Table 1. Hydrogen bond formation propensity for the C-HBs of MDM2, both in the apo protein and in the p53-MDM2 wild-type complex.
In both cases, we denote as PDB-BHB the state value of the BHB in the PDB (1 = formed; 0 = not formed), D-BHB is the fraction of time the BHB is formed in the dynamics and the value D is given by: D = PDB-BHB—D-BHB. We note there that the C-HBs are determined in the apo protein and they are named as such also when considered in the complex. From their behavior in the protein complex we would not identify them as C-HBs. Thus, C-BHs are “quenched” upon association.
| C HBs | MDM2 apo protein | MDM2-p53 complex | |||||
|---|---|---|---|---|---|---|---|
| PDB-BHB | D-BHB | D | PDB-BHB | D-BHB | D | ||
| 57 | 53 | 0 | 0.9007 | -0.9007 | 1 | 0.9275 | 0.0725 |
| 62 | 58 | 1 | 0.3081 | 0.6919 | 1 | 0.94325 | 0.05675 |
| 99 | 95 | 1 | 0.4368 | 0.5632 | 1 | 0.82825 | 0.17175 |
| 100 | 96 | 1 | 0.5519 | 0.44809997 | 1 | 0.904 | 0.096 |
| 103 | 99 | 1 | 0.1549 | 0.8451 | 1 | 0.8375 | 0.1625 |