2.9 Molecular docking analysis
Molecular docking simulations were performed by Autodock 4.2 (Rashtbari
et al., 2017;
Yektaet al., 2017). All water molecules were removed by Auto Dock
Tools and polar hydrogen atoms, KOLLMAN atoms charge were added to PsbA
and PsbS, and docking calculations were performed using Lamarckian
genetic algorithm (LGA). The Grid Box was placed at center of PsbA (X
center: -8.337, Y center: -50.07, Z center: 38.514) and PsbS (X center:
-13.053, Y center: -5.89, Z center: 23.526). The grid map for spacing
the midpoints of XXĂ… for PsbA and PsbS were 0.508 and 0.375 angstroms,
respectively. The numbers of points in the XYZ dimension were
126*126*126 angstroms, respectively. After docking analysis, the lowest
binding energy conformation was selected for each target. The
interactions of the PsbA and PsbS protein complexes with thymol,
carvacrol, beta-elemene, trans-caryophyllene, germacrene-D, spathulenol,
and 5alpha-pregnane compounds were also analyzed using UCSFChimera and
Discovery Studio 4.1 Client.