Figure 5.

Probability distributions of the inter-core-domain Q-score from the CG MD simulation with all of the $ϵ$’s in Eq. 1 set to 0.0 (left) and from the CG MD simulation with the updated parameters (right and right inset). The Q-score represents the ratio of the transiently formed contacts to the natively formed contacts. Natively formed contacts are defined using the x-ray crystal structure in which four core domains bind to its specific DNA (PDB ID: 3KMD) as a template structure. We calculated the probability distribution of each pair of the core domains. Because of the symmetry of the molecule, these pairs can be divided into three classes. Therefore, we mapped these three classes on to the cartoon of tetramerized CTetD (left inset). The color assignment is the same as that of Fig. 1A and B. To see this figure in color, go online.