Computational protocol: Crystal and EM Structures of Human Phosphoribosyl Pyrophosphate Synthase I (PRS1) Provide Novel Insights into the Disease-Associated Mutations

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Protocol publication

[…] MODELLER[] was used to build the full-length model of D65N, E43T, Q133P, A87T, M115T mutants and WT using their crystal structures respectively. Starting from each structure model, a MD simulation was carried out with a parallel implementation of the GROMACS-4.5.5 package[], using the CHARMM27 force field[]. The MD simulation procedure was described as following. The periodic boundary condition (PBC) with a dodecahedron box type was used, with the minimal distance of 1.2 nm between the solute and the box boundary. TIP3P[] water molecules were added into the box. The steepest descent method was used for the energy-minimization of the system until the maximum force on any atom was less than 1000kJ/(mol.nm). Na+ ions were added to the system to neutralize the net negative charge of the system by replacing water molecules with the most favorable electrostatic potential. The final system was energy minimized using the steepest descent followed by the conjugate gradient method until the maximum force on any atom was less than 400kJ/(mol.nm). Verlet integration scheme[] was used with a 2 fs time-step. A 100 ps equilibration simulation with positional restraint was firstly performed, using a force constant of 1000 kJ mol−1 nm−2. The initial atomic velocities were generated according to a Maxwell distribution at 310 K. The following production run was 100 ns long. The simulation was performed in a constant NPT ensemble, and the system was coupled to a temperature bath of 310 K through use of an velocity rescaling thermostat[]. The pressure was adjusted to 1 bar with a relaxation time of 0.5 ps, and the compressibility was 4.5×10–5 bar−1[]. Covalent bonds were constrained using the LINCS algorithm[]. The cutoff distances for the Coulomb and van der Waals interactions were chosen to be 0.9 and 1.4 nm, respectively, and the neighbor list was updated every 10 fs. The long-range electrostatic interactions were treated by the PME algorithm[], with a tolerance of 10–5 and an interpolation order of 4. […]

Pipeline specifications

Application Protein structure analysis
Organisms Homo sapiens
Diseases Neural Tube Defects