Skip to main content
. 2012 Nov 8;22(1):56–64. doi: 10.1002/pro.2184

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.

HHS Vulnerability Disclosure