Fig. 4.

Two different approaches for modeling biochemical processes under crowding. (A) The direct simulation approach follows the horizontal paths whereas the postprocessing approach follows the vertical paths, illustrated on the folding process of a protein. The same free energy difference δΔG, here representing the effect of crowding on the folding free energy, is obtained by following either the horizontal paths (δΔG = ΔG_f −ΔG_f0) or the vertical paths (δΔG = Δμ_F − Δμ_U). (b) In the direct simulation approach, one follows the folding transition in the presence of crowders. Here the protein is shown in a folded conformation. (c) In the postprocessing approach, one simulates only the folded state and the unfolded state, not their inter-conversion, and does so in the absence of crowders [73]. To calculate Δμ_F, folded conformations are fictitiously inserted into the crowders. An analogous calculation yields Δμ_U.