Explicit Solvent Molecular Dynamics Simulation Studies of the Dissociation of Human Insulin Hexamer into the Dimeric Units

The molecular dynamics (MD) simulation of two structures of human insulin hexamers (Zn-hexamer and Znfree-hexamer) in explicit solvent was performed and the role of the Zn2+ ions in the hexamer’s cavity as it may affect the propensities of the dissociation of insulin hexamer into dimers and monomers investigated. The starting structure of the Zn-hexamer contains two cavity water molecules and two Zn2+ ions in addition to the amino acids residues of the insulin hexamer while the starting structure Znfree-hexamer is made up of only the amino acids residues of the insulin hexamer. The MD simulation was performed for 1 µs under the isothermal-isobaric conditions (NPT) conditions using the GROMACS software, amber ff99-SB force field, TIP 3P water model with periodic boundary conditions imposed on x-, y- and z- directions. Structural analyses of the two experimental structures were carried out and root mean square deviations (RMSD) and root mean square fluctuations (RMSF) computed from the referenced initial structures. The average RMSD value of the backbone atoms for the Zn-hexamer is 0.293 nm and Znfree-hexamer is 0.785 nm. The structural analysis revealed that, there were dimer’s dissociation and pronounced fluctuations of the amino acids residues in the Znfree-hexamer compared to the Zn-hexamer during the MD simulation. This is evident in the higher inter-dimer distances of the six glutamate-13(β) residues in the Znfree-hexamer which confirmed the influence of the removal of the Zn2+ ions and cavity water molecules on dissociation of the insulin hexamer. 

کلیدواژه ها:

insulin ، Zn-hexamer ، Znfree-hexamer ، Explicit solvent ، Cavity water