dppc cholesterol mixture  (Revvity)

Journal: Biochimica et biophysica acta. Biomembranes

Article Title: Boundary lipids of the nicotinic acetylcholine receptor: spontaneous partitioning via coarse-grained molecular dynamics simulation

doi: 10.1016/j.bbamem.2019.01.005

Figure Lengend Snippet: nAChR boundary lipids in binary mixtures of DPPC and CHOL. A: Representative frame from a simulated trajectory of a single nAChR embedded in a small membrane, colored by subunit (α:green, β:purple, δ:gray, γ:cyan) in a 4:1 DPPC (blue):Chol (red) mixture. B: Extent of demixing (MDPPC defined in Eq. 1) and depletion of saturated lipids from the boundary (Qsat defined in Eq.2) in small binary membranes. In this binary system, cholesterol depletion/enrichment is directly related to the saturated lipid depletion/enrichment: Qchol = −xsat Qsat/xChol. Error bars represent standard error for a blocking average over 50 ns. C: Average normalized density (Eq. 4) of cholesterol for the system in A. Data is equivalent to that in Figure 5: Binary Mixture “Chol” row.

Article Snippet: In binary Dipalmitoylphosphatidylcholine:Cholesterol (DPPC:CHOL) mixtures, both CHOL and DPPC acyl chains were observed spontaneously entering deep “non-annular” cavities in the nAChR TMD, particularly at the subunit interface and the β subunit center, facilitated by the low amino acid density in the cryo-EM structure of nAChR in a native membrane.

Techniques: Blocking Assay

Journal: Biochimica et biophysica acta. Biomembranes

Article Title: Boundary lipids of the nicotinic acetylcholine receptor: spontaneous partitioning via coarse-grained molecular dynamics simulation

doi: 10.1016/j.bbamem.2019.01.005

Figure Lengend Snippet: Lipid density enrichment or depletion around a single central nAChR. Heatmaps are colored according to the normalized density ρ˜a (left, defined in eq 4) or ln ρ ρ˜a (right), averaged over the final 5µs of a 10 µs simulation. Membrane column (left) depicts density across the simulated membrane; ρ˜a<1 indicates depletion compared to a random mixture, while ρ˜a>1 indicates enrichment. Boundary column (right) shows a zoomed-in region around the protein, with circles corresponding to average position of the protein helices, colored as in Figure 1, and black indicating no detected lipid density. If no non-annular or embedded lipid binding was observed, the entire protein footprint would be black for all lipids. Binary mixture contains 4:1 DPPC:CHOL as in Figure 1, while both ternary mixtures contain 2:2:1 DPPC:PUFA:Chol.

Article Snippet: In binary Dipalmitoylphosphatidylcholine:Cholesterol (DPPC:CHOL) mixtures, both CHOL and DPPC acyl chains were observed spontaneously entering deep “non-annular” cavities in the nAChR TMD, particularly at the subunit interface and the β subunit center, facilitated by the low amino acid density in the cryo-EM structure of nAChR in a native membrane.

Techniques: Binding Assay

Journal: Biochimica et biophysica acta. Biomembranes

Article Title: Boundary lipids of the nicotinic acetylcholine receptor: spontaneous partitioning via coarse-grained molecular dynamics simulation

doi: 10.1016/j.bbamem.2019.01.005

Figure Lengend Snippet: Trajectories of ternary mixtures at ratios of 2:2:1 DPPC:PUFA:Chol. A and B: Trajectories of simulation systems with a single nAChR embedded within small membranes, using lipids containing DHA acyl chains or LA acyl chains. Both simulations were run for 2 µs. C: Final snapshot of 4 µs trajectory of a system within a large ~ 75×75 nm2 membrane with the same composition as in A. Subunits are colored: α: green, β: purple, δ: gray, γ: cyan. Lipids are colored: Chol: red, DPPC: blue, dDHA-PE: white, dLA-PC: tan.

Article Snippet: In binary Dipalmitoylphosphatidylcholine:Cholesterol (DPPC:CHOL) mixtures, both CHOL and DPPC acyl chains were observed spontaneously entering deep “non-annular” cavities in the nAChR TMD, particularly at the subunit interface and the β subunit center, facilitated by the low amino acid density in the cryo-EM structure of nAChR in a native membrane.

Techniques:

Journal: Biochimica et biophysica acta. Biomembranes

Article Title: Boundary lipids of the nicotinic acetylcholine receptor: spontaneous partitioning via coarse-grained molecular dynamics simulation

doi: 10.1016/j.bbamem.2019.01.005

Figure Lengend Snippet: Embedded lipids in the nAChR. Main image: Representative frame from equilibrated small membrane simulation of nAChR in 2:2:1 DPPC:DHA-PE:CHOL. Backbone beads of the TMD helices are colored by subunit as in Figure 2; side-chain beads are not shown. Both DHA-PE (white) and cholesterol (red) equilibrate to embedded sites in the subunit center and subunit interfaces, although most cholesterol is found in the lo phase with DPPC (blue). Inset : Cryo-EM density of nAChR from (117) as rendered in (98); dark blue indicates high density, white is medium density, and red is low density.

Article Snippet: In binary Dipalmitoylphosphatidylcholine:Cholesterol (DPPC:CHOL) mixtures, both CHOL and DPPC acyl chains were observed spontaneously entering deep “non-annular” cavities in the nAChR TMD, particularly at the subunit interface and the β subunit center, facilitated by the low amino acid density in the cryo-EM structure of nAChR in a native membrane.

Techniques: Cryo-EM Sample Prep