Mechanism and Determinants of Amphipathic Helix-Containing Protein Targeting to Lipid Droplets

Abstract

Cytosolic lipid droplets (LDs) are the main storage organelles for metabolic energy in most cells. They are unusual organelles that are bounded by a phospholipid monolayer and specific surface proteins, including key enzymes of lipid and energy metabolism. Proteins targeting LDs from the cytoplasm often contain amphipathic helices, but how they bind to LDs is not well understood. Combining computer simulations with experimental studies in vitro and in cells, we uncover a general mechanism for targeting of cytosolic proteins to LDs: large hydrophobic residues of amphipathic helices detect and bind to large, persistent membrane packing defects that are unique to the LD surface. Surprisingly, amphipathic helices with large hydrophobic residues from many different proteins are capable of binding to LDs. This suggests that LD protein composition is additionally determined by mechanisms that selectively prevent proteins from binding LDs, such as macromolecular crowding at the LD surface.

Keywords: all-atom molecular dynamics simulations; amphipathic helices; cell biology; lipid droplets; phospholipid bilayers; phospholipid monolayers; phospholipid packing defects; protein targeting; reconstitution assay.

Figure 1. Molecular Dynamics Simulations Reveal that LDs Have Larger and More Persistent Surface Packing Defects than Bilayer Membranes

(A) Simulation snapshots of the monolayer system (phospholipids: 65:27:8 POPC:DOPE:SAPI, neutral lipids: TG:SE 1:1, neutral lipid thickness: 4nm). Arrow indicates a neutral lipid that has inserted all the way to the surface. (B) z-Density profile for the 4-nm LD. The relative density is normalized by the maximum number density. Note the mixing between the neutral lipids and the tails of the phospholipids. See also Table S1 for a summary of all simulations run. (C) Distribution of packing defect sizes for bilayer and LD surfaces. The monolayer exhibits increases in the frequency of larger defects. Normalized frequency: number of defects for a given size range is normalized by the total number of defects over the simulation time frame. Solid lines are least-square fits to exponential decays. See also Figure S1. (D) Distribution of packing defect sizes taking into account only the defects with characteristic lifetimes,τ, longer than 5 ns. Compared with the defects on the bilayer, the defects on the monolayer are roughly 10 times as likely to last longer than 5 ns for all defect sizes. Solid lines are least-square fits to exponential decays.

Figure 2. Molecular Dynamics Simulations Show that Amphipathic Helices Insert Bulky Hydrophobic Residues into Large Lipid Packing Defects

(A) Representative sequence of insertion of a stretch of residues from the M-domain into the LD surface. The inserting residues are depicted in a space-filling representation, and the rest of the peptide is depicted by a ribbon. The horizontal line in the side view represents the phosphate level. Residues labeled are the hydrophobic residues that have inserted below the phosphate plane. See also Movie S1. (B) Amino acid sequence of the M-domain and helical plots of both halves (P1 and P2). Dashed lines indicate the ends of both peptides within the full M-domain sequence. (C) Binding success of AHs with (ArfGAP1 ALPS, M-domain, P2) or without (P1) large hydrophobic residues at the LD surface in MD simulations. Binding success is defined as the number of simulations in which at least one residue inserted in the lipid monolayer and remained inserted for the duration of the simulation. See also Figure S2 and Table S2. A total of four simulations were run for each peptide. (D) Binding success of P2 to different surfaces. Monolayer: phospholipids: POPC:DOPE:SAPI 65:27:8, neutral lipids: TG: SE 1:1, bilayer: POPC: DOPE: SAPI 65: 27: 8, bilayer large defects: DOPC: DOG 85: 15. See also Tables S1 and S2.

