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Research Article | Open Access

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

Zahra Karimi1, Shokoufeh Heydaripour2, Rozita Farhadi3, Bita Farhadi4( ), Fariba Karami Moghadam5, Mohammad Omidi6
State key laboratory of Fine Chemicals, Department of Pharmaceutical Science, School of Chemical Engineering, Dalian University of Technology, Dalian 116024, People's Republic of China
Department of Neurology, Kermanshah University of Medical Science, Kermanshah, Iran
Health Center of Tuyserkan, Hamadan University of Medical Science, Hamadan, Iran
School of Physics & School of Microelectronics, Dalian University of Technology, Dalian 116023, People's Republic of China
Kermanshah University of Medical Science, Kermanshah, Iran
School of Energy and Power Engineering, Dalian University of Technology, Dalian, People's Republic of China
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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.

Keywords

temperatureMolecular dynamicspressure3LPU proteindynamical behaviour

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Nano Biomedicine and Engineering
Volume 14 Issue 2,
June 2022
Pages 159-166
DOI: 10.5101/nbe.v14i2.p159-166
Cite this article:
Karimi Z, Heydaripour S, Farhadi R, et al. A Molecular Dynamic Approach to a Theory on the Dynamical Behaviour of HIV (3LPU Protein) - Water Molecules Interactions in Atomic Structures. Nano Biomedicine and Engineering, 2022, 14(2): 159-166. https://doi.org/10.5101/nbe.v14i2.p159-166

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Received: 13 April 2022
Accepted: 07 October 2022
Published: 22 October 2022
© Zahra Karimi, Shokoufeh Heydaripour, Rozita Farhadi, Bita Farhadi, Fariba Karami Moghadam, and Mohammad Omidi.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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