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Table 2 Binding free energy of pre-pore Cry4Aa trimer in solution

From: Combined molecular dynamics and continuum solvent studies of the pre-pore Cry4Aa trimer suggest its stability in solution and how it may form pore

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)
  1. 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.
  2. 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.
  3. b Error in energy was calculated as the standard error of the mean.
  4. c Energies in square brackets were guessed values based on data from simulations of protein complexes [45, 46].
  5. d Energies in round brackets were theoretical estimated values using statistical mechanics and the entropic energies of Cry4Aa monomer.
  6. e Error in adding or subtracting two values of energies E1 ± ΔE1 and E2 ± ΔE2 was estimated as .