scholarly journals Hydrophobic aggregation and collective absorption of dioxin into lipid membranes: insights from atomistic simulations

2015 ◽  
Vol 17 (4) ◽  
pp. 2344-2348 ◽  
Author(s):  
M. Casalegno ◽  
G. Raos ◽  
G. Sello
Keyword(s):  
Lipid Membranes ◽  
Cell Membranes ◽  
Md Simulations ◽  
Atomistic Simulations ◽  
Hydrophobic Aggregation

MD simulations show that dioxin molecules quickly aggregate in water and jointly penetrate into cell membranes.

scholarly journals From dioxin to dioxin congeners: understanding the differences in hydrophobic aggregation in water and absorption into lipid membranes by means of atomistic simulations

2016 ◽  
Vol 18 (26) ◽  
pp. 17731-17739 ◽  
Author(s):  
Mosé Casalegno ◽  
Guido Raos ◽  
Guido Sello
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Lipid Membranes ◽  
Cell Membranes ◽  
Atomistic Simulations ◽  
Dynamics Simulations ◽  
Hydrophobic Aggregation

Molecular dynamics simulations indicate that dioxin likely accumulates in cell membranes more than its congeners (anthracene, tetrahydrodioxin, 3,3′,5,5′-tetrachlorobiphenyl, and 1,2-dihydroxytetrahydrodibenzo-p-dioxin).

scholarly journals Sequential water and headgroup merger: Membrane poration paths and energetics from MD simulations

2020 ◽  
Author(s):  
Greg Bubnis ◽  
Helmut Grubmüller
Keyword(s):  
Lipid Membranes ◽  
Lipid Membrane ◽  
Quantitative Description ◽  
Md Simulations ◽  
Nucleation Mechanism ◽  
Membrane Topology ◽  
Atomistic Simulations ◽  
Cellular Transport ◽  
Membrane Pore ◽  
Reaction Coordinates

Membrane topology changes such as poration, stalk formation, and hemi-fusion rupture are essential to cellular function, but their molecular details, energetics, and kinetics are still not fully understood. Here we present a unified energetic and mechanistic picture of metastable pore defects in tensionless lipid membranes. We used an exhaustive committor analysis to test and select optimal reaction coordinates and also to determine the nucleation mechanism. These reaction coordinates were used to calculate free energy landscapes that capture the full process and end states. The identified barriers agree with the committor analysis. To enable sufficient sampling of the complete transition path for our atomistic simulations, we developed a novel “gizmo” potential biasing scheme. The simulations suggest that the essential step in the nucleation is the initial merger of lipid head-groups at the nascent pore center. To facilitate this event, an indentation pathway is energetically preferred to a hydrophobic defect. Continuous water columns that span the indentation were determined to be on-path transients that precede the nucleation barrier. This study gives a quantitative description of the nucleation mechanism and energetics of small metastable pores and illustrates a systematic approach to uncover the mechanisms of diverse cellular membrane remodeling processes.STATEMENT OF SIGNIFICANCEThe primary steps and nucleation of lipid membrane pore formation are key to membrane fusion, viral infection, and vesicular cellular transport. Despite decades experimental and theoretical studies, the underlying mechanisms are still not fully understood at the atomic level. Using a committor-based reaction coordinate and atomistic simulations, we report new structural and energetics insight into the full poration process. We find that the pore nucleates via an elastic indentation rather than by forming a hydrophobic defect. Subsequently, water pierces the thinned slab as a prerequisite for the following axial merger of the first lipid headgroups from opposite monolayers, which precedes and best characterizes the transition state. We also identify a metastable prepore basin, thereby explaining previous indirect experimental evidence.

scholarly journals Effects of lipid heterogeneity on model human brain lipid membranes

Soft Matter ◽  
2021 ◽  
Vol 17 (1) ◽  
pp. 126-135
Author(s):  
Sze May Yee ◽  
Richard J. Gillams ◽  
Sylvia E. McLain ◽  
Christian D. Lorenz
Keyword(s):  
Human Brain ◽  
Lipid Membranes ◽  
Cell Membranes ◽  
Brain Lipid ◽  
Lipid Distribution

Cell membranes naturally contain a heterogeneous lipid distribution.

Elucidation of molecular interactions between lipid membranes and ionic liquids using model cell membranes

Soft Matter ◽  
2012 ◽  
Vol 8 (20) ◽  
pp. 5501 ◽  
Author(s):  
Seunghwan Jeong ◽  
Sung Ho Ha ◽  
Sang-Hyun Han ◽  
Min-Cheol Lim ◽  
Sun Min Kim ◽  
...  
Keyword(s):  
Ionic Liquids ◽  
Molecular Interactions ◽  
Lipid Membranes ◽  
Cell Membranes ◽  
Model Cell

Molecular Dynamics Simulation of a Pullout Test on a Carbon Nanotube in a Polymer Matrix

2014 ◽  
Vol 1700 ◽  
pp. 61-66
Author(s):  
Guttormur Arnar Ingvason ◽  
Virginie Rollin
Keyword(s):  
Molecular Dynamics ◽  
Polymer Matrix ◽  
Large Scale ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Atomistic Simulations ◽  
Polymer Molecules ◽  
Molecular Potential ◽  
Pull Out ◽  
Walled Carbon Nanotubes

