Fig 1.
A snapshot of a simulated membrane, the used lipid moieties, and the thermodynamic cycle for estimation of the free energy of transfer of a membrane protein between the Ld and Lo phases.
A) Lo membrane with 8 mol% SDPE after 10 μs of equilibration. In panel A), A2AR is shown in green, DSPC in blue, CHOL in red, and SDPE in yellow. CG structures of B) DSPC, C) DOPC, D) SDPE, and E) CHOL. In panels B)–E), phosphate is shown in brown, choline/ethanolamine in blue, and the CHOL ring in green. The saturated chain segments and glycerol are shown in cyan, while the unsaturated chains are shown in purple. F) The thermodynamic cycle. The horizontal arrows represent the transformations used in this work, whereas the vertical arrows represent the alternative transformations employed commonly for smaller molecules (see Section A.1 in S1 File for details). Lipids having a low main transition temperature Tm (here DOPC, present in the Ld phase) and lipids having a high Tm (here DSPC, present in the Lo phase) are shown in cyan and green, respectively. Cholesterol is shown in yellow and the protein in orange.
Fig 2.
Average 2nd rank acyl chain order parameters (Sn).
A) Average order parameter of the mutated lipid (DSPC→DOPC) in (top) the system containing A2AR, and (bottom) the protein-free system. The cholesterol content was 20 mol% in all systems. The Lo→Ld transformation takes place as the coupling parameter λ changes from zero to one. In Section B.1 in the S1 File, we demonstrate that these end points indeed correspond to the Lo and Ld phases. Error bars showing standard error are smaller than the marker size. B) Effects of SDPE and A2AR on average 2nd rank acyl chain order parameters (). Data are shown for both coarse-grained and all-atom (fine-grained) simulations. For the latter, the order parameter is estimated from the average deuterium order parameter as
, and the error bars show the standard error.
Fig 3.
The effect of SDPE on the free energies of transfer of proteins between the Lo and Ld phases.
A) Values for A2AR are shown in black solid line. A negative sign of the free energy of transfer indicates A2AR to favor the Ld phase. Inset shows the free energy changes and
of the alchemical transformations (DSPC→DOPC) with and without A2AR, respectively. B) Free energies of all studied proteins in the absence and presence (16 mol%) of SDPE. The more realistic membrane compositions are denoted with “real.”.
Fig 4.
2D radial distribution functions of different lipid chains around the center of mass of A2AR and cholesterol density maps.
A) The radial distribution functions are shown as a function of distance from the A2AR COM for the Lo phase membrane (DSPC/CHOL) with 4 mol% SDPE. Data are extracted from the last 5 μs of the 10 μs simulation using the gmx rdf tool. Error bars show standard error. Data for other SDPE concentrations are shown in Fig. E in the S1 File. B & C) Cholesterol density around A2AR in systems B) without SDPE and C) with 16 mol% SDPE is shown as a blue isosurface. The residues involved in binding cholesterol, suggested by earlier studies, are shown in orange [27] and yellow [28]. The vicinity of these residues to the observed cholesterol density (blue) suggests that cholesterol reaches the protein surface and often finds the proper binding sites in our simulations. Note that the isosurfaces are not in scale.
Fig 5.
Radial distribution functions of different lipid chains around the centers of mass of four representative proteins.
Leftmost column: RDF plots. The distance was measured in the membrane plane, and the last 500 ns of the simulations were used in the analysis. The gmx rdf tool was used. Error bars show standard error. The dashed line shows the approximate position of the protein surface. Two rightmost columns: Protein structures used in the solvation simulations, as well as snapshots of them residing in the membranes. For membranes, only fatty acid chains are rendered with the protein. The coloring is as follows: blue for saturated chains (both DPPC chains and the stearic acid chain of SDPC), red for monounsaturated chains (both DOPC chains), yellow for diunsaturated chains (both DLiPC chains), green for polyunsaturated chains (docosahexaenoic acid chain of SDPC), and orange for cholesterol.
Fig 6.
Observed conformations of SDPE due to the flexibility of DHA in the fine-grained simulations.
A) An example configuration, where the DHA chain adapts to the A2AR surface. B) An example configuration, where the DHA chain penetrates into the core of A2AR. The DHA chain is shown in orange, the rest of the lipid (including the stearic acid chain) in yellow, and A2AR in green.