Table 2 Binding free energy of pre-pore Cry4Aa trimer in solution
Contributions | Trimer | 3 × Monomer | Difference | Notes |
|---|---|---|---|---|
1. G sol | -11,722.5a ± 17.6b | -11,319.6 ± 37.9 | -402.9 ± 42.8 | Solvation free energy |
1-1. | 0.9 ± 0.0 | 446.6 ± 1.0 | -445.7 ± 1.0 | Non-polar part |
1-2. | -11,723.5 ± 17.6 | -11,766.2 ± 37.9 | 42.8 ± 41.8 | Polar part |
2. H MM | -36,968.6 ± 22.1 | -37,206.5 ± 46.5 | 237.9 ± 51.4 | Molecular mechanical energy |
2-1. H elec | -50,075.3 ± 20.2 | -50,218.7 ± 43.7 | 143.4 ± 48.1 | Electrostatic energy |
2-2. H vdW | -9,430.9 ± 5.8 | -9,420.8 ± 13.7 | -10.2 ± 14.9 | van der Waals energy |
2-3. H conf | 22,537.6 ± 6.6 | 22,432.9 ± 7.5 | 104.7 ± 10.0 | Conformational energy |
3. - TS tot | [~-19,430]c | -19,488.5 | [~60] | Entropic energy |
3-1.-TS tran | (-18.6)d | -52.9 | (34.4) | Translational part |
3-2. TS rot | (-20.0) | -56.3 | (36.3) | Rotational part |
3-3. TS vib | [~-19,390] | -19,379.3 | [~ -10] | Vibrational part |
4. G tot | -48,691.1 ± 28.2e | -48,526.1 ± 60.0 | -165.0 ± 66.3 | Free energy (1+2) |
[~-100] | Free energy (1+2+3) |
- Binding free energy (in kcal/mol) calculated as the difference between the free energy of Cry4Aa trimer in solution and that of three separated Cry4Aa monomers in solution.
- a Energy was calculated as an average over 50 snapshots taken at 100 ps interval from the last 5 ns of the 10-ns MD simulations.
- b Error in energy was calculated as the standard error of the mean.
- c Energies in square brackets were guessed values based on data from simulations of protein complexes [45, 46].
- d Energies in round brackets were theoretical estimated values using statistical mechanics and the entropic energies of Cry4Aa monomer.
- e Error in adding or subtracting two values of energies E1 ± ΔE1 and E2 ± ΔE2 was estimated as
.
.