Table 1.
Binding free energy computations for LC3C‐ATG4B complexes
| System/Energy terms (kJ/mol) | LC3C‐ATG4B (unphosphorylated) | LC3C‐ATG4B (unphosphorylated + LIR) | LC3C‐ATG4B (S93/S96‐PO4 + LIR) |
|---|---|---|---|
| van der Waals | −1,036.2 ± 110.2 | −985.9 ± 91.6 | −970.1 ± 128.4 |
| Electrostatic | −4,652.7 ± 536.4 | −4,495.8 ± 315.7 | −1,610.2 ± 293.4 |
| Polar solvation | 2,940.0 ± 406.0 | 2,883.0 ± 339.2 | 2,672.4 ± 311.0 |
| SASA | −136.2 ± 14.5 | −134.8 ± 10.2 | −125.2 ± 14.0 |
| Total binding energy | −2,885.1 ± 305.2 | −2,733.5 ± 204.0 | −33.1 ± 202.4 |
| ΔΔG | – | 151.6 ± 367.1 | 2,851.9 ± 366.2 |
The table lists different energetic contributions (mean ± SD) to the binding of LC3C and ATG4B in different phosphorylation states and with modeled LIR‐WXXL interactions. The different binding energy contributions were computed using the MM‐PBSA approach implemented in g_mmpbsa (see Materials and Methods) from MD simulations of LC3C‐ATG4B complexes. The non‐bonded energy terms (van der Waals and electrostatic) contribute significantly to the molecular mechanics interaction energy of the complex, whereas changes in the bonded terms (bond length, angle, and dihedral terms) do not contribute significantly to the interaction energy during complex formation.