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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

Molecular dynamics3LPU proteintemperaturepressuredynamical behaviour

References

[1]
HIV/AIDS., J.U.N.P. o. and W.H. Organization, 2008 report on the global AIDS epidemic. 2008: World Health Organization.
[2]

Latha, G.M. and E.S.N. Murthy, Clinical study on ocular manifestations in HIV/AIDS relation to CD4 count in tertiary care hospital, Andhra Pradesh. virus. 11: 12.
Google Scholar
[3]

Nguyen, P.T., et al., Factors associated with high-risk behaviors of people newly diagnosed with HIV/AIDS: results from a cross-sectional study in Vietnam. AIDS care, 2021, 33(5): 607-615.
Crossref Google Scholar
[4]

Diehr, M.C., et al., The 50 and 100-item short forms of the Paced Auditory Serial Addition Task (PASAT): demographically corrected norms and comparisons with the full PASAT in normal and clinical samples. Journal of clinical and experimental neuropsychology, 2003, 25(4): 571-585.
Crossref Google Scholar
[5]
HIV/AIDS., J.U.N.P. o. and W.H. Organization, AIDS epidemic update, December 2006. 2006: World Health Organization.
[6]

MacNeil, A., et al., Global epidemiology of tuberculosis and progress toward achieving global targets — 2017. Morbidity and Mortality Weekly Report, 2019, 68(11): 263.
Crossref Google Scholar
[7]

Corbett, E.L., et al., The growing burden of tuberculosis: global trends and interactions with the HIV epidemic. Archives of internal medicine, 2003, 163(9): 1009-1021.
Crossref Google Scholar
[8]
Organization, W.H., Report on global sexually transmitted infection surveillance 2018, 2018.
[9]
Koppaka, R., Ten great public health achievements—worldwide, 2001-2010, 2011.
[10]

Edition, F., Guidelines for drinking-water quality. WHO chronicle, 2011, 38(4): 104-108.
Google Scholar
[11]

Koonin, E.V., T.G. Senkevich, and V.V. Dolja, The ancient Virus World and evolution of cells. Biology direct, 2006, 1(1): 1-27.
Crossref Google Scholar
[12]
Krämer, A., M. Kretzschmar, and K. Krickeberg, Modern infectious disease epidemiology: Concepts, methods, mathematical models, and public health. 2010: Springer.
Crossref
[13]
Kirch, W., Encyclopedia of Public Health: Volume 1: A-H Volume 2: I-Z. 2008: Springer Science & Business Media.
Crossref
[14]

Parkhurst, J.O., The Ugandan success story? Evidence and claims of HIV-1 prevention. The Lancet, 2002, 360(9326): 78-80.
Crossref Google Scholar
[15]

Lyles, C.M., et al., Evidence–based HIV behavioral prevention from the perspective of the CDC's HIV/AIDS Prevention Research Synthesis Team. AIDS Education & Prevention, 2006, 18(supp): 21-31.
Crossref Google Scholar
[16]

Rahier, J.F., et al., European evidence-based Consensus on the prevention, diagnosis and management of opportunistic infections in inflammatory bowel disease. Journal of Crohn's and Colitis, 2009, 3(2): 47-91.
Crossref Google Scholar
[17]

Mishra, S.K., et al., Role of the ubiquitin-like protein Hub1 in splice-site usage and alternative splicing. Nature, 2011, 474(7350): 173-178.
Crossref Google Scholar
[18]

Christ, F., et al., Rational design of small-molecule inhibitors of the LEDGF/p75-integrase interaction and HIV replication. Nature chemical biology, 2010, 6(6): 442-448.
Crossref Google Scholar
[19]

Karplus, M. and G.A. Petsko, Molecular dynamics simulations in biology. Nature, 1990, 347(6294): 631-639.
Crossref Google Scholar
[20]

Liu, X. and Y.P. Zhao, Generating artificial homologous proteins according to the representative family character in molecular mechanics properties–an attempt in validating an underlying rule of protein evolution. FEBS letters, 2010, 584(5): 1059-1065.
Crossref Google Scholar
[21]

Jolfaei, N.A., et al., Investigation of thermal properties of DNA structure with precise atomic arrangement via equilibrium and non-equilibrium molecular dynamics approaches. Computer methods and programs in biomedicine, 2020, 185: 105169.
Crossref Google Scholar
[22]

Alipour, P., et al., Molecular dynamics simulation of fluid flow passing through a nanochannel: Effects of geometric shape of roughnesses. Journal of Molecular Liquids, 2019, 275: 192-203.
Crossref Google Scholar
[23]

