Figure 4. Individual-based models of chaperone protein diffusion and aggregation.

(A) Geometry of the 3D model used in individual-based models for E. coli intracellular space. Numbers indicate distances in µm. The blue boxes inside the bacteria locate the nucleoids, where increased molecular crowding is modeled by the insertion of bulk immobile obstacles. (B) Comparison between simulations and experiments of the localization at first detection of the protein aggregates along the long axis (x-axis). The full lines show the spatial distributions extracted from the simulations with different detection thresholds (an aggregate must contain at least 5, 10, 20 or 50 monomeric proteins, respectively, to be detected). Total number of proteins in the simulations N_p = 100. The dashed line is an histogram showing the distribution of the experimental data. (C–E) Time-evolution of the probabilities to observe exactly 1 (red), 2 (green), 3 (blue) or more than for 4 (brown) distinct aggregates simultaneously in the simulations. The simulations emulated non-stressed conditions (C), with N_p = 100 total proteins and aggregate detection threshold = 30 or heat-shock triggered aggregation, with N_p = 7,000 total proteins and aggregate detection threshold = 30 (D) or 1750 (E).