Table 1.
Results of Thr-In 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, nine 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 | 5.4 ± 0.4 | 2.1 ± 0.1 | −53.7 ± 0.9 | −172.2 ± 5.7 | 190.1 ± 5.2 | −6.4 ± 0.1 | 29.1 | −12.9 ± 1.2 |
| 2 | 3.3 ± 0.3 | 1.6 ± 0.1 | −54.2 ± 1.7 | −133.4 ± 11.9 | 154.7 ± 11.2 | −6.3 ± 0.1 | 27.9 | −11.2 ± 2.5 |
| 3 | 3.7 ± 0.2 | 2.1 ± 0.1 | −57.0 ± 1.1 | −142.3 ± 7.0 | 172.1 ± 6.9 | −6.3 ± 0.1 | 30.4 | −3.1 ± 1.7 |
| 4 | 4.1 ± 0.3 | 1.9 ± 0.1 | −50.4 ± 1.5 | −141.7 ± 14.3 | 164.9 ± 13.7 | −6.0 ± 0.1 | 28.2 | −5.0 ± 2.8 |
| 5 | 3.6 ± 0.1 | 1.7 ± 0.1 | −51.2 ± 1.1 | −141.5 ± 5.9 | 158.6 ± 5.5 | −6.2 ± 0.1 | 28.5 | −11.8 ± 1.4 |
| 6 | 3.1 ± 0.2 | 2.7 ± 0.2 | −52.4 ± 0.9 | −125.8 ± 6.0 | 145.4 ± 5.5 | −6.2 ± 0.1 | 27.7 | −11.4 ± 1.4 |
| 7 | 3.4 ± 0.1 | 1.7 ± 0.1 | −53.5 ± 1.0 | −201.2 ± 6.4 | 215.7 ± 5.9 | −6.6 ± 0.1 | 26.7 | −18.8 ± 1.4 |
| 8 | 3.4 ± 0.1 | 2.2 ± 0.1 | −52.0 ± 1.1 | −130.7 ± 5.8 | 158.2 ± 5.6 | −6.2 ± 0.1 | 26.2 | −4.4 ± 1.0 |
| 9 | 3.1 ± 0.1 | 2.6 ± 0.1 | −54.1 ± 0.5 | −150.8 ± 3.2 | 160.7 ± 3.0 | −6.4 ± 0.1 | 27.0 | −23.5 ± 0.6 |
|
| ||||||||
| 10 | 9.9 ± 0.8 | 5.3 ± 0.4 | −41.6 ± 1.3 | −100.8 ± 9.1 | 125.0 ± 8.6 | −5.3 ± 0.1 | 34.9 | 12.3 ± 1.8 |
|
| ||||||||
| Average ΔGtotal for SS bound states (simulations 1-9): | −11.3 ± 2.4 | |||||||