Table 3.
Average RMS Differences (Å) with respect to the Canonical Forms of DNA for the Drude and CHARMM36 Simulations a
| DNA system | Drude |
C36 |
||
|---|---|---|---|---|
| vs A | vs B | vs A | vs B | |
| EcoR11 | 4.93 ± 0.67 4.00 ± 0.68 |
1.85 ± 0.39 1.73 ± 0.37 |
4.61 ± 0.651 3.54 ± 0.461 |
2.29 ± 0.501 1.88 ± 0.361 |
| JunFos | 6.19 ± 0.60 5.33 ± 0.55 |
1.89 ± 0.35 1.68 ± 0.29 |
6.06 ± 0.69 | 2.61 ± 0.57 |
| 3BSE | 6.29 ± 0.67 5.75 ± 0.68 |
2.32 ± 0.55 1.89 ± 0.44 |
5.21 ± 0.65 | 3.71 ± 0.91 |
| 1AXP | 5.20 ± 0.67 3.63 ± 0.49 |
2.26 ± 0.63 2.04 ± 0.56 |
4.02 ± 0.57 | 2.42 ± 0.58 |
| 1ZF7 | 4.24 ± 0.66 3.04 ± 0.47 |
1.49 ± 0.26 1.27 ± 0.25 |
4.23 ± 0.57 | 2.07 ± 0.51 |
| 2L8Q | 5.73 ± 0.73 4.58 ± 0.59 |
1.77 ± 0.42 1.55 ± 0.29 |
||
| 1ZF1(EtOH) | 1.95 ± 0.24 1.64 ± 0.20 |
4.23 ± 0.42 3.31 ± 0.36 |
1.34 ± 0.22 | 4.43 ± 0.31 |
| 1ZF1(H2O) | 3.32 ± 0.56 2.35 ± 0.39 |
2.21 ± 0.48 1.81 ± 0.36 |
4.06 ± 0.50 | 2.07 ± 0.52 |
a
Results over all non-hydrogen atoms obtained by excluding one terminal residue (first row) and the first two terminal residues (second row) on each end of the DNA molecule from the analysis. Errors represent the RMS fluctuations about the average. Data are based on 100 ns MD simulations for all systems except EcoR1. For EcoR1 sequence RMSD is calculated based on 200 ns simulations. (1) Additive C36 results for EcoR1 are from MD simulations carried out in this study. All other C36 results are from Ref.8