Figure 6. Analysis of transient complexes formed in the US simulations.

The US window corresponding to 3 nm COM distance of separation was analyzed. (A) The transient complex of UBC13 and TRAF6^RING at t = 2.50 ns is shown. A transient intermolecular salt-bridge between R14 and D57 is indicated by a red dotted circle. (B) The plot of COM separation against time for the UBC13/TRAF6^RING and dUBC13/TRAF6^RING complexes. (C) The distance between the R14-D57 transient contact is compared between the two complexes. The distances were measured between R14-Cζ and D57-Cγ atoms. (D) Coulombic interaction energy (CIE) plotted against time. (E) The contact distance of E100-D57 and R14-E100 contacts are shown against time for the dUBC13/TRAF6^RING complex. The distances were measured between R14-Cζ, E100-Cδ, and D57-Cγ atoms. (F) The transient complex of dUBC13 and TRAF6 at t = 0.35 ns, where E100 contacted D57.

Figure 6—figure supplement 1. Analysis of interaction energy and COM separation between UBC13 and dUBC13 complexes from multiple umbrella sampling windows.

(A) Coulombic interaction energy between E100^UBC13 and TRAF6^RING in US windows from 2.7 to 3.1 nm COM separation. Beyond 3.1 nm, the energy profile is negligible. Repulsive interactions represented by positive CIE values were observed between E100 (carboxylate oxygens) and TRAF6^RING within 3.0 nm COM separation in US simulations. (B) and (D) are the plots of COM separation against time for the UBC13/TRAF6^RING and dUBC13/TRAF6^RING complexes at 2.8 nm and 2.9 nm US windows, respectively. (C) and (E) are the plots of CIE between UBC13 (or dUBC13) and TRAF6^RING at 2.8 nm and 2.9 nm US windows, respectively.