Computational Investigation of the Atomic Interactions and Physical Effects of Herpesvirus and Alzheimer’s Protein for Co-localization

Abstract

Computational analysis via the Molecular Dynamics (MD) approach has been used to investigate atomic interactions between Herpesvirus 1 (2GV9) and the Alzheimer's protein (1OWT). The results of MD simulation on the dynamic behavior of this colony have been ascertained with the calculation of numerous physical parameters such as total energy, center of mass (COM) distance and volume of atomic structures. Manipulation of these parameters enabled analysis of the atomic interaction. The calculated COM distances varied from 7.94 Å to 3.72 Å after 1ns which confirmed the traction between the 2GV9 virus and the 1OWT protein. Structurally, the volume of the 1OWT protein increased from 1,056,000 Å3 to 1,786,000 Å3 after atomic interaction with the virus. Moreover, the simulation results showed that temperature is the most critical environmental parameter for the interaction of 1OWT protein and Herpesvirus. Thermal conductivity calculations were performed using t = 1,000,000 time steps to discover the physical stability in the simulated structures. The obtained Green-Kubo results showed that as the temperature changed from 300K to 350K, the thermal conductivity of structures modeled in an aquatic environment increased from 1,233 W/mK to 1,957 W/mK.