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Study and Simulation of Nanoparticle Translocation Through Cell Membrane

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Iranian Journal of Science and Technology, Transactions of Mechanical Engineering Aims and scope Submit manuscript

Abstract

In this research, nanoparticle translocation through cell membrane has been studied and simulated. To this end, gold nanoparticles have been selected as the main carrier of the drug and have been functionalized with some selected ligands. The partial charges of the ligands have been calculated using quantum mechanics based on HF technique with 6-31Gd basis set. To achieve the realistic shape of a drug, the number and arrangement of ligands loaded on the gold nanoparticle have been optimized. After determining the properties such as diffusion coefficient and validating the results with experimental data, a MARTINI coarse-grained mapping of the drugs is created. The coarse-grained model of the drug has been placed in a cellular microenvironment containing a solvent. The cytoplasmic membranes investigated in this study consists of more than 60 types phospholipids similar to animal cell membranes. After minimizing the system and performing procedures for controlling temperature and pressure, ions are added to the system and a potential difference is applied to the membrane and translocation of the drug is studied.

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Authors and Affiliations

  1. Computational Nano-Mechanics Laboratory, Mechanical Engineering Department, Sharif University of Technology, Tehran, Iran

    Hossein Nejat Pishkenari, Mohammad Reza Barzegar & Ali Taghibakhshi

Authors
  1. Hossein Nejat Pishkenari
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  2. Mohammad Reza Barzegar
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  3. Ali Taghibakhshi
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Corresponding author

Correspondence to Hossein Nejat Pishkenari.

Appendix

Appendix

See Figs. 25, 26, 27, 28, 29 and Tables 8, 9, 10, 11, 12, 13.

Fig. 25
figure 25

Percentage of the phospholipids constitute the cell membrane (those with percentages more than 2%)

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Fig. 26
figure 26

Coarse-grained cell membrane used in the simulations (the periodic boundary condition is applied to the two surface directions)

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Fig. 27
figure 27

Partial load obtained by GAUSSIAN software. Atom name and charge are written on each atom, and the atoms are colored according to the load

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Fig. 28
figure 28

Energy stability in all-atomic simulation of gold nucleus with ligand SC12H24NH +3 . In this simulation, the temperature reached from 250 to 310 K

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Fig. 29
figure 29

Temperature equilibration in all-atomic simulation of gold nucleus with ligand SC2H24NH3+. In this simulation, the temperature reached from 250 to 310 K

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Table 8 Partial charges on SC8H16NH3+ atoms in related drug
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Table 9 Partial charges in all-atomic simulation with SC12H24NH3+ ligand
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Table 10 Partial charges in all-atomic simulation with SC16H32NH3+ ligand
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Table 11 The average distances between the atoms of SC8H24NH3+ ligand and the center of the gold core
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Table 12 The average distances between the atoms of SC8H24NH3+ ligand and the center of the gold core
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Table 13 The average distances between the atoms of SC16H32NH3+ ligand and the center of the gold core
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Nejat Pishkenari, H., Barzegar, M.R. & Taghibakhshi, A. Study and Simulation of Nanoparticle Translocation Through Cell Membrane. Iran J Sci Technol Trans Mech Eng 45, 939–960 (2021). https://doi.org/10.1007/s40997-019-00326-8

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  • DOI: https://doi.org/10.1007/s40997-019-00326-8

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