Figure 6
From: Dynamic recognition and linkage specificity in K63 di-ubiquitin and TAB2 NZF domain complex
MD simulations of linear di-Ub/TAB2 NZF and K33 di-Ub/TAB2 NZF. (A) FES of linear di-Ub/TAB2 NZF obtained in the MSES simulation, plotted on a two-dimensional space, Cα RMSD values of TAB2 NZF and di-Ub from the initial homology model, after superimposing Cα atoms of di-Ub (1–70). (B) The same as (A), but plotted on the two distances, dR42-Q686 and dE140-R683. (C) Two representative structures whose positions in the FES are indicated in (A,B). TAB2 NZF changes the position by rotation while maintaining the salt bridge, R72-E688. (D) Time courses of Cα RMSD value of K33 di-Ub/TAB2 NZF from the initial homology model, after superimposing Cα atoms of di-Ub (1–70), obtained in the three 150-ns MD simulations (colored in red, blue, and green). The blue curve overshoots the range of the figure. (E) Two representative structures indicated in (D).
