Molecular dynamics simulations of model micelles. 4. Effects of chain length and head group characteristics

1990 ◽  
Vol 94 (6) ◽  
pp. 2624-2631 ◽  
Author(s):  
S. Karaborni ◽  
J. P. O'Connell
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Chain Length ◽  
Head Group ◽  
Dynamics Simulations ◽  
Group Characteristics

scholarly journals Molecular dynamics simulations and experimental studies reveal differential permeability of withaferin-A and withanone across the model cell membrane

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Renu Wadhwa ◽  
Neetu Singh Yadav ◽  
Shashank P. Katiyar ◽  
Tomoko Yaguchi ◽  
Chohee Lee ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Cell Membrane ◽  
Molecular Dynamics Simulations ◽  
Experimental Studies ◽  
Bilayer Membrane ◽  
Withaferin A ◽  
Head Group ◽  
Polar Head Group ◽  
Natural Drugs ◽  
Dynamics Simulations

AbstractPoor bioavailability due to the inability to cross the cell membrane is one of the major reasons for the failure of a drug in clinical trials. We have used molecular dynamics simulations to predict the membrane permeability of natural drugs—withanolides (withaferin-A and withanone) that have similar structures but remarkably differ in their cytotoxicity. We found that whereas withaferin-A, could proficiently transverse through the model membrane, withanone showed weak permeability. The free energy profiles for the interaction of withanolides with the model bilayer membrane revealed that whereas the polar head group of the membrane caused high resistance for the passage of withanone, the interior of the membrane behaves similarly for both withanolides. The solvation analysis further revealed that the high solvation of terminal O5 oxygen of withaferin-A was the major driving force for its high permeability; it interacted with the phosphate group of the membrane that led to its smooth passage across the bilayer. The computational predictions were tested by raising and recruiting unique antibodies that react to withaferin-A and withanone. The time-lapsed analyses of control and treated cells demonstrated higher permeation of withaferin-A as compared to withanone. The concurrence between the computation and experimental results thus re-emphasised the use of computational methods for predicting permeability and hence bioavailability of natural drug compounds in the drug development process.

Multiscale Simulations of Polymer Flow Between Two Parallel Plates

2021 ◽  
Vol 143 (4) ◽  
Author(s):  
Hong-Ji Yan ◽  
Zhen-Hua Wan ◽  
Feng-Hua Qin ◽  
De-Jun Sun
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Chain Length ◽  
Multiscale Method ◽  
Time Averaging ◽  
Parallel Plates ◽  
Large Spatial Scale ◽  
Dynamics Simulations ◽  
Pressure Driven Flow ◽  
Pressure Driven

Abstract A modified multiscale method without constitutive equation is proposed to investigate the microscopic information and macroscopic flow properties of polymeric fluid with the memory effect between parallel plates. In this method, the domain is entirely described by macromodel with isolated molecular dynamics simulations applied to calculate the necessary local stresses. The present method is first verified by the creep-recovery motion and pressure-driven flow, and all results are in excellent agreement with the available numerical solutions in literature. Then, the method is extended to simulate two typical problems of relatively large spatial scale in general beyond the capability of molecular dynamics simulations. In the planar Couette flow, the relationship between macroscopic properties and the time evolution of local molecular information is investigated in detail without long time averaging. All results that are consistent with nonequilibrium molecular dynamics and literature qualitatively or quantitatively demonstrate the validity of present multiscale method in simulating transient viscoelastic flows and the capacity to obtain the polymer information. In the pressure-driven flow, a general monotonically decreasing relationship between the maximum or average velocities and the polymer concentrations has been found regardless of the polymer chain length. Particularly, the reference concentration that satisfies a power law with chain length is closely related to the overlap concentration, and the reference velocity is exactly the relevant velocity of Newtonian fluid with corresponding zero shear rate viscosity.

scholarly journals Transmembrane Potential of Physiologically Relevant Model Membranes: Effects of Membrane Asymmetry

2020 ◽  
Author(s):  
Xubo Lin ◽  
Alemayehu A. Gorfe
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Transmembrane Potential ◽  
Model Membranes ◽  
Head Group ◽  
Asymmetric Distribution ◽  
Symmetric Model ◽  
Lipid Dynamics ◽  
Dynamics Simulations ◽  
The Impact

<div><div>Transmembrane potential difference (𝑉௠) plays important roles in regulating various biological</div><div>processes. At the macro level, 𝑉௠ can be experimentally measured or calculated using the Nernst</div><div>or Goldman-Hodgkin-Katz equation. However, the atomic details responsible for its generation</div><div>and impact on protein and lipid dynamics still need to be further elucidated. In this work, we</div><div>performed a series of all-atom molecular dynamics simulations of symmetric model membranes of</div><div>various lipid compositions and cation contents to evaluate the relationship between membrane</div><div>asymmetry and 𝑉௠. Specifically, we studied the impact of the asymmetric distribution of POPS (1-</div><div>palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine), PIP2 (phosphatidylinositol 4,5-bisphosphate),</div><div>𝑁𝑎ା, 𝐾ା and 𝐶𝑎ଶା on 𝑉௠ using atomically detailed molecular dynamics simulations of symmetric</div><div>model membranes. The results suggest that, for an asymmetric POPC-POPC/POPS bilayer in the</div><div>presence of NaCl, enrichment of the monovalent anionic lipid POPS in the inner leaflet polarizes</div><div>the membrane (∆𝑉௠ < 0). Intriguingly, replacing a third of the POPS lipids by the polyvalent</div><div>anionic signaling lipid PIP2 counteracts this effect, resulting in a smaller negative membrane</div><div>potential. We also found that replacing 𝑁𝑎ା ions in the inner region by 𝐾ା depolarizes the</div><div>membrane (∆𝑉௠ > 0), whereas replacing by 𝐶𝑎ଶା polarizes the membrane. These divergent effects</div><div>arise from variations in the strength of cation-lipid interactions and are correlated with changes in</div><div>lipid chain order and head group orientation. </div></div>

Molecular dynamics simulations of conformation and chain length dependent terahertz spectra of alanine polypeptides

2015 ◽  
Vol 42 (5) ◽  
pp. 398-404 ◽  
Author(s):  
Mingkun Zhang ◽  
Dongshan Wei ◽  
Mingjie Tang ◽  
Changcheng Shi ◽  
Hong-liang Cui ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Chain Length ◽  
Dynamics Simulations

scholarly journals Open Collaboration that uses NMR Data to Judge the Correctness of Phospholipid Glycerol and Head Group Structures in Molecular Dynamics Simulations

2015 ◽  
Vol 108 (2) ◽  
pp. 411a
Author(s):  
Patrick F.J. Fuchs ◽  
Matti Javanainen ◽  
Antti Lamberg ◽  
Markus S. Miettinen ◽  
Luca Monticelli ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Head Group ◽  
Open Collaboration ◽  
Nmr Data ◽  
Dynamics Simulations ◽  
Group Structures
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