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. 2019 Oct 22;8:e49223. doi: 10.7554/eLife.49223

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© 2019, Mohanty et al

This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

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Figure 3. — (A) Surface electrostatic potentials of UBC13 and TRAF6^RING. Circled regions indicate the complementary electrostatic surfaces on UBC13 and TRAF6^RING interfaces. The color scale ranges from −8 to +8 kT/e. (B) Potential of mean force (PMF) profiles as a function of COM separation along the x-axis for the association between UBC13 variants and TRAF6^RING. PMF profiles were calculated by averaging over five PMF profiles ranging from 2.5 ns to 10 ns. Error bars represent ± one standard error of the mean (SEM). (C) Stability and occupancy of the R14-E69 salt-bridge in the native window for the wild-type complex. D) Stability and occupancy of the R14-E69 and R14-E100 salt-bridge in the native window for the dUBC13/ TRAF6^RING complex. In (C) and (D), distance plots indicate the distance between R14 Cζ and E69/E100 Cδ atoms. The salt-bridge occupancy plots were generated as in Figure 2B. The salt-bridge occupancies are provided in Supplementary file 1-table S5. (E) Coulombic interaction energies (CIE) between UBC13 wild-type/Q100E and TRAF6^RING in native windows (mean COM separation = 2.7 nm) from the US simulations. The table in (F) reports the Mean ± SD of the interaction energies over 10 ns. (G) RMSD of TRAF6^RING (aa:70–109) against time in the UBC13 and dUBC13 complexes.

Figure 3—figure supplement 1. — (A) Surface electrostatic potentials of UBC13 and TRAF6^RING. Circled regions indicate the complementary electrostatic surfaces on UBC13 and TRAF6^RING interfaces. The color scale ranges from −8 to +8 kT/e. (B) Potential of mean force (PMF) profiles as a function of COM separation along the x-axis for the association between UBC13 variants and TRAF6^RING. PMF profiles were calculated by averaging over five PMF profiles ranging from 2.5 ns to 10 ns. Error bars represent ± one standard error of the mean (SEM). (C) Stability and occupancy of the R14-E69 salt-bridge in the native window for the wild-type complex. D) Stability and occupancy of the R14-E69 and R14-E100 salt-bridge in the native window for the dUBC13/ TRAF6^RING complex. In (C) and (D), distance plots indicate the distance between R14 Cζ and E69/E100 Cδ atoms. The salt-bridge occupancy plots were generated as in Figure 2B. The salt-bridge occupancies are provided in Supplementary file 1-table S5. (E) Coulombic interaction energies (CIE) between UBC13 wild-type/Q100E and TRAF6^RING in native windows (mean COM separation = 2.7 nm) from the US simulations. The table in (F) reports the Mean ± SD of the interaction energies over 10 ns. (G) RMSD of TRAF6^RING (aa:70–109) against time in the UBC13 and dUBC13 complexes.