Table I.
Summary of the Barley LTP-Palmitate Simulations Reported in This Work
Simulation name | Sequence | Starting structure | NOE restraints | Ligand temperature | Number water molecules | Simulation length (ns) |
---|---|---|---|---|---|---|
WT_LA_310 | WT | 1be2 | No | 310 K | 8428 | 20 |
WT_LA_NOE_310 | WT | 1be2 | Yes | 310 K | 8428 | 20 |
WT_LAH_310 | WT | LAH | No | 310 K | 8254 | 20 |
WT_LB_NOE_400 | WT | LB | Yes | 400 K | 8428 | 10 |
M12_LAH_310 | P12V | LAH | No | 310 K | 8635 | 10 |
M12,70_LAH_310 | P12V, P70V | LAH | No | 310 K | 8330 | 10 |
The simulation name used, the protein sequence (either wild type (WT) or the mutations made), the starting structure for the simulation, whether NOE restraints (protein-ligand and intraligand) were applied, the ligand temperature in the simulations, the number of SPC water molecules in the rectangular periodic simulation box and the length of simulation used in the analysis are indicated. 1be2 refers to simulations that were started from the NMR structure of the LTP-palmitate complex. LB refers to simulations started from the final structure of a 5 ns simulation where the 54B7 (vacuum) force-field parameters were used for the ligand and the 54A7 parameters were used for the protein and solvent. LAH refers to simulations started from final structures taken from 20 ns simulations with protonated palmitate as a ligand. Full details are given in the Methods section.