Table 1. Computational predictions by osprey/fries/EWAK* that were selected for experimental validation.
Each row of the table shows the results of the redesign of a residue position in c-Raf-RBD in the c-Raf-RBD:KRas PPI that were also selected for experimental validation (all of the computational results are listed in S3 Table). The table contains the values for upper and lower bounds on log(K*) values (the calculation of these bounds is described in detail in [32]). Mutations highlighted in yellow, blue, and pink were selected for experimental testing and validation. The two residues highlighted in blue are the best previously discovered [60] mutations that improve binding (independently and additively) and are included in our tightest binding variant, c-Raf-RBD(RKY) (Figs 8, 9 and 10). The variants highlighted in yellow are, to the best of our knowledge, never-before-tested variants that are predicted to increase the binding of c-Raf-RBD to KRasGTP. The variant highlighted in pink was selected for experimental testing to act as a mutation predicted to be comparable to wild-type to test how accurately osprey predicted the effects of these mutations.
| Mutation | Lower Bound log(K*) | Upper Bound log(K*) |
|---|---|---|
| T57M | 3.43 | 3.46 |
| T57 | 3.82 | 3.92 |
| T57K | 5.01 | 5.07 |
| N71 | 7.25 | 7.49 |
| N71R | 9.66 | 10.10 |
| A85 | 26.3 | 26.9 |
| A85K | 30.7 | 32.3 |
| K87 | 13.4 | 14.1 |
| K87Y | 14.1 | 14.2 |
| V88 | 16.5 | 16.6 |
| V88Y | 17.3 | 17.6 |
| V88F | 18.0 | 18.2 |