Table 4.
Adaptation free energy of the PDZ domains upon binding: ΔGadaptP in kcal/mola.
| Protein | ΔEintb | ΔGelec | ΔGnpd | −TΔSadapte | ΔG*adaptf | ΔGadaptg |
|---|---|---|---|---|---|---|
| NHERF a | −6.0 (41.5) | 4.0 (9.1) | 1.4 (32.2) | 95 (8) | −0.6 (42.3) | 94.4 (50.3) |
| NHERF b | −4.2 (40.5) | 3.3 (9.4) | −2.1 (34.0) | 85(3) | −3.0 (41.9) | 82.0 (44.9) |
| NHERF c |
−14.8 (41.3) |
3.1 (10.2) |
10.2 (31.8) |
95 (3) |
−1.5 (42.1) |
93.5 (45.1) |
| PSD-95 |
30.0 (47.1) |
−1.2 (10.4) |
7.5 (35.7) |
20 (10) |
36.3 (47.2) |
56.3 (57.2) |
| Dishevelle d |
−15.8 (41.2) |
−1.2 (8.2) |
44.3 (30.7) |
−17 (5) |
27.3 (41.1) |
10.3 (46.1) |
| Shank |
8.2 (44.6) |
0.1 (8.9) |
5.8 (32.3) |
−1 (3) |
14.1 (44.7) |
13.1 (47.7) |
| Syntenin I | 7.9 (38.0) | −0.6 (7.2) | 11.1 (26.7) | −15 (7) | 18.4 (36.8) | 3.4 (43.8) |
| Syntenin II |
−2.4 (37.2) |
3.6 (7.0) |
4.2 (26.8) |
15 (2) |
5.3 (36.8) |
20.3 (38.8) |
| Erbin I | 17.2 (42.0) | 6.2 (16.4) | 4.7 (31.3) | 4 (2) | 28.0 (45.2) | 32.0 (47.2) |
| Erbin II |
2.0 (41.4) |
3.3 (9.8) |
6.7 (32.2) |
0 (11) |
12.0 (41.9) |
12.0 (52.9) |
| GRIP |
10.0 (40.8) |
−3.1 (9.2) |
17.7 (32.4) |
10 (10) |
24.7 (43.2) |
34.7 (53.2) |
| Inad |
−0.8 (42.6) |
−0.2 (10.7) |
8.5 (34.2) |
15 (8) |
7.6 (43.6) |
22.6 (51.6) |
| Average | 2.6 (13.1) | 1.4 (2.8) | 10.0 (11.9) | 26 (42) | 14.1 (13.0) | 39.6 (33.5) |
Standard deviations of averages are shown in parentheses. The last line is the average of each column and its corresponding standard deviation.
Difference in internal energy (sum of the bond, angle and dihedral energies).
Difference in electrostatic free energy (sum of the intra-molecular electrostatic energy and the electrostatic solvation free energy).
Difference in non-polar free energy (sum of the van der Waals energy and the non-polar part of the solvation free energy).
−TΔSadaptP ≈ −T(SconfP_holo — SconfP_apo) where SconfP_holo and SconfP_apo are calculated with the quasi-harmonic approximation, respectively from the holo and the apo simulations. The error is calculated as |-TΔS(5−20ns)+TΔS(5−15ns)|.
ΔG*adapt = ΔEint+ ΔGele + ΔGnp.
ΔGadapt = ΔG*adapt −TΔSadapt.