Computational protocol: EGCG in Green Tea Induces Aggregation of HMGB1 Protein through Large Conformational Changes with Polarized Charge Redistribution

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Protocol publication

[…] The protein was solvated with SPC water molecules and its excess negative charge was neutralized by Na+. GROMACS v4.6.5 was used to conduct the simulation with the GROMOS96 53a6 force field. The parameters for EGCG were adopted from a previous study in Sun’s Lab. Long range electrostatics were calculated using the particle mesh Ewald (PME) method with a 12 Å cut-off. Van der Waal interactions were modeled using Lennard-Jones 6–12 potentials with a 14 Å cut-off. All production runs were performed with the NPT ensemble, with a constant temperature at 300 K using the Berendsen thermostats, and a constant isotropic pressure at 1 bar using the Berendsen barostats. All bonds were constrained with the LINCS algorithm. The time step was set to 2 fs and the neighboring list was updated at every 10 time steps.Prior to production runs, following similar protocols in our previous studies, energy minimization of 3000 steps with steepest descent method were carried out on each system followed by a 0.1 ns equilibration process in which position restrain was applied to the backbone of the protein and EGCG molecule using a constant force of 1000 kJmol−1 nm−2. Production runs with lengths of 100–300 ns were conducted and coordinates were saved every10 ps for analysis. VMD and Chimera programs were used for visualization. Electrostatics potential of proteins were calculated using DelPhi module in Discovery Studio software (Accelrys Inc., San Diego, CA, USA) with default parameters (grid points per axis is 65 and 50% grids is filled by solute; the dielectric constant of the solvent and solute interior is 80 and 2, respectively; ionic strength 0.145 mol L−1 was used). […]

Pipeline specifications

Software tools GROMACS, P-LINCS, VMD
Application Protein structure analysis
Organisms Homo sapiens
Diseases Genetic Diseases, Inborn