Simulation of nanoparticles interacting with a cell membrane: probing the structural basis and potential biomedical application

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Abstract

Nanoparticles (NPs), owing to their ultrasmall size, have been extensively researched for potential applications in biomedicine. During their delivery and functionalization within the organism, they frequently interact with cells. The resulting nano-bio interfaces between the NPs and cell membrane play an important role in dominating the physiological effects of NPs. Therefore, understanding how the properties of NPs affect their nano-bio interface interactions with the cell membrane is important. Compared to experimental and theoretical analyses, simulations can provide atomic-level accuracy regarding dynamic changes in structure, which can reveal the mechanisms of nano-bio interface interactions for feasible modulation. Thus, we reviewed the current advances in nano-bio interfaces from the perspective of simulations. This study will determine how the properties of NPs affect their interactions with cell membranes to provide insights for the design of NPs and summarize their corresponding biomedical applications.

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Most cited references 69

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An improved method for the preparation of graphene oxide (GO) is described. Currently, Hummers' method (KMnO(4), NaNO(3), H(2)SO(4)) is the most common method used for preparing graphene oxide. We have found that excluding the NaNO(3), increasing the amount of KMnO(4), and performing the reaction in a 9:1 mixture of H(2)SO(4)/H(3)PO(4) improves the efficiency of the oxidation process. This improved method provides a greater amount of hydrophilic oxidized graphene material as compared to Hummers' method or Hummers' method with additional KMnO(4). Moreover, even though the GO produced by our method is more oxidized than that prepared by Hummers' method, when both are reduced in the same chamber with hydrazine, chemically converted graphene (CCG) produced from this new method is equivalent in its electrical conductivity. In contrast to Hummers' method, the new method does not generate toxic gas and the temperature is easily controlled. This improved synthesis of GO may be important for large-scale production of GO as well as the construction of devices composed of the subsequent CCG.

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A significant modification to the additive all-atom CHARMM lipid force field (FF) is developed and applied to phospholipid bilayers with both choline and ethanolamine containing head groups and with both saturated and unsaturated aliphatic chains. Motivated by the current CHARMM lipid FF (C27 and C27r) systematically yielding values of the surface area per lipid that are smaller than experimental estimates and gel-like structures of bilayers well above the gel transition temperature, selected torsional, Lennard-Jones and partial atomic charge parameters were modified by targeting both quantum mechanical (QM) and experimental data. QM calculations ranging from high-level ab initio calculations on small molecules to semiempirical QM studies on a 1,2-dipalmitoyl-sn-phosphatidylcholine (DPPC) bilayer in combination with experimental thermodynamic data were used as target data for parameter optimization. These changes were tested with simulations of pure bilayers at high hydration of the following six lipids: DPPC, 1,2-dimyristoyl-sn-phosphatidylcholine (DMPC), 1,2-dilauroyl-sn-phosphatidylcholine (DLPC), 1-palmitoyl-2-oleoyl-sn-phosphatidylcholine (POPC), 1,2-dioleoyl-sn-phosphatidylcholine (DOPC), and 1-palmitoyl-2-oleoyl-sn-phosphatidylethanolamine (POPE); simulations of a low hydration DOPC bilayer were also performed. Agreement with experimental surface area is on average within 2%, and the density profiles agree well with neutron and X-ray diffraction experiments. NMR deuterium order parameters (S(CD)) are well predicted with the new FF, including proper splitting of the S(CD) for the aliphatic carbon adjacent to the carbonyl for DPPC, POPE, and POPC bilayers. The area compressibility modulus and frequency dependence of (13)C NMR relaxation rates of DPPC and the water distribution of low hydration DOPC bilayers also agree well with experiment. Accordingly, the presented lipid FF, referred to as C36, allows for molecular dynamics simulations to be run in the tensionless ensemble (NPT), and is anticipated to be of utility for simulations of pure lipid systems as well as heterogeneous systems including membrane proteins.

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Andre E. Nel, Lutz Mädler, Darrell Velegol … (2009)

Rapid growth in nanotechnology is increasing the likelihood of engineered nanomaterials coming into contact with humans and the environment. Nanoparticles interacting with proteins, membranes, cells, DNA and organelles establish a series of nanoparticle/biological interfaces that depend on colloidal forces as well as dynamic biophysicochemical interactions. These interactions lead to the formation of protein coronas, particle wrapping, intracellular uptake and biocatalytic processes that could have biocompatible or bioadverse outcomes. For their part, the biomolecules may induce phase transformations, free energy releases, restructuring and dissolution at the nanomaterial surface. Probing these various interfaces allows the development of predictive relationships between structure and activity that are determined by nanomaterial properties such as size, shape, surface chemistry, roughness and surface coatings. This knowledge is important from the perspective of safe use of nanomaterials.

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Author and article information

Contributors

Xiao Zhang: (View ORCID Profile)

Wei Wei: (View ORCID Profile)

Journal

Title: NPG Asia Materials

Abbreviated Title: NPG Asia Mater

Publisher: Springer Science and Business Media LLC

ISSN (Print): 1884-4049

ISSN (Electronic): 1884-4057

Publication date Created: December 2021

Publication date (Electronic): July 16 2021

Publication date (Print): December 2021

Volume: 13

Issue: 1

Article

DOI: 10.1038/s41427-021-00320-0

SO-VID: 38b53d67-e6b0-4f14-988d-6650b58a5a9c

License:

https://creativecommons.org/licenses/by/4.0

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