Computational protocol: A molecular dynamics simulation study decodes the Zika virus NS5 methyltransferase bound to SAH and RNA analogue

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Protocol publication

[…] First, we modified a partial length of the Zika NS5 protein structure (PDB ID: 5kqs), and we used PyMOL software to modify the ligand (m7GDP to m7GTP). Second, we aligned the partial length of the Zika NS5 protein structure and the full length of the Zika NS5 protein structure (PDB ID: 5u0b). We then inserted the ligand (m7GTP) into the full-length Zika NS5 protein structure. The initial complex structures are Zika NS5 with SAH and Zika NS5 with m7GTP. These complex structures were generated and then inserted into TIP3P solvent molecules. The size of the complex structures was approximately 10.00 × 11.00 × 11.00 nm. These initial complexes were then simulated using the AMBER 16 package with the AMBER FF12SB all-hydrogen amino acid and amber GAFF parameters. The geometries of the SAH and m7GTP were fully optimized, and their electrostatic potentials were obtained using a single-point calculation at the Hatree–Fock level with the 6–31 G(d,p) basis set using the GAUSSIAN 09 program. Subsequently, partial charges were obtained by employing the restrained electrostatic potential procedure using the Antechamber package. All cMD simulations were performed in the isothermal–isobaric (NPT) assembly with a simulation temperature of 310 K, unless stated otherwise, by using the Verlet integrator with an integration time step of 0.002 ps and SHAKE constraints for all covalent bonds involving hydrogen atoms. In the electrostatic interactions, atom-based truncation was performed using the PME method, and the switch van der Waals function was used with a 2.00 nm cut-off for atom-pair lists. These complex structures were minimized for 100,000 conjugate gradient steps and then subjected to a 100-ns, isothermal, constant-volume MD simulation. Moreover, the final structures from these simulations were used in five dependent 5000-ns GaMD simulation calculations, and these structures were used in the umbrella sampling simulations. [...] For the Zika NS5 protein with SAH (RC1 = 3–8 Å) and m7GTP (RC2 = 6–11 Å), all residues were obtained using preresidue displacement calculations. The preresidue displacement calculations were applied to the major barriers: RC1 = 3–8 Å and RC2 = 6–11 Å). The reaction coordinate profiles and preresidue displacement calculations were analysed using the AmberTools 16 and VMD software packages. The reaction coordinates profiles were calculated for the reaction coordinates used for the potential of mean force (PMF) calculations. The PyReweighting toolkit was used to reweight the GaMD simulations for the PMF profile calculations and to examine the boost potential distributions. One-dimensional PMF profiles were also constructed using the reaction coordinates for the Zika NS5 protein with a bin size of 1.0 Å. When the number of simulation frames within a bin was lower than a certain limit, the bin was insufficiently sampled and thus was excluded for reweighting. […]

Pipeline specifications

Software tools PyMOL, AMBER, VMD
Application Protein structure analysis
Organisms Zika virus
Diseases Protein S Deficiency