Membrane-mediated aggregation of anisotropically curved nanoparticles

2016 ◽  
Vol 186 ◽  
pp. 265-275 ◽  
Author(s):  
Alexander D. Olinger ◽  
Eric J. Spangler ◽  
P. B. Sunil Kumar ◽  
Mohamed Laradji
Keyword(s):  
Adhesion Strength ◽  
Self Assembly ◽  
Lipid Membranes ◽  
Lipid Vesicles ◽  
Membrane Curvature ◽  
Coarse Grained ◽  
Implicit Solvent ◽  
High Adhesion ◽  
Solvent Model ◽  
Chain Aggregates

Using systematic numerical simulations, we study the self-assembly of elongated curved nanoparticles on lipid vesicles. Our simulations are based on molecular dynamics of a coarse-grained implicit-solvent model of self-assembled lipid membranes with a Langevin thermostat. Here we consider only the case wherein the nanoparticle–nanoparticle interaction is repulsive, only the concave surface of the nanoparticle interacts attractively with the lipid head groups and only the outer surface of the vesicle is exposed to the nanoparticles. Upon their adhesion on the vesicle, the curved nanoparticles generate local curvature on the membrane. The resulting nanoparticle-generated membrane curvature leads in turn to nanoparticle self-assembly into two main types of aggregates corresponding to chain aggregates at low adhesion strengths and aster aggregates at high adhesion strength. The chain-like aggregates are due to the fact that at low values of adhesion strength, the nanoparticles prefer to lie parallel to each other. As the adhesion strength is increased, a splay angle between the nanoparticles is induced with a magnitude that increases with increasing adhesion strength. The origin of the splay angles between the nanoparticles is shown to be saddle-like membrane deformations induced by a tilt of the lipids around the nanoparticles. This phenomenon of membrane mediated self-assembly of anisotropically curved nanoparticles is explored for systems with varying nanoparticle number densities, adhesion strength, and nanoparticle intrinsic curvature.

Stability of membrane-induced self-assemblies of spherical nanoparticles

Soft Matter ◽  
2018 ◽  
Vol 14 (24) ◽  
pp. 5019-5030 ◽  
Author(s):  
Eric J. Spangler ◽  
P. B. Sunil Kumar ◽  
Mohamed Laradji
Keyword(s):  
Molecular Dynamics ◽  
Self Assembly ◽  
Lipid Membranes ◽  
The Self ◽  
Coarse Grained ◽  
Implicit Solvent ◽  
Spherical Nanoparticles ◽  
Implicit Solvent Model ◽  
Solvent Model ◽  
Dynamics Simulations

The self-assembly of spherical nanoparticles, resulting from their adhesion on tensionless lipid membranes, is investigated through molecular dynamics simulations of a coarse-grained implicit-solvent model for self-assembled lipid membranes.

Coarse-grained simulation of the self-assembly of lipid vesicles concomitantly with novel block copolymers with multiple tails

Soft Matter ◽  
2021 ◽  
Author(s):  
Alexander Kantardjiev
Keyword(s):  
Molecular Dynamics ◽  
Block Copolymers ◽  
Self Assembly ◽  
Lipid Vesicles ◽  
The Self ◽  
Coarse Grained ◽  
Copolymer Concentration ◽  
Copolymer Structure ◽  
Coarse Grained Molecular Dynamics

We carried out a series of coarse-grained molecular dynamics liposome-copolymer simulations with varying extent of copolymer concentration in an attempt to understand the effect of copolymer structure and concentration on vesicle self-assembly and stability.

scholarly journals A natural product inhibits the initiation of α-synuclein aggregation and suppresses its toxicity

2017 ◽  
Vol 114 (6) ◽  
pp. E1009-E1017 ◽  
Author(s):  
Michele Perni ◽  
Céline Galvagnion ◽  
Alexander Maltsev ◽  
Georg Meisl ◽  
Martin B. D. Müller ◽  
...  
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Natural Product ◽  
Self Assembly ◽  
Lipid Membranes ◽  
Neuroblastoma Cells ◽  
Lipid Vesicles ◽  
Human Neuroblastoma

The self-assembly of α-synuclein is closely associated with Parkinson’s disease and related syndromes. We show that squalamine, a natural product with known anticancer and antiviral activity, dramatically affects α-synuclein aggregation in vitro and in vivo. We elucidate the mechanism of action of squalamine by investigating its interaction with lipid vesicles, which are known to stimulate nucleation, and find that this compound displaces α-synuclein from the surfaces of such vesicles, thereby blocking the first steps in its aggregation process. We also show that squalamine almost completely suppresses the toxicity of α-synuclein oligomers in human neuroblastoma cells by inhibiting their interactions with lipid membranes. We further examine the effects of squalamine in a Caenorhabditis elegans strain overexpressing α-synuclein, observing a dramatic reduction of α-synuclein aggregation and an almost complete elimination of muscle paralysis. These findings suggest that squalamine could be a means of therapeutic intervention in Parkinson’s disease and related conditions.

