Molecular Dynamics Simulation of MDM2-Polyphenol Complex

MD simulation of the complex was carried out using the GROMOS96 43a1 force field [23 , 24 ] of the GROMACS 4.5.4 package. Autodock generated lowest binding energy (most negative) docking conformation of MDM2–polyphenol complex which was taken as the initial conformation for MD simulation. The topology parameters of proteins were created by means of the Gromacs program. The topology parameters of taxifolin were built using the Dundee PRODRG server [25 ]. The complex was immersed in a cubic box of extended simple point charge water molecules [26 , 27 ]. Energy minimization was performed using the steepest descent method of 10,000 steps followed by the conjugate gradient method for 10,000 steps, to release conflicting contacts. Position-restrained dynamics simulation (equilibration phase) (NVT and NPT) of the system was done at 300 K for 200 ps followed by MD production run for 15 ns. For the purpose of analysis, the atomic coordinates were recorded every 1.0 ps during the MD simulation. All the structural images were generated using Chimera [28 ].