Table 3. Changes in the interaction energies and hydrogen bond numbers.
| Mutants | ΔCoulomb*(kJ/mol) | ΔLJ*(kJ/mol) | ΔHB† |
| M41E | −86.32 (−48.14) | 4.53 (5.14) | 1.27 (0.63) |
| F63W | −17.08 (3.82) | −11.02 (−2.08) | 0.80 (0.04) |
| V134L | −1.49 (−1.38) | −4.97 (−1.80) | 0 (0) |
| H159Q | −26.10 | 3.93 | 0.35 |
| D181E | −9.00 | 0.60 | 0.38 |
| M41E/F63W | −150.41 | 0.30 | 2.53 |
| F63W/D181E | 21.79 | 4.68 | −0.01 |
| V134L/H159Q | −32.28 | −1.75 | 0.50 |
*Differences in the interaction energies between the mutants and wild-type decoy receptor (Emut-Ewild, kJ/mol) were calculated using Gromacs4 package with an Amber03 force field. Each energy value represents the average of 3-ns molecular dynamics trajectories.
†
The number of hydrogen bonds was analyzed for each 3-ns molecular dynamics trajectory snapshot, and differences in their average values between the mutants and wild-type decoy receptor are shown as ΔHB.
Values in parenthesis were obtained by molecular dynamics simulations with the crystal structures of the single mutants (M41E, F63W, and V134L).