Fig. 6.
In order to understand how stability of binding affects the dynamics of ligand receptor interactions and patterns of oligomerization, we turned the binding affinity into different values by keeping the on rates of trans and cis interactions as constant and changing their values of off rate. TNF ligands are in their trimeric state. Simulations were carried out for all different combinations. At the end of each simulation trajectory, we calculated and plot the histograms for the distributions of (a) the number of ligand-receptor trans-interactions, (b) the number of receptor-receptor cis-interactions, (c) the average size of formed oligomers, and (d) the largest oligomer found in the system, respectively. We found that large oligomers cannot be derived from the strongest cis-interactions. For instance, we compared the simulations between the weak and strong cis-interactions, but with the same trans-interactions. (e) We plot the configuration with weak cis-interactions (off rate equals 1 × 103s−1). (f) Under the same trans-interactions (off rate equals 1 × 102s−1), we plot the configuration with strong cis-interactions (off rate equals 1 × 100s−1).