Figure 3.

(A) Concentration-dependent diffusion slowdown from simulations. The slowdown is expressed relative to the diffusion coefficient for the least concentrated sub-box (134 g/L). The dashed lines represent fits with a second-order polynomial fraction. (B) Snapshots showing folded (upper row) and unfolded (lower row) simulation boxes at different protein concentrations. (C) Snapshots of sub-boxes (288 g/L) with a progressively increasing unfolded fraction r_u. Folded proteins are blue while unfolded proteins are shown in red. (D) Translational diffusion coefficients in sub-boxes (288 g/L; see panel C) with a varying fraction of unfolded proteins. The insets show the dependence, fitted to a power law, of the apparent unfolded fraction a_u on r_u. (E, F) The decrease in the translational diffusion coefficient of folded and unfolded proteins inside the partially unfolded sub-box (288 g/L) with increasing r_u. The values shown in panels A, E, and F as well as in the inset of panel D are averages across all temperatures, with error bars expressing the standard deviations. The results presented in this figure were obtained with the a99SB-disp force field; analogous plots for CHARMM36m, exhibiting qualitatively the same behavior, can be found in the SI.