Table 1.
MM-PBSA estimates of free energies of binding (dG) together with all important energetic components and numbers of dendrimer/protein H-bonds detected in final configurations
| Dendrimer | dH | TdS | dG | VDW | EEL | EPB | ENP | H-bonds |
|---|---|---|---|---|---|---|---|---|
| G2_S16 (A) | −106.78 (26.15) |
−46.70 (9.30) |
−60.08 (27.76) |
−59.03 (14.15) |
−526.49 (130.25) |
516.57 (129.77) |
−37.83 (7.82) |
21 |
| G2_S16 (B) | −109.21 (19.36) |
−50.57 (11.17) |
−58.64 (22.35) |
−71.34 (7.13) |
−343.05 (70.77) |
345.61 (69.53) |
−40.43 (2.02) |
11 |
| G2_S16 (C) | −101.43 (20.43) |
−47.45 (8.99) |
−53.97 (22.32) |
−62.41 (6.91) |
117.49 (137.20) |
−119.16 (137.33) |
−37.34 (3.62) |
7 |
| G2_S16 (D) | −70.98 (17.53) |
−50.09 (7.08) |
−20.89 (18.90) |
−41.51 (7.58) |
−341.54 (66.61) |
340.26 (68.62) |
−28.19 (3.99) |
15 |
| G2_S16 (E) | −66.65 (22.11) |
−42.12 (10.18) |
−24.54 (24.34) |
−36.58 (5.73) |
297.45 (92.03) |
−299.85 (95.06) |
−27.67 (2.42) |
11 |
| G2_S16 (F) | −151.57 (21.33) |
−60.13 (12.62) |
−91.44 (24.79) |
−89.16 (7.83) |
−413.22 (67.98) |
402.39 (69.24) |
−51.58 (2.11) |
19 |
| G2_S16 (N-term) | −140.61 (10.98) |
−64.97 (5.60) |
−75.65 (12.33) |
−74.32 (5.77) |
−3,682.17 (170.52) |
3,663.67 (169.95) |
−47.80 (2.65) |
22 |
| G1_S4 (A) | −120.80 (8.49) |
−45.54 (4.34) |
−75.26 (9.54) |
−74.92 (6.55) |
−269.87 (44.99) |
265.27 (44.09) |
−41.28 (2.19) |
7 |
| G1_S4 (B) | −113.17 (12.74) |
−43.17 (11.74) |
−70.01 (17.32) |
−73.51 (9.51) |
−188.86 (40.40) |
186.81 (39.35) |
−37.61 (2.97) |
6 |
| G1_S4 (C) | −100.13 (12.99) |
−41.24 (5.45) |
−58.88 (14.08) |
−63.51 (9.33) |
−197.97 (63.33) |
196.96 (62.63) |
−35.61 (3.58) |
5 |
| G1_S4 (D) | −88.92 (8.28) |
−34.52 (9.66) |
−54.40 (12.73) |
−55.02 (6.01) |
−246.20 (46.48) |
242.40 (45.52) |
−30.10 (2.76) |
6 |
| G1_S4 (E) | −104.28 (10.37) |
−45.43 (7.08) |
−58.85 (12.56) |
−65.73 (7.48) |
20.09 (30.60) |
−21.39 (30.10) |
−37.25 (3.23) |
6 |
| G1_S4 (F) | −126.48 (8.64) |
−44.02 (4.16) |
−82.46 (9.59) |
−81.21 (5.78) |
−190.90 (35.65) |
188.06 (36.18) |
−42.43 (1.71) |
5 |
| G1_S4 (N-term) | −99.86 (8.50) |
−38.60 (2.08) |
−61.27 (12.33) |
−58.89 (5.21) |
−1,321.18 (54.82) |
1,311.29 (54.22) |
−31.09 (1.58) |
9 |
Notes: The units are in kcal/mol. dH = VDW + EEL + EPB + ENPOLAR, dG = dH − TdS. Values of dH and TdS were not calculated from the identical MD frames so the standard deviation for dG obtained from the population of dH − TdS values are not available. Instead, the square root of the sum of squares of the standard deviations for dH and TdS is provided as the upper bound estimate for dG deviation. The significance of the bold values are the total enthalpic contribution to free binding energy deviation.
Abbreviations: dH, total enthalpic contribution to free binding energy; dS, solute entropy change due to binding; EEL, electrostatic contribution in vacuum (ie, without considering solvent); ENP, estimate for nonpolar contribution; EPB, energetic contribution that arises from electrostatic solvent–solute interaction (desolvation penalty); MD, molecular dynamics; MM/PBSA, molecular mechanics/Poisson–Boltzmann surface area; T, absolute temperature; VDW, van der Waals contribution to binding enthalpy.