Computational protocol: Characterization of the Interaction between Gallic Acid and Lysozyme by Molecular Dynamics Simulation and Optical Spectroscopy

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Protocol publication

[…] The three-dimensional structure of LYS in complex with its 1,2-ethanediol ligand was obtained from the Protein Data Bank (PDB ID: 1GWD) (http://www.pdb.org). All the C1, I, Na and CO atoms were removed by Autodock program. After correcting atom types and adding all the hydrogen atoms, molecular building was done for GA ligand with molecular sketch program based on the structure of 1,2-ethanediol ligand. The ESP CHELPG charges calculated from B3LYP/6-31G* by Gaussian 98 was used for GA. RESP charges parameters were used for all LYS residues. Atomic partial charge generation and assignment of the force field were performed using Antechamber suite. Docking studies were performed with the AutoDock 4.02 suite of programs, and all of the calculations were performed on a Silicon Graphics Octane 2 workstation. Molecular dynamics simulations were carried out on the GA-LYS system using the SANDER module of AMBER11 with the Amber FF03 and GAFF force fields. The atomic charges and force field parameters of GA were added into the Amber FF03 force field to generate the topology file and coordinate file. The initial structure was placed in a truncated octahedral periodic box of TIP3P water molecules. We used the periodic boundary conditions and the distance between water box edges and the closest atom of the solutes was at least 10 angstrom. All of the simulations were carried out at neutral pH, and an adequate number of Cl ions were added to a simulation box in order to preserve neutrality. The system was minimized with the SANDER module with constant volume by 500 cycles of steepest descent minimization followed by 500 cycles of conjugate gradient minimization. These procedures ensured that the initial experimental structure was maintained while the solvent was allowed to relax. The steps above all featured 2000 cycles of steepest descent followed by conjugate gradient minimization. After energy minimization, canonical ensemble (NVT)-MD was carried out for 100 ps, during which the system was heated from 0 to 298/310 K. A 10 Å cut-off was set for the GA-LYS system. Finally, a 2 ns isothermal isobaric ensemble (NPT)-MD simulation was performed without any constraints. The time-step for the MD simulation was 2 fs, and every 2 ps a track file was recorded. The MD simulations of GA binding to LYS were analyzed using the Discovery Studio software package, followed by Origin8.0 and Pymol software. […]

Pipeline specifications

Software tools AutoDock, PyMOL
Application Protein interaction analysis
Diseases Genetic Diseases, Inborn
Chemicals Gallic Acid, Hydrogen