Table 2.
Results of Thr-Out MD simulations. For each of the ten, 25 ns MD simulations, two RMSD measurements and the results of an MM-PBSA analysis are shown. Based on visual inspection, the RMSDs, and the energetics, five of the 10 simulations exhibited stable SS binding.
| # | Complete SS RMSD (Å) |
Core SS RMSD (Å) |
ΔEelec
(kcal/mol) |
ΔEvdw
(kcal/mol) |
ΔGpolar
(kcal/mol) |
ΔGnonpolar
(kcal/mol) |
–TΔSconfig
(kcal/mol) |
ΔGtotal
(kcal/mol) |
|---|---|---|---|---|---|---|---|---|
| 1 | 3.7 ± 0.3 | 2.2 ± 0.2 | −58.7 ± 1.5 | −86.7 ± 11.3 | 125.8 ± 10.2 | −6.5 ± 0.1 | 26.9 | 0.8 ± 2.6 |
| 2 | 3.1 ± 0.1 | 2.0 ± 0.1 | −50.8 ± 0.5 | −124.5 ± 4.3 | 145.4 ± 4.0 | −5.8 ± 0.1 | 28.5 | −7.2 ± 0.7 |
| 3 | 4.2 ± 0.1 | 3.5 ± 0.1 | −50.0 ± 0.8 | −187.1 ± 6.2 | 210.3 ± 6.6 | −6.4 ± 0.1 | 26.0 | −7.3 ± 1.1 |
| 4 | 3.0 ± 0.1 | 2.6 ± 0.1 | −54.3 ± 1.8 | −191.8 ± 11.0 | 210.4 ± 10.2 | −6.4 ± 0.1 | 26.1 | −16.1 ± 2.8 |
| 5 | 2.7 ± 0.1 | 2.6 ± 0.1 | −60.4 ± 0.6 | −166.5 ± 3.2 | 196.3 ± 2.9 | −6.1 ± 0.1 | 26.1 | −10.5 ± 0.8 |
|
| ||||||||
| 6 | 14.2 ± 0.8 | 9.7 ± 0.7 | −30.4 ± 1.9 | −94.8 ± 8.6 | 110.6 ± 7.9 | −4.1 ± 0.2 | 34.0 | 15.2 ± 1.4 |
| 7 | 6.8 ± 0.3 | 4.5 ± 0.1 | −50.4 ± 0.8 | −112.8 ± 5.9 | 143.1 ± 5.5 | −6.0 ± 0.1 | 28.8 | 2.8 ± 1.4 |
| 8 | 7.4 ± 1.1 | 4.5 ± 1.0 | −45.7 ± 4.0 | −82.6 ± 26.2 | 111.3 ± 24.7 | −5.7 ± 0.2 | 34.2 | 11.5 ± 3.7 |
| 9 | 6.0 ± 1.3 | 4.1 ± 1.3 | −44.1 ± 4.1 | −81.4 ± 17.2 | 102.2 ± 18.3 | −5.5 ± 0.4 | 30.2 | 1.4 ± 3.8 |
| 10 | 7.9 ± 0.9 | 4.6 ± 0.5 | −40.6 ± 2.0 | −95.2 ± 16.2 | 117.4 ± 15.5 | −5.5 ± 0.2 | 35.8 | 11.9 ± 2.7 |
|
| ||||||||
| Average ΔGtotal for SS bound states (simulations 1-5): | −8.1 ± 2.5 | |||||||