Computational protocol: Robust Denaturation of Villin Headpiece by MoS2 Nanosheet: Potential Molecular Origin of the Nanotoxicity

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Protocol publication

[…] The HP35 is a protein that folds independently into a three-helix bundle, which has been widely used as a model scaffold in protein folding studies. The initial protein structure used in this study was downloaded from the Protein Data Bank with the PDB code 1YRF. The simulation system consisted of a HP35 protein, and a MoS2 nanosheet with a size of 6.735 nm × 6.600 nm. The MoS2 nanosheet parameters were adopted from a previous study (see for details). The initial distance between the protein and the MoS2 nanosheet was set to be 0.8 nm. The complex system was then solvated in a rectangular water box (6.924 nm × 6.744 nm × 5.000 nm), containing 6,568 water molecules (21,728 atoms in total). Two chloride ions were also added to this water box to neutralize the system. This fully solvated complex was then simulated with molecular dynamics simulations, which are widely used in the studies of biomolecules and nanomaterials.The MD simulation was performed with the software package GROMACS (version 4.6.6). The VMD software was used to analyze and visualize the simulation results. We adopted CHARMM 27 force field and TIP3P water model for the protein and water molecules, respectively. Temperature was fixed at 300 K using v-rescale thermostat and the volume of the simulation box also remained constant during the simulation (NVT). Periodic boundary conditions were applied in all directions. To avoid the “artificial collapsing” of nanosheets with their mirror images due to the limited size of simulation box (which is due to the limited computational resource), the MoS2 nanosheet was frozen throughout the simulation process. The long-range electrostatic interactions were treated with PME method, and the van der Waals (vdW) interactions were calculated with a cutoff distance of 1.0 nm. All solute bonds were maintained constant at their equilibrium values with the LINCS algorithm, and water geometry was also constrained using the SETTLE algorithm. During the production runs, a time step of 2.0 fs was used, and data were collected every 20 ps. The total aggregated simulation time was larger than 2 μs. […]

Pipeline specifications

Software tools GROMACS, VMD, P-LINCS
Application Protein structure analysis