Molecular Dynamics Simulation of TLR-4 Protein

Molecular dynamic simulation was performed using YASARA structure software (version 14.12.2) (Wien, Austria) by selecting the AMBER14 force field [35 ]. The whole protein was embedded in the water-filled simulation cell (20 Å). During the entire simulation process, the experimental condition was maintained at a constant pressure (107p) and a temperature of 298 K. The TLR-4 protein and rutin molecule was placed at the center of the cubic box, adding the counterion to adjust the pH to the physiological level (i.e., 7.4) [36 (link)]. The simulation was commenced for 150 ns with a 2.5 fs time step at a constant temperature and pressure (NPT ensemble) [37 (link)]. A pre-established macro script (md run.mcr) within the YASARA package was used during the simulation steps and the output of the conformation was 100 ps [38 (link)]. The results of the simulations were visualized using Discovery Studio Visualizer version 2018.