Table III.
Calculated free energy and standard deviations calculated with MM-PBSA with its components (Kcal/mol) for the tandem repeats cylindrins and the steric-zipper fibril models
| MM-PBSA binding energy components of the different tandem repeat cylindrins amyloid | |||||||
|---|---|---|---|---|---|---|---|
| System | ΔEvdw | ΔEele | ΔGPB | ΔGSA | ΔGsolv | ΔGbinding | |
| WT-TR | −70.06† (0.1)‡ | −469.67(10.9) | 473.43(9.7) | −7.72(0.1) | 465.71(9.6) | −74.03(1.4) | |
| V2L-TR | −80.09(0.2) | −500.61(16.9) | 501.94(15.6) | −8.34(0.1) | 493.59(15.8) | −87.10(1.3) | |
| V4AV8A-TR | −69.36(1.9) | −499.05(65.8) | 502.15(60.9) | −8.43(0.5) | 493.72(60.4) | −74.69(7.3) | |
| V4GV8G-TR | −86.45(9.3) | −495.73(65.2) | 522.81(70.3) | −9.94(0.9) | 512.86(69.3) | −69.31(5.3) | |
| VTL-TR | −78.85(1.9) | −429.72(35.3) | 441.59(37.9) | −8.39(0.3) | 433.20(38.2) | −75.37(4.8) | |
| MM-PBSA binding energy components of doublelayer (SH2-ST6) steric-zipper fibril models | |||||||
| System | ΔEvdw | ΔEele | ΔGPB | ΔGSA | ΔGsolv | ΔGbinding | ΔΔG§ |
| WT-SZ | −127.29(1.7) | −266.89(3.6) | 294.59(7.6) | −12.69(0.1) | 281.91(7.5) | −112.27(2.2) | −38.27 |
| V2L-SZ | −124.72(2.5) | −354.23(36.7) | 371.56(31.6) | −12.81(0.2) | 358.74(31.8) | −120.21(2.4) | −31.11 |
| V4AV8-SZ | −117.14(9.8) | −352.87(38.5) | 380.08(42.9) | −11.83(0.1) | 368.25(42.9) | −101.76(5.4) | −27.06 |
| V4GV8G-SZ | −105.55(1.3) | −534.37(78.2) | 558.37(78.2) | −12.53(0.4) | 545.84(78.5) | −94.64(1.2) | −25.32 |
| VTL-SZ | −139.72(4.3) | −323.53(24.6) | 353.31(20.2) | −13.35(0.2) | 339.96(20.4) | −123.29(0.1) | −47.86 |
ΔEele, non-solvent electrostatic potential energy; ΔGPB, electrostatic contributions to the solvation free energy calculated with Poisson-Boltzmann equation; GSA, nonpolar contributions to solvation free energy; ΔEvdw, van der Waals potential energy; and ΔGbinding, calculated bindingΔGsolv are the polar, nonpolar and total solvation energies. Data are shown as mean with the standard deviation (SD) in brackets. ΔGbinding = ΔEvdw + ΔEele + ΔGsol; ΔGsol = ΔGPB + ΔGSA.
Mean values are calculated from the two trajectories for each model resulting from two independent simulations.
The standard deviation (SD) therefore describes the deviation between the two independent simulations.
ΔΔG§(the difference in binding free energy between the tandem repeat cylindrins amyloid and steric-zipper fibril models. The negative values indicates the steric zippers are more stable than the corresponding tandem repeat cylindrins)