Table 3.
Interaction results from MD simulations of BF2 and DesHDAP1 with DNA. H-bonding data reports the average percentages of all peptide•DNA hydrogen bonds that involved the nucleic acid phosphate groups. ΔΔGphos:ΔΔGbases is the ratio of the electrostatic free energy contributions of the phosphate groups to the electrostatic free energy contributions of the nucleic acid bases, as determined from Poisson-Boltzmann electrostatics calculations. All values are averaged over structures taken from the last 10 ns of simulations.
| BF2 | DesHDAP1 | |||
|---|---|---|---|---|
| Simulations | % H-bonds to phosphate | ΔΔGphos:ΔΔGbases | % H-bonds to phosphate | ΔΔGphos:ΔΔGbases |
| 1 | 100.0 | 23.5 | 84.9 | 6.5 |
| 2 | 100.0 | 14.8 | 75.9 | 9.8 |
| 3 | 96.3 | 10.9 | 98.5 | 19.4 |
| 4 | 88.0 | 10.5 | 72.8 | 5.6 |
| 5 | 97.4 | 12.9 | 76.6 | 6.4 |
| average ± SE | 96.3±2.2 | 14.5±2.4 | 81.7±4.6 | 9.6±2.6 |