Diffusion, Crowding & Protein Stability in a Dynamic Molecular Model of the Bacterial Cytoplasm
Figure 2
Parameterization and sampling in the cytoplasm model.
A. Extrapolated long-time Dtrans values for GFP from BD simulations performed with different energy models; ‘ε’ refers to the well-depth (in kcal/mol) of the Lennard-Jones potential used to describe hydrophobic interactions (see Methods). Solid, long-dash, short-dash and dotted lines are the experimental Dtrans values from refs. 14, 15, 16 and 17 respectively. The vertical arrow indicates the energy model selected for further BD simulation. B. Average of the maximum distance moved during the 15µs of production for all molecule types plotted versus their molecular weights. Upper error bars indicate the largest value of the maximum distance moved found for any molecule of that type; lower error bars indicate the smallest value of the maximum distance moved. All distances expressed in terms of the molecular diameters (obtained by doubling the hydrodynamic radius calculated by HydroPro [88]. C. Average number of unique neighbors encountered by each molecule type as a function of simulation time; each line refers to a different molecule type. D. Average number of neighbors possessed by each molecule type at any instant, plotted versus molecular weight. E. Time constant for the slower of the two exponentials describing the rate at which neighbors are lost, plotted for each molecule type versus molecular weight. F. Average number of times that each molecule type's immediate neighbors exchange during 15µs simulation plotted versus molecular weight of each molecule type.