Effects of fullerene on lipid bilayers displaying different liquid ordering: a coarse-grained molecular dynamics study

Sastre, Judit; Mannelli, Ilaria; Reigada, Ramón

doi:10.1016/j.bbagen.2017.08.004

Cited by 18 publications

(20 citation statements)

References 51 publications

(62 reference statements)

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“…Slower diffusion was observed at higher fullerene concentrations in agreement with Sastre et al . 39 . Perhaps surprisingly, the differences in lateral fullerene diffusion in the three cases are very small.…”

Section: Resultsmentioning

confidence: 99%

“…The coarse grained fullerene molecule (F16) consist of 16 beads and the latest updated fullerene parameters were used to reproduce the atomistic potential of mean force (PMF) profile of transferring a fullerene through a lipid membrane 49 . This fullerene model has been previously validated against experimental solvation free energies and atomistic simulations and it has been used in numerous independent studies with various lipid bilayers (DPPC, POPC, DOPC, DSPC and DUPC) and shown to work well 14,19,21,28,34,39,42,49–53 . The models and atom numberings are shown in Fig.…”

Section: Methodsmentioning

confidence: 99%

“…The above explanation, however, holds only at low fullerene concentrations 36 . Several experimental and computational studies have shown that fullerene aggregates are harmful to biological membranes 17,19–21,37–39 . However, the experimental results of fullerene aggregation in lipid membrane are still controversial especially since the aggregate sizes are not known 20,40–42 .…”

Section: Introductionmentioning

confidence: 99%

“…However, the experimental results of fullerene aggregation in lipid membrane are still controversial especially since the aggregate sizes are not known 20,40–42 . Importantly, the mechanisms of fullerene aggregation inside the lipid membrane remain poorly understood 14,20,28,37,39,43 . Computer simulations offer a complementary method 44,45 , however, fullerene aggregation may depend on the concentration and the accessible time and length scales set some limitations that necessitate the use of coarse-grained (CG) methods 46 .…”

Section: Introductionmentioning

confidence: 99%

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Dependence of fullerene aggregation on lipid saturation due to a balance between entropy and enthalpy

Nalakarn

Boonnoy

Nisoh

et al. 2019

Sci Rep

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It is well-known that fullerenes aggregate inside lipid membranes and that increasing the concentration may lead to (lethal) membrane rupture. It is not known, however, how aggregation and rupture depend on the lipid type, what physical mechanisms control this behavior and what experimental signatures detect such changes in membranes. In this paper, we attempt to answer these questions with molecular simulations, and we show that aggregation and membrane damage depend critically on the degree of saturation of the lipid acyl chains: unsaturated bonds, or “kinks”, impose a subtle but crucial compartmentalization of the bilayer into core and surface regions leading to three distinct fullerene density maxima. In contrast, when the membrane has only fully saturated lipids, fullerenes prefer to be located close to the surface under the head groups until the concentration becomes too large and the fullerenes begin clustering. No clustering is observed in membranes with unsaturated lipids. The presence of “kinks” reverses the free energy balance; although the overall free energy profiles are similar, entropy is the dominant component in unsaturated bilayers whereas enthalpy controls the fully saturated ones. Fully saturated systems show two unique signatures: 1) membrane thickness behaves non-monotonously while the area per lipid increases monotonously. We propose this as a potential reason for the observations of low fullerene concentrations being effective against bacteria. 2) The fullerene-fullerene radial distribution function (RDF) shows splitting of the second peak indicating the emergence short-range order and the importance of the second-nearest neighbor interactions. Similar second peak splitting has been reported in metal glasses.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Dependence of fullerene aggregation on lipid saturation due to a balance between entropy and enthalpy

Nalakarn

Boonnoy

Nisoh

et al. 2019

Sci Rep

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“…[25] for details). A large variety of lipid membrane phenomena have been successfully investigated using the Martini force field [26], in some cases also by involving the interaction with carbon-based nanomaterials [27].…”

Section: Coarse-grained Descriptionmentioning

confidence: 99%

Interaction modes between nanosized graphene flakes and liposomes: Adsorption, insertion and membrane fusion

Santiago

Reigada

2019

Biochimica et Biophysica Acta (BBA) - General Subjects

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Background: Understanding the effects of graphene-based nanomaterials on lipid membranes is critical to determine their environmental impact and their efficiency in the biomedical context. Graphene has been reported to favourably interact with biological and model lipid membranes. Methods: We report on a systematic coarse-grained molecular dynamics study of the interaction modes of graphene nanometric flakes with POPC/cholesterol liposome membranes. We have simulated graphene layers with a variety of sizes and oxidation degrees, and we have analyzed the trajectories, the interaction modes, and the energetics of the observed phenomena. Results: Three interaction modes are reported. Graphene can be transiently adsorbed onto the liposome membrane and/or inserted in its hydrophobic region. Inserted nanosheets prefer a perpendicular orientation, and tilt in order to maximize the contact with phospholipid tails while avoiding the contact with cholesterol molecules. When placed between two liposomes, graphene facilitates their fusion in a single vesicle. Conclusions: Graphene can be temporary adsorbed on the liposome before insertion. Bilayer curvature has an influence on the orientation of inserted graphene particles. Cholesterol molecules are depleted from the surrounding of graphene particles. Graphene layers may catalyse membrane fusion by bypassing the energy barrier required in stalk formation. General significance: Nanometric graphene layers can be adsorbed/inserted in lipid-based membranes in different manners and affect the cholesterol distribution in the membrane, implying important consequences on the structure and functionality of biological cell membranes, and on the bioaccumulation of graphene in living organisms. The graphene-mediated mechanism opens new possibilities for vesicle fusion in the experimental context.

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Development of a bottom‐up coarse‐grained model for interactions of lipids with TiO 2 nanoparticles

Ivanov,

Lyubartsev

2024

J Comput Chem

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Understanding interactions of inorganic nanoparticles with biomolecules is important in many biotechnology, nanomedicine, and toxicological research, however, the size of typical nanoparticles makes their direct modeling by atomistic simulations unfeasible. Here, we present a bottom‐up coarse‐graining approach for modeling titanium dioxide (TiO) nanomaterials in contact with phospholipids that uses the inverse Monte Carlo method to optimize the effective interactions from the structural data obtained in small‐scale all‐atom simulations of TiO surfaces with lipids in aqueous solution. The resulting coarse‐grained models are able to accurately reproduce the structural details of lipid adsorption on different titania surfaces without the use of an explicit solvent, enabling significant computational resource savings and favorable scaling. Our coarse‐grained simulations show that small spherical TiO nanoparticles ( nm) can only be partially wrapped by a lipid bilayer with phosphoethanolamine headgroups, however, the lipid adsorption increases with the radius of the nanoparticle. The current approach can be used to study the effect of the size and shape of TiO nanoparticles on their interactions with cell membrane lipids, which can be a determining factor in membrane wrapping as well as the recently discovered phenomenon of nanoquarantining, which involves the formation of layered nanomaterial–lipid structures.

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Effects of fullerene on lipid bilayers displaying different liquid ordering: a coarse-grained molecular dynamics study

Abstract: Background:

Cited by 18 publications

References 51 publications

Dependence of fullerene aggregation on lipid saturation due to a balance between entropy and enthalpy

Dependence of fullerene aggregation on lipid saturation due to a balance between entropy and enthalpy

Interaction modes between nanosized graphene flakes and liposomes: Adsorption, insertion and membrane fusion

Development of a bottom‐up coarse‐grained model for interactions of lipids with TiO 2 nanoparticles

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