Diffusion, Crowding & Protein Stability in a Dynamic Molecular Model of the Bacterial Cytoplasm
Figure 4
Thermodynamic effects of the cytoplasm model on protein folding and association equilibria.
A. Computed stabilization of the folded state relative to the unfolded state for two experimentally-studied proteins; experimental data for Lrp (λ6-85) and CRABP taken from refs [4] and [32] respectively. ‘steric sampling’ indicates that insertions were performed on snapshots taken from a BD simulation performed with the ‘steric’ energy function; ‘steric scoring’ etc. indicates that the ‘steric’ energy function was used to calculate the cytoplasm-interaction energies, Eint, of the inserted proteins. B. Histogram of interaction energies, Eint, obtained for all non-clashing insertions of the folded and unfolded state conformations of CRABP with snapshots sampled from the ‘full’ model BD simulations; inset shows the same for λ6-85. C. Distribution of radius of gyration values for the 1000 unfolded conformations generated with the RCG software [31]; distributions are plotted in order of increasing molecular weight of the studied proteins. D. Same as A. but showing computed results for six other proteins, listed in order of increasing molecular weight. E. Computed stabilization of dimeric form relative to two separated monomers for eleven proteins, listed in order of increasing molecular weight. F. Computed stabilization of oligomeric form relative to separated monomers for three proteins.