the radius of gyration of Ub (or (Ub)₃) in the unfolded state. Examination of the unfolding pathways shows that, relative to Φ_c = 0, crowding promotes reassociation of ruptured secondary structural elements. Both the nature of the unfolding pathways and ⟨f_u(Φ_c)⟩ for (Ub)₃ are altered in the presence of crowding particles, with the effect being most dramatic for the subunit that unfolds last. We predict, based on SOP simulations and theoretical arguments, that ⟨f_u(Φ_c)⟩ ∼ Φ_c^1/3ν, where ν is the Flory exponent that describes the unfolded (random coil) state of the protein.