Extraction Of Lipids From Phospholipid Membranes By Steered Molecular Dynamics

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Extraction of Lipids from Phospholipid Membranes by Steered

Steered molecular dynamics (SMD) simulations were employed to investigate the extraction step of the lipid head group cleavage reaction by human synovial phospholipase A 2 (PLA 2) by pulling a lipid molecule from a monolayer of dilauroyl-phosphatidyl-ethanolamin lipids into the active site of PLA 2 and into the aqueous phase.

Effect of Shape on the Entering of Graphene Quantum Dots into

Apr 16, 2021 degeneration.26 Chen et al. pointed out that the phospholipid extraction by graphene can activate integrin on the cell membrane.27 Li et al. first pointed out that graphene could spontaneously pass through the cell membrane through edge protrusion or corner sites.28 Puigpelat et al. used the MD method to study the spontaneous entry of graphene

Influence of Single-Stranded DNA Coatings on the Interaction

The literature, in particular aided by molecular dynamics (MD) simulation, has established that the hydrophobicity of graphitic materials is a significant driving force in terms of their interactions with lipid membranes. For example, MD simulation calculations of the free energy of C60 buckyballs penetrating phospholipid membranes revealed a

Application of Graphene as a Nanoindenter Interacting with

Jul 22, 2020 GN sheets and phospholipid bilayers are examined using steered molecular dynamics simulations. GN sheets of different sizes were inserted into a bilayer and subsequently withdrawn from it at two different rates (1 and 2 m/s). In some cases, nanoindentation led to substantial damage of the phospholipid bilayer;

Reconstructing Potentials of Mean Force through Time Series

Steered molecular dynamics (SMD) simulates a biopolymer system under the influence of an applied external force; such simulations can describe AFM-style micromanipulations in atomic-level detail and employ stiffer springs than those used in present AFM experi-ments. As a result, more detailed information about interaction energies as well as

Partitioning of Anesthetics into a Lipid Bilayer and their

Steered molecular dynamics (SMD) simulations (43,44), using NAMD2, were also carried out on a system consisting of a single halothane molecule dragged from the DOPC lipid into the water phase. SMD calculations in-volve the application of external forces to accelerate the processes to overcome energy barriers.

Stability and dynamics of membrane-spanning DNA nanopores

simulations to explore the structure, stability and dynamics of an archetypical DNA nanotube inserted via a ring of membrane anchors into a phospholipid bilayer. Coarse-grained MD reveals that the lipids reorganize locally to interact closely with the membrane-spanning section of the DNA tube. Steered simulations along the bilayer normal

Membrane Localization and Dynamics of Geranylgeranylated Rab5

full-atomistic and coarse-grained molecular dynamics simulations of the truncated Rab5 HVR206-215 in three model membranes of increasing complexity (pure phospholipid bilayer, ternary membrane with cholesterol, six-component early endosome) were performed.

Molecular Dynamics Simulations of Bacterial Outer Membrane

Jun 11, 2020 97 extraction of lipids from both Gram-negative bacterial OM and IM models, using a range 98 of CVs (Table 1). The OM model was comprised of an extracellular leaflet of ReLPS and 99 an inner leaflet of 90% 16:0 18:1 phosphatidyl-ethanolamine (POPE), 5% 16:0 18:1 100 phosphatidyl-glycerol (POPG) and 5% CDL, with LPS lipids neutralized by calcium