Table 5.
Effect of salt concentration on the calculated binding free energy
| Slope of the change in binding free energy ΔΔGbinding (kcal/mol) |
||
|---|---|---|
| Bound reference | Free reference | |
| Wild-type | 5.62 | 4.79 |
| Asn-1 | 5.63 | 4.80 |
| Lys-3 | 4.74 | 4.00 |
| Thr-4 | 5.61 | 4.80 |
| Arg-5 | 4.88 | 4.10 |
| Arg-6 | 4.69 | 4.00 |
| His-7 | 4.83 | 4.10 |
| Glu-8 | 6.22 | 5.42 |
| Arg-9 | 4.81 | 4.11 |
| Arg-10 | 4.72 | 4.00 |
| Arg-11 | 4.99 | 4.17 |
| Ile-15 | 5.60 | 4.79 |
Slope was calculated over the last 10 ns of the MD trajectories. Residues were substituted by alanine. Bound and free reference indicates that the trajectories from the complex or the isolated RNA and peptide, respectively, were used to represent the individual partner structures for calculating the binding free energies.