A Molecular Dynamic Approach to a Theory on the Dynamical Behaviour of HIV (3LPU Protein) - Water Molecules Interactions in Atomic Structures

Zahra Karimi, Shokoufeh Heydaripour, Rozita Farhadi, Bita Farhadi, Fariba Karami Moghadam, Mohammad Omidi

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Abstract

Molecular dynamics simulation was used to investigate the structure of the H2O molecule and its dynamical behaviour near an HIV (3LPU protein). This study simulated the atomic interaction between 3LPU protein and H2O molecules using a precise atomic arrangement. The interaction between 3LPU protein and H2O molecules is influenced by temperature and pressure. According to our simulated findings, the amplitude of atomic oscillation increases as the atom's temperature rises to 400 K. As a result of this occurrence, the interatomic force of structures increases. As a result, as the temperature rises, the diffusion coefficient of H2O molecules into 3LPU protein changes from 0.421 to 0.861 μm2/ms. The dynamical behaviour of atomic structures is also influenced by pressure. The diffusion coefficient of H2O molecules into the 3LPU protein structure fell from 0.587 to 0.052 μm2/ms when the pressure of the simulated structures was increased from 0 to 4 bar.

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Nano Biomedicine and Engineering.

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