Figure 7. Transient complexes observed during unbiased association simulations.

(A) Black open circles denote TRAF6^RING (aa:70–109) centers of mass around UBC13 in the Cartesian coordinate space. Red, pink and blue colored symbols denote projections of the centers of masses on the coordinate planes. Projections of the centers of mass of TRAF6^RING in the native complex are shown as black open circles on the coordinate planes. The center of mass of the UBC13 helix α1, which is at the center of UBC13 interface, is shown as a yellow sphere at the origin. (B) Same as in (A) for dUBC13. (C) TRAF6^RING clusters calculated based on pairwise RMSD between UBC13/TRAF6^RING complexes (cutoff = 0.45 nm) are shown as orange spheres. Only representatives for clusters with greater than ten structures are shown. The UBC13 is represented in ribbon and colored green. The center of mass of UBC13 interface is shown as a green transparent sphere with 1 nm radius. The sidechain of R14 is shown and colored red. (D) Same as (C) for dUBC13. The region near R14, where TRAF6^RING clusters were absent in dUBC13 is shown as a red dotted curve in (C) and (D).

Figure 7—figure supplement 1. Free energy landscapes obtained from association MD (10 mM NaCl).

(A) and (B) are 2D-free energy landscapes of UBC13/TRAF6^RING and dUBC13/TRAF6^RING association, respectively. Both (A) and (B) are calculated as a function of minimum intermolecular salt-bridge distance (see Materials and methods) and TRAF6^RING RMSD with respect to its crystallographic orientation. Dotted black boxes indicate the native-like transient complex ensemble while the red dotted box in A indicates the native complex. Bins equal to or greater than 2.4 kcal mol⁻¹ are colored white.

Figure 7—figure supplement 2. RMSD analysis of UBC13/dUBC13 and TRAF6^RING association trajectories.

(A) RMSD analysis of the UBC13/TRAF6^RING trajectories, which show a native-like association. One trajectory at 10 mM NaCl showed TRAF6^RING RMSD values close (~0.25 nm) to its crystallographic orientation. (B) RMSD analysis of the dUBC13/TRAF6^RING association trajectories, which show a native-like association. In only one trajectory at 100 mM NaCl (black lines), TRAF6^RING RMSD values were transiently below 0.5 nm.