Table 1.
Binding free energies computed by the MM-GBSA methoda
| Componentb | scFv:METH | scFv:AMP-H2O | scFv:AMP |
|---|---|---|---|
| Δ Eele | -107.14 ± 6.99 | -132.96 ± 6.43 | -142.15 ± 7.31 |
| Δ Evdw | -24.56 ± 2.23 | -20.39 ± 2.12 | -22.89 ± 2.31 |
| Δ Gnonpol | -3.67 ± 0.08 | -2.56 ± 0.07 | -3.23 ± 0.07 |
| Δ Gpol | 107.15 ± 5.95 | 132.21 ± 7.20 | 135.20 ± 6.05 |
| Δ Gele+pol | 0.01 | -0.75 | -6.95 |
| Δ Gvdw+nonpol | -28.23 | -22.95 | -26.12 |
| Δ H | -28.21 ± 2.13 | -23.70 ± 3.49 | -33.07 ± 2.89 |
| T Δ S | -15.60 ± 6.59 | -15.4 ± 4.88 | -16.13 ± 6.42 |
| Δ Gbind | -12.61 | -8.30 | -16.94 |
| Δ Gexpc | -10.98 | -6.43 | |
a
All values are given in kcal/mol, and the symbols are explained in the text.
b
Component: ΔEele: electrostatic energy in the gas phase; ΔEvdW: van der Waals energy; ΔGnonpol: non-polar solvation energy; ΔGpol: polar solvation energy; ΔGele+pol = ΔGele +ΔGpol; ΔGvdw+nonpol = ΔEvdw +ΔGnonpol; ΔH = ΔEele +ΔEvdW +ΔGnonpol +ΔGpol; ΔTS: total entropy contribution.
c
The experimental binding free energies are calculated using the equation ΔGexp= - RTlnKi.