scholarly journals Molecular dynamics simulations of membrane deformation induced by the amphiphilic helices of Epsin, Sar1p and Arf1

2017 ◽  
Author(s):  
Zhen-lu Li
Keyword(s):  
Lipid Membranes ◽  
Critical Role ◽  
Membrane Curvature ◽  
Coarse Grained ◽  
Insertion Depth ◽  
Membrane Deformation ◽  
Specific Distribution ◽  
Amphiphilic Helix ◽  
Coarse Grained Simulations ◽  
Dynamics Simulations

AbstractThe N-terminal amphiphilic helices of proteins Epsin, Sar1p and Arf1 play a critical role in initiating membrane deformation. We present here the study of the interactions of these amphiphilic helices with the lipid membranes by combining the all-atom and coarse-grained simulations. In the all-atom simulations, we find that the amphiphilic helices of Epsin and Sar1p have a shallower insertion depth into the membrane compared to the amphiphilic helix of Arf1, but remarkably, the amphiphilic helices of Epsin and Sar1p induce higher asymmetry in the lipid packing between the two monolayers of the membrane. The insertion depth of amphiphilic helix into the membrane is determined not only by the overall hydrophobicity but also by the specific distribution of polar and non-polar residues along the helix. To directly compare their ability of deforming the membrane, we further apply coarse-grained simulations to investigate the membranes deformation under the insertion of multiple helices. Importantly, it is found that the amphiphilic helices of Epsin and Sar1p generate a larger membrane curvature than that of Arf1, in accord with the experimental results qualitatively. These findings enhance our understanding of the molecular mechanism of the protein-driven membrane remodeling.

scholarly journals Developing Martini Coarse-Grained Nitrogen Gas Model for Lipid Nanobubble Simulations

2021 ◽  
Author(s):  
Fujia Tian ◽  
Xubo Lin
Keyword(s):  
Cell Membrane ◽  
Lipid Membranes ◽  
Molecular Mechanisms ◽  
Membrane Curvature ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Atomistic Simulations ◽  
Nitrogen Gas ◽  
Hydrophobic Region

<p>By integrating the advantages of lipids’ biocompatibility and nanobubbles’ potent physicochemical properties, lipid nanobubbles show a great potential in ultrasound molecular imaging and biocompatible drug/gene delivery. However, under the interactions of the ultrasound, lipid nanobubbles may fuse with the cell membrane, changing the local membrane component and re-distributing encapsulated gas molecules into the hydrophobic region of the cell membrane, which may greatly affect the dynamics of certain membrane proteins and thus functions of cells. Although molecular dynamics simulation provides a useful computational tool to reveal the related molecular mechanisms, the lack of coarse-grained gas model greatly restricts this purpose. In the current work, we developed a Martini-compatible coarse-grained gas model based on the results of previous experiments and atomistic simulations, which could be used for lipid nanobubble simulations with complicated lipid components. By comparing the results of well-designed lipid nanobubble, lipid bi-monolayer and lipid bilayer simulations, we further revealed the role of membrane curvature and interleaflet coupling in the liquid-liquid phase separation of lipid membranes. It is worth mention that our developed coarse-grained nitrogen gas model can also be used for other gas-water interface systems such as pulmonary surfactant, which may overcome the possible artefacts arising from the usage of vacuum for gas phase. </p>

scholarly journals Explicit and implicit modeling of nanobubbles in hydrophobic confinement

2010 ◽  
Vol 82 (1) ◽  
pp. 3-12 ◽  
Author(s):  
Joachim Dzubiella
Keyword(s):  
Large Scale ◽  
Md Simulations ◽  
Energy Functional ◽  
Coarse Grained ◽  
Implicit Solvent ◽  
Implicit Solvent Model ◽  
Solvent Model ◽  
Nanofluidic Devices ◽  
Capillary Evaporation ◽  
Hydrophobic Solutes

Water at normal conditions is a fluid thermodynamically close to the liquid-vapor phase coexistence and features a large surface tension. This combination can lead to interesting capillary phenomena on microscopic scales. Explicit water molecular dynamics (MD) computer simulations of hydrophobic solutes, for instance, give evidence of capillary evaporation on nanometer scales, i.e., the formation of nanometer-sized vapor bubbles (nanobubbles) between confining hydrophobic surfaces. This phenomenon has been exemplified for solutes with varying complexity, e.g., paraffin plates, coarse-grained homopolymers, biological and solid-state channels, and atomistically resolved proteins. It has been argued that nanobubbles strongly impact interactions in nanofluidic devices, translocation processes, and even in protein stability, function, and folding. As large-scale MD simulations are computationally expensive, the efficient multiscale modeling of nanobubbles and the prediction of their stability poses a formidable task to the'nanophysical' community. Recently, we have presented a conceptually novel and versatile implicit solvent model, namely, the variational implicit solvent model (VISM), which is based on a geometric energy functional. As reviewed here, first solvation studies of simple hydrophobic solutes using VISM coupled with the numerical level-set scheme show promising results, and, in particular, capture nanobubble formation and its subtle competition to local energetic potentials in hydrophobic confinement.

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