The atomic interactions between Histone and 3LPT protein using an equilibrium molecular dynamics simulation

Abstract

The atomic interactions between histone molecule and 3LPT protein are reported using the molecular dynamics (MD) method in this computational work. This computational study is done for the first time. The results of the MD simulations on the dynamical manner of these structures have been reported by calculating various physical parameters. Physically, our results show that the attraction forces between the histone molecule and 3LPT protein destructed the 3LPT protein after 2 ns. Further, the temperature and pressure of these structures are important parameters in their atomic interactions. Numerically, by increasing these two parameters from 300 K to 350 K and 0 to 1 bar, respectively, the interatomic distance between these structures decreases from 7 Å to 2.54 Å and 7 Å to 2.79 Å (respectively). Further, bonding energy in these simulations varies from 23.51 eV to 31.78 eV. The diffusion coefficient of histone structure into 3LPT protein is another important parameter. Numerically, this physical coefficient changes from 0.58μm2/s to 0.89 μm2/s.