Figure 3 .

Two simulation scenarios were designed to elucidate the functional importance of TRAF clustering in regulation of downstream signaling pathway. The TRAF trimers in the first scenario contain three binding sites and can simultaneously form cis-interactions with three structural neighbors, whereas in a control system, only one binding site was assigned to each TRAF protein. The numbers of cis-interactions formed along the simulations in these two scenarios are plotted in (a). The distributions of fluctuations in the number of cis-interactions are shown as histograms in (b). The final configurations at the end of two simulation systems are compared with each other in (c) and (d). Finally, the outputs from the downstream signaling networks of these two systems, e.g. the numbers of NF-κB molecules, which bind to IκB and DNA, are also compared with each other in (e) and (f), respectively.