ABSTRACTAdding single walled carbon nanotubes (SWCNT) to a polymer matrix can improve the delamination properties of the composite. Due to the complexity of polymer molecules and the curing process, few 3-D Molecular Dynamics (MD) simulations of a polymer-SWCNT composite have been run. Our model runs on the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS), with a COMPASS (Condensed phase Optimized Molecular Potential for Atomistic Simulations Studies) potential. This potential includes non-bonded interactions, as well as bonds, angles and dihedrals to create a MD model for a SWCNT and EPON 862/DETDA (Diethyltoluenediamine) polymer matrix. Two simulations were performed in order to test the implementation of the COMPASS parameters. The first one was a tensile test on a SWCNT, leading to a Young’s modulus of 1.4 TPa at 300K. The second one was a pull-out test of a SWCNT from an originally uncured EPON 862/DETDA matrix.

scholarly journals Study of interactions between polymer nanoparticles and cell membranes at atomistic levels

2015 ◽  
Vol 370 (1661) ◽  
pp. 20140036 ◽  
Author(s):  
Chin W. Yong
Keyword(s):  
Cell Membranes ◽  
Membrane Surface ◽  
Animal Health ◽  
Md Simulations ◽  
Industrial Applications ◽  
Polymer Nanoparticles ◽  
Head Groups ◽  
Structure Of Nanoparticles ◽  
Hydrocarbon Chains ◽  
Modelling Techniques

Knowledge of how the structure of nanoparticles and the interactions with biological cell membranes is important not only for understanding nanotoxicological effects on human, animal health and the environment, but also for better understanding of nanoparticle fabrication for biomedical applications. In this work, we use molecular modelling techniques, namely molecular dynamics (MD) simulations, to explore how polymer nanoparticles interact with 1-palmitoyl-2-oleoyl- sn -glycero-3-phosphocholine (POPC) lipid cell membranes. Two different polymers have been considered: 100 monomer units of polyethylene (approx. 2.83 kDa) and polystyrene (approx. 10.4 kDa), both of which have wide industrial applications. We found that, despite the polar lipid head groups acting as an effective barrier to prevent the nanoparticles from interacting with the membrane surface, irreversible adhesion can be initiated by insertion of dangling chain ends from the polymer into the hydrophobic interior of the membrane. In addition, alignment of chain segments from the polymers with that of hydrocarbon chains in the interior of the membrane facilitates the complete immersion of the nanoparticles into the cell membrane. These findings highlight the importance of the surface and the topological structures of the polymer particles that dictate the absorption behaviour into the membrane and, subsequently, induce the possible translocation into the cell.

Singlet oxygen effects on lipid membranes: implications for the mechanism of action of broad-spectrum viral fusion inhibitors

2014 ◽  
Vol 459 (1) ◽  
pp. 161-170 ◽  
Author(s):  
Axel Hollmann ◽  
Miguel A. R. B. Castanho ◽  
Benhur Lee ◽  
Nuno C. Santos
Keyword(s):  
Singlet Oxygen ◽  
Mechanism Of Action ◽  
Broad Spectrum ◽  
Lipid Membranes ◽  
Cell Membranes ◽  
Viral Fusion ◽  
Fusion Inhibitors ◽  
Oxygen Effects

By studying the interaction of LJ001 and JL103 with lipid membranes, we demonstrate that singlet oxygen produced by both compounds induces changes on lipid properties, preventing the fusion between viral and cell membranes.

scholarly journals Cation-containing lipid membranes – experiment and md simulations

2017 ◽  
Vol 64 (2) ◽  
pp. 9-14
Author(s):  
N. Kučerka ◽  
E. Dushanov ◽  
Kt. Kholmurodov ◽  
J. Katsaras ◽  
D. Uhríková
Keyword(s):  
Lipid Membranes ◽  
Metal Ion ◽  
Md Simulations ◽  
Molar Ratio ◽  
Bilayer Thickness ◽  
Dipalmitoyl Phosphatidylcholine ◽  
Dppc Bilayer ◽  
Divalent Metal Ion ◽  
Gel Phase ◽  
Dynamics Simulations

AbstractUsing small angle neutron diffraction and molecular dynamics simulations we studied the interactions between calcium (Ca2+) or zinc (Zn2+) cations, and oriented gel phase dipalmitoyl-phosphatidylcholine (DPPC) bilayers. For both cations studied at ~1:7 divalent metal ion to lipid molar ratio (Me2+:DPPC), bilayer thickness increased. Simulation results helped reveal subtle differences in the effects of the two cations on gel phase membranes.

Comment on “Cholesterol solubility limit in lipid membranes probed by small angle neutron scattering and MD simulations” by S. Garg et al., Soft Matter, 2014, 10, 9313

Soft Matter ◽  
2015 ◽  
Vol 11 (27) ◽  
pp. 5580-5581
Author(s):  
Richard M. Epand ◽  
Diana Bach ◽  
Ellen Wachtel
Keyword(s):  
Phase Separation ◽  
Neutron Scattering ◽  
Small Angle ◽  
Lipid Membranes ◽  
Small Angle Neutron Scattering ◽  
Soft Matter ◽  
Md Simulations ◽  
Solubility Limit ◽  
Phospholipid Bilayers ◽  
Cholesterol Solubility

As consistently described in the literature, the solubility limit of cholesterol in phospholipid bilayers is defined by its phase separation and crystallization.

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