Table 5.
Binding free energies and different Components of the binding free energy using the MM PBSA approximations for interaction within symmetrically segmented proto-filaments (single layer, between the first pentameric and the second pentameric units) and proto-filament pairs (double layer, between the upper and the lower β-hairpin units)
| Energy components | WT (SL) | F15L (SL) | F23L (SL) | Y37L (SL) | WT- F15L (SL) | WT- F23L (SL) | WT- Y37L (SL) | WT (DL) | F23L (DL) | Y37L (DL) |
|---|---|---|---|---|---|---|---|---|---|---|
| Δ Eelec | 1038.7±182.0 | 1055.1±94.9 | 1006.1±38.2 | 1047.9±146.2 | 1148.5±118.5.4 | 960.9±9.9 | 1057.5±162.8 | 453.7±20.0 | 570.2±12.0 | 482.8±25.4 |
| Δ Evdw | −188.9±6.1 | −187.3±2.6 | −187.5±11.1 | −187.0±4.5 | −190.8±5.0 | −186.7±6.2 | −190.9±0.1 | −206.5±17.7 | −98.8±12.0 | −211.8±3.7 |
| Δ EPB | −1004.7±179.0 | −1008.3±95.0 | −969.1±26.2 | −1007.7±145.0 | −1104.1±117.0 | −921.5±5.4 | −1020.7±159.1 | −395.5±24.9 | −531.4±18.6 | −397.4±14.8 |
| Δ ESA | 108.3±0.8 | 108.9±0.1 | 108.3±6.4 | 107.1±2.1 | 109.1±3.2 | −78.5±3.4 | 108.3±0.1 | 120.9±0.5 | 58.5±7.3 | 126.7±2.6 |
| Δ Epolar | 34.4±2.7 | 46.9±0.1 | 37.1±12.0 | 40.2±1.3 | 44.4±1.5 | 39.4±4.4 | 36.7±3.7 | 58.2±4.7 | 38.8±6.6 | 85.4±10.6 |
| Δ Enonpolar | −118.3±49.9 | −109.4±41.3 | −79.2±4.6 | −80.1±2.4 | −146.4±6.6 | −78.5±3.4 | −82.5±0.3 | −85.6±17.2 | −38.4±6.7 | −85.2±6.4 |
| Δ Gbinding | −46.3±2.6 | −31.6±2.6 | −42.1±7.4 | −39.9±1.1 | −37.3±3.3 | −39.1±7.8 | −45.8±3.4 | −27.5±12.5 | 0.4±0.2 | 0.2±4.2 |
*
The data are averages of two independent 40 ns simulation with the corresponding standard deviations. All values are in kcal/mol. The polar term is the sum of Coulomb interaction energy (Eelec) and polar contribution to the solvation free energy (EPB). The nonpolar term consists of takes the van der Waals interaction energies (EvdW) and the nonpolar contribution to the solvation free energy (ESA)