Computational protocol: Characterization of a Deswapped Triple Mutant Bovine Odorant Binding Protein

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Protocol publication

[…] Three MD simulations were performed on the crystal structure of GCC-bOBP, obtained from the Brookhaven Protein Data Bank (pdb id code 2hlv []), with the GROMACS program [] and the Gromos96 force field []: at neutral pH, in the absence and in the presence of the co-crystallized 3, 6-bis(methylen)decanoic acid ligand [] and at acidic pH.For each simulation, the protein was solvated with a pre-equilibrated water box, keeping a water layer of 8 Å around the solute molecule (corresponding to about 6500 water molecules for each system), sodium ions were added to keep the system neutral and the periodic boundary conditions were applied to the system. The two Cys residues were kept in the oxy state to form a disulfide bridge and, according to the experimental pH value, all histidine residues were kept in the neutral form. As previously stated [], the residue Glu117 was substituted with Gly117.An energy minimization was first performed on the whole system up to a gradient of 500 kJ/(mol nm). Afterwards, a position restrained dynamics was run for 50 ps, to let the solvent relax around the protein. Finally, a full molecular dynamics was run for 20 ns (simulations at neutral pH) or 30 ns (simulation at acidic pH) at 300 K and 1 atm, with a time step of 1 fs.The ligand parameters were obtained by means of the PRODRG server []. To reproduce highly acidic conditions, all Asp and Glu residues and the C-terminus carboxyl group were protonated.Structural analysis was performed with the VMD software package [] (particularly regarding the MD trajectories) and the Swiss-Pdb Viewer program [], whereas the H-bonds calculations were made by the DSSP program []. […]

Pipeline specifications

Software tools GROMACS, PRODRG, VMD, Swiss-PdbViewer
Applications Drug design, Protein structure analysis
Organisms Bos taurus