Figure 2

FES of K63 di-Ub/TAB2 NZF. (A) FES plotted on a two-dimensional space, Cα RMSD values of TAB2 NZF, and di-Ub from the crystal structure (PDB: 2wwz) after superimposing Cα atoms of the core regions of di-Ub (1–70). The inset is the same plot but calculated from five 150-ns MD simulations (Fig. S1A). The lower free energy region (<10 KJ/mol) is named as the “near-native” ensemble, while the higher free energy region (>10 KJ/mol) is named as the “non-native” ensemble. (B) The FES for the subset with the condition that TAB2 NZF contacts (any non-hydrogen atom pairs whose distance is less than 4 Å) both distal and proximal Ubs. (C) The same as (A) but plotted on the two Cα RMSD values of TAB2 NZF, one superimposing the distal Ub (1–70) and the other superimposing the proximal Ub (1–70). (D) Three representative structures of the complex whose position in the FES are indicated by the numbers in (A,C).