Fig 1.
Full-scale model of a realistic HIV-1 lipid vesicle at united atom resolution (MARTINI force-field).
A Full-view representation of the 150 nm vesicle model. B Clipped view of the vesicle and C close-up view of the clipped vesicle, the latter demonstrating lipid packing across the bilayer. In each panel, the headgroup of each chemical species is colored differently according to the legend provided. Tails are shown in licorice representation, and Cholesterol is shown in ball-and-stick representation.
Fig 2.
Hydrophobic thickness analysis.
A Clipped view of the carbon bead selection used for thickness calculation. The selection is superimposed with the volume grid employed to determine the leaflet in which each ‘C2B’ bead resides; blue represents the outer monolayer and green the inner monolayer. The inset shows a zoomed in view of the leaflets delineated by the volume grid, the latter yielded by measure volinterior. B The uniform point distribution (N = 1024) used to sample thickness, yielded via Poisson disk sampling. C Uniform distribution with the volume grid. The inset demonstrates the carbon beads isolated about each test point, in a search radius rsearch of 46 Å. Hydrophobic thickness is considered as the center of mass distance between groups of C2B beads in each leaflet. D Resulting analysis over the 5.2 μs trajectory. The dark line shows the mean hydrophobic thickness per frame, while the transparent region shows the standard deviation at each frame for the 1024 values calculated. The mean thickness over the time series, dotted line, is 26 Å with a standard deviation of 1 Å between frames.
Fig 3.
Diffusion of lipids on the complex vesicle model.
A Trans-bilayer rates of lipids present in the vesicle after 5.2 μs of MD production. The average outer to inner rate (blue) and outer to inner (red) rates were estimated by calculating the cumulative number of flipping events per lipid species from three different starting points during the simulation: 0, 200 and 4,000 ns. The values reported are normalized per number of events per molecule. B Lipid lateral diffusion coefficient and C scaling factor. The average is reported at windows sizes of 25, 50, 100, 250, 500 and 1,000 ns.
Fig 4.
Mobility analysis of lipids and lipid regions.
A Mobility of lipid headgroups after 1 μs of production MD, in the outer leaflet. Each column shows lipids with decreasing mobility cutoffs, down to 15 Å. B Visualization of the low-mobility domains, circled in panel A, below 15 Å mobility. Chemical species are colored according to the legend provided.
Fig 5.
Bending rigidity of the HIV-1 lipid vesicle.
A Undulating surface of the radial fluctuations as obseverd after 5 μs of MD production. Units of fluctuations are given as percent of the average radius. B Undulation spectra from the expansion in spherical harmonic of the undulating surface for a single simulation snapshot of the liposome; the fit is shown for wave-number q cutoffs [38] of 0.75 nm-1, 0.85 nm-1 and 1 nm-1. A linear fit is shown for the initial l-degrees for the three different cutoffs. C Ensemble average undulation spectra of the HIV-1 liposome. The bending rigidity is estimated from the Helfrich continuum model [38] for bilayer undulations yielding a value of 109 kbT at 298 K.
Table 1.
Summary of HIV-1 vesicle lipid composition.
Lipid names match those used in the MARTINI 2.1 forcefield. There are 24 lipid species in total.