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. 2015 Aug 7;34(20):2506–2521. doi: 10.15252/embj.201592337

Figure 4.

Figure 4

Mechanism of phosphoubiquitin binding and conformational change in parkin
  1. Chemical shift perturbation map of R0RBR upon the addition of pUb. A colour gradient is used to show residues and the corresponding surface with little or no changes (grey) and scaled from light pink (average chemical shift change) to magenta (greater than average + 2 standard deviations). Parkin is shown as a transparent surface over a ribbon, and the orientation of the molecule is similar to that shown in Fig1C (bottom).
  2. Representative model of pUb interaction with parkin derived from HADDOCK calculations using chemical shift perturbation and paramagnetic relaxation enhancement experiments. One hundred water-refined structures were calculated that all showed a similar pUb orientation. The best twenty complexes showed excellent agreement (backbone rmsd 0.37 Å, pUb + R0RBR). The model shown has been rotated 90° (x) and 20° (y) with respect to Fig1C (top). The colours used are the same as in Fig1C with pUb shown in orange. The pS65 is shown as red sticks, and the basic triad consisting of K151, H302 and R305 are shown as blue sticks. Several important residues that had significant chemical shift changes in pUb upon R0RBR interaction are indicated.
  3. Representative isothermal titration calorimetry experiments showing the exothermic binding of pUbl to R0RBR parkin (left) and endothermic binding of pUb to R0RBR parkin (right).
  4. Bar graph showing the thermodynamic properties for Ubl, pUbl, Ub and pUb binding to R0RBR. The data show Ubl binding and pUbl binding are driven by enthalpy (ΔH) changes, while Ub binding and pUb binding are driven by entropy changes (ΔS) indicative of a pUb-induced conformational change.