scholarly journals Orientation of Fluorescent Lipid Analogue BODIPY-PC to Probe Lipid Membrane Properties: Insights from Molecular Dynamics Simulations

2011 ◽  
Vol 115 (19) ◽  
pp. 6157-6165 ◽  
Author(s):  
Kevin C. Song ◽  
Philip W. Livanec ◽  
Jeffery B. Klauda ◽  
Krzysztof Kuczera ◽  
Robert C. Dunn ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Lipid Membrane ◽  
Membrane Properties ◽  
Dynamics Simulations ◽  
Fluorescent Lipid

scholarly journals Molecular Dynamics Simulations of the Permeation of Bisphenol A and Pore Formation in a Lipid Membrane

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Liang Chen ◽  
Junlang Chen ◽  
Guoquan Zhou ◽  
Yu Wang ◽  
Can Xu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Bisphenol A ◽  
Molecular Dynamics Simulations ◽  
Pore Formation ◽  
Lipid Membrane ◽  
Dynamics Simulations

Interaction of fullerene chains and a lipid membrane via computer simulations

RSC Advances ◽  
2014 ◽  
Vol 4 (57) ◽  
pp. 30215-30220 ◽  
Author(s):  
Wen-de Tian ◽  
Kang Chen ◽  
Yu-qiang Ma
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Computer Simulations ◽  
Membrane Structure ◽  
Lipid Membrane ◽  
Coarse Grained ◽  
Structure Dynamics ◽  
Dynamics Simulations ◽  
Fullerene Polymers ◽  
Coarse Grained Molecular Dynamics

Coarse-grained molecular dynamics simulations were employed to study the fullerene polymers with various functionalization degrees interacting with the DPPC membrane. Structure, dynamics, and thermodynamics of systems were analyzed.

Size-dependent formation of membrane nanotubes: continuum modeling and molecular dynamics simulations

2018 ◽  
Vol 20 (5) ◽  
pp. 3474-3483 ◽  
Author(s):  
Falin Tian ◽  
Tongtao Yue ◽  
Wei Dong ◽  
Xin Yi ◽  
Xianren Zhang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Lipid Membrane ◽  
Continuum Theory ◽  
Mechanical Behaviors ◽  
Continuum Modeling ◽  
Membrane Nanotubes ◽  
Size Dependent ◽  
Structural Lipid ◽  
Dynamics Simulations

With continuum theory and molecular dynamics simulations we demonstrated that the lipid membrane upon extraction exhibits size- and tension-dependent mechanical behaviors, and different structural lipid rearrangements in different leaflets.

scholarly journals Curvature induction and sensing of the F-BAR protein Pacsin1 on lipid membranes via molecular dynamics simulations

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Md. Iqbal Mahmood ◽  
Hiroshi Noguchi ◽  
Kei-ichi Okazaki
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Lipid Membranes ◽  
Lipid Membrane ◽  
Complex Structure ◽  
Membrane Curvature ◽  
Coarse Grained ◽  
Lateral Interaction ◽  
Bar Domain ◽  
Dynamics Simulations

Abstract F-Bin/Amphiphysin/Rvs (F-BAR) domain proteins play essential roles in biological processes that involve membrane remodelling, such as endocytosis and exocytosis. It has been shown that such proteins transform the lipid membrane into tubes. Notably, Pacsin1 from the Pacsin/Syndapin subfamily has the ability to transform the membrane into various morphologies: striated tubes, featureless wide and thin tubes, and pearling vesicles. The molecular mechanism of this interesting ability remains elusive. In this study, we performed all-atom (AA) and coarse-grained (CG) molecular dynamics simulations to investigate the curvature induction and sensing mechanisms of Pacsin1 on a membrane. From AA simulations, we show that Pacsin1 has internal structural flexibility. In CG simulations with parameters tuned from the AA simulations, spontaneous assembly of two Pacsin1 dimers through lateral interaction is observed. Based on the complex structure, we show that the regularly assembled Pacsin1 dimers bend a tensionless membrane. We also show that a single Pacsin1 dimer senses the membrane curvature, binding to a buckled membrane with a preferred curvature. These results provide molecular insights into polymorphic membrane remodelling.

scholarly journals Kinetics, Statistics, and Energetics of Lipid Membrane Electroporation Studied by Molecular Dynamics Simulations

2008 ◽  
Vol 95 (4) ◽  
pp. 1837-1850 ◽  
Author(s):  
Rainer A. Böckmann ◽  
Bert L. de Groot ◽  
Sergej Kakorin ◽  
Eberhard Neumann ◽  
Helmut Grubmüller
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Lipid Membrane ◽  
Dynamics Simulations
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