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Contributions
|
Trimer
|
3 × Monomer
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Difference
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Notes
|
|---|
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1. G
sol
|
-11,722.5a ± 17.6b
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-11,319.6 ± 37.9
|
-402.9 ± 42.8
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Solvation free energy
|
1-1.
|
0.9 ± 0.0
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446.6 ± 1.0
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-445.7 ± 1.0
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Non-polar part
|
1-2. 
|
-11,723.5 ± 17.6
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-11,766.2 ± 37.9
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42.8 ± 41.8
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Polar part
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|
2. H
MM
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-36,968.6 ± 22.1
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-37,206.5 ± 46.5
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237.9 ± 51.4
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Molecular mechanical energy
|
|
2-1. H
elec
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-50,075.3 ± 20.2
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-50,218.7 ± 43.7
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143.4 ± 48.1
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Electrostatic energy
|
|
2-2. H
vdW
|
-9,430.9 ± 5.8
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-9,420.8 ± 13.7
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-10.2 ± 14.9
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van der Waals energy
|
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2-3. H
conf
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22,537.6 ± 6.6
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22,432.9 ± 7.5
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104.7 ± 10.0
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Conformational energy
|
|
3. -
TS
tot
|
[~-19,430]c
|
-19,488.5
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[~60]
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Entropic energy
|
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3-1.-TS
tran
|
(-18.6)d
|
-52.9
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(34.4)
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Translational part
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3-2. TS
rot
|
(-20.0)
|
-56.3
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(36.3)
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Rotational part
|
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3-3. TS
vib
|
[~-19,390]
|
-19,379.3
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[~ -10]
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Vibrational part
|
|
4. G
tot
|
-48,691.1 ± 28.2e
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-48,526.1 ± 60.0
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-165.0 ± 66.3
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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
.
.