Ibrahim, M., et al., Investigation of dynamical behavior of 3LPT protein-water molecules interactions in atomic structures using molecular dynamics simulation. Journal of Molecular Liquids, 2021, 329: 115615.
Crossref Google Scholar
[24]

Yin, J. and Y.P. Zhao, Hybrid QM/MM simulation of the hydration phenomena of dipalmitoylphosphatidylcholine headgroup. Journal of colloid and interface science, 2009, 329(2): 410-415.
Crossref Google Scholar
[25]

Yin, J. and Y.P. Zhao, Molecular dynamics simulation of adhesion forces in a dipalmitoylphosphatidylcholine membrane. Surface Review and Letters, 2007, 14(04): 671-675.
Crossref Google Scholar
[26]

Lemkul, J.A., et al., An empirical polarizable force field based on the classical drude oscillator model: development history and recent applications. Chemical reviews, 2016, 116(9): 4983-5013.
Crossref Google Scholar
[27]

Fermi, E., J. Pasta, and S. Ulam, Los alamos report la-1940. Fermi, Collected Papers, 1955. 2: 977-988.
Google Scholar
[28]

Alder, B.J. and T.E. Wainwright, Studies in molecular dynamics. I. General method. The Journal of Chemical Physics, 1959, 31(2): 459-466.
Crossref Google Scholar
[29]

Rahman, A., Correlations in the motion of atoms in liquid argon. Physical review, 1964, 136(2A): A405.
Crossref Google Scholar
[30]
Schlick, T., Pursuing Laplace's vision on modern computers, in Mathematical Approaches to Biomolecular Structure and Dynamics. 1996, Springer, 219-247.
Crossref
[31]

Ashkezari, A.Z., et al., Calculation of the thermal conductivity of human serum albumin (HSA) with equilibrium/non-equilibrium molecular dynamics approaches. Computer methods and programs in biomedicine, 2020, 188: 105256.
Crossref Google Scholar
[32]

Tohidi, M. and D. Toghraie, The effect of geometrical parameters, roughness and the number of nanoparticles on the self-diffusion coefficient in Couette flow in a nanochannel by using of molecular dynamics simulation. Physica B: Condensed Matter, 2017, 518: 20-32.
Crossref Google Scholar
[33]

Rappé, A.K., et al., UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations. Journal of the American chemical society, 1992, 114(25): 10024-10035.
Crossref Google Scholar
[34]

Mayo, S.L., B.D. Olafson, and W.A. Goddard, DREIDING: a generic force field for molecular simulations. Journal of Physical chemistry, 1990, 94(26): 8897-8909.
Crossref Google Scholar
[35]

Lennard-Jones, J.E., The determination of molecular orbitals. Proceedings of the Royal Society of London. Series A. Mathematical and Physical Sciences, 1949, 198(1052): 1-13.
Crossref Google Scholar
[36]

Berendsen, H., J. Grigera, and T. Straatsma, The missing term in effective pair potentials. Journal of Physical Chemistry, 1987, 91(24): 6269-6271.
Crossref Google Scholar
[37]

Farhadi, B., et al., Carbon doped lead-free perovskite with superior mechanical and thermal stability. Molecular Physics, 2021: e2013555.
Crossref Google Scholar
[38]

Farhadi, B., et al., Influence of contact electrode and light power on the efficiency of tandem perovskite solar cell: Numerical simulation. Solar Energy, 2021. 226: 161-172.
Crossref Google Scholar
[39]
Wang, L.P., T.J. Martinez, and V.S. Pande, Supporting Information for: Building Force Fields-an Automatic, Systematic and Reproducible Approach.
[40]

Plimpton, S., Fast parallel algorithms for short-range molecular dynamics. Journal of computational physics, 1995, 117(1): 1-19.
Crossref Google Scholar
[41]

Brown, W.M., et al., Implementing molecular dynamics on hybrid high performance computers–short range forces. Computer Physics Communications, 2011, 182(4): 898-911.
Crossref Google Scholar
[42]

Brown, W.M., et al., Implementing molecular dynamics on hybrid high performance computers–Particle–particle particle-mesh. Computer Physics Communications, 2012, 183(3): 449-459.
Crossref Google Scholar
[43]

Zheng, Y., et al., Potential energy and atomic stability of H2O/CuO nanoparticles flow and heat transfer in non-ideal microchannel via molecular dynamic approach: the green–Kubo method. Journal of Thermal Analysis and Calorimetry, 2021, 144(6): 2515-2523.
Crossref Google Scholar
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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