Figure 3. Amphipathic Helix Sequences with Large Hydrophobic Residues Bind LDs and Packing Defect-Rich Membranes in In Vitro Systems

(A) Binding of AHs with (P2, P1 LH) or without (P1, P2 SH) large hydrophobic residues to artificial lipid droplets. Emulsion droplets prepared from a mixture of triolein and phospholipids (POPC: DOPE: liver phosphatidylinositol (liver PI) 65: 27: 8) were incubated with Alexa488-labeled synthetic peptides and imaged by fluorescence confocal microscopy. Upper panel: bright field and confocal images of the droplets after incubation with Alexa488-P1 and -P2. The inset highlights the ring-shaped protein signal. Lower panel: boxplot representation of the fluorescence signal on droplets. Over 200 droplets per condition were quantified in each of two independent experiments. Scale bar, 50 μm (larger field), and 10 μm (inset). (B) Binding of AH peptides to a membrane-LD system. GUVs (POPC: DOPE: liver PI 65: 27: 8) were incubated with an emulsion of triolein in buffer, and the resulting TG-containing GUVs were incubated with labeled AHs and imaged with fluorescence confocal microscopy. Top: schematic of the experimental protocol. Middle: Representative image of a TG-loaded GUV after incubation with Alexa488-P2. Confocal images show the peptide and phospholipid signals. Two membrane-embedded droplets are visible in the bright field image, however only the one in focus is visible in the confocal images. Bottom left: representative images for each peptide. The protein channel is shown (see also Figure S3A for more examples); Bottom right: quantification (mean and standard deviation) of the fluorescence signal at the surface of the LD and membrane. 10–40 GUVs were imaged in each of two independent experiments. Scale bar, 5 μm. (C) Binding of AH peptides to liposomes of increasing curvature. Liposomes (POPC: DOPE: liver PI 65: 27: 8) of different curvatures were incubated with NBD-labeled peptides and fluorescence emission spectra of the resulting mixtures were recorded. Left: normalized fluorescence emission spectra of NBD-P2 in the presence and absence of liposomes. Right: normalized fluorescence emission signal at 540 nm as a function of the extrusion pore diameter. Mean and standard deviation from three independent experiments with duplicate measurements are shown. Fluorescence values at each wavelength were normalized by the fluorescence at 540 nm in buffer averaged over the six measurements. (D) Binding of Alexa488-P2 to TG-loaded GUVs of varying surface tensions. Same as (B) except GUVs were aspirated in micropipettes to change their tension. Top left: schematic of the experimental protocol. Arrows represent aspiration pressure. Bottom left: representative images of a GUV aspirated to two different tensions. Scale bar, 5 μm (merge), 2 μm (inlay). Right: quantification of the fluorescence in the protein channel on the monolayer and bilayer parts of the GUV as a function of membrane tension. Each different marker corresponds to a different GUV (N=5). Quantification of fluorescence in the lipid channel is shown in Figure S3B.

Figure 4. Large Hydrophobic Residues Are Crucial for LD Targeting of the M-domain in Cells

(A) Analysis of the LD-targeting ability of a series of M-domain mutants. Drosophila cells were transfected with mCherry-tagged constructs and incubated 14-18 hours with 0.5 mM oleic acid. LDs were stained with BODIPY. Representative images are shown. Scale bar, 5 μm (merge), 1 μm (inlay). (B) Quantification of the protein signal on droplets. Data are represented as mean + SD. At least 10 cells were analyzed in each independent experiment.

Figure 5. Binding of Amphipathic Helices to Cellular Lipid Droplets Correlates with the Number of Large Hydrophobic Residues

(A) Analysis of the LD-targeting ability of WT and “small hydrophobic residues” (SH) mutants of ArfGAP1 ALPS and Lsd1 H6-7. (B) Quantification of the protein signal on droplets. Data are represented as mean + SD. Each construct was included in at least two independent experiments, and least 10 cells were analyzed in each experiment. (C) Analysis of the LD-targeting ability of a range of amphipathic helices from non-LD proteins. More examples are shown in Figure S4. ApoA-I: Apolipoprotein A-I. (A) and (C) Drosophila cells were transfected with mCherry-tagged constructs and incubated 14-18 hours with 0.5 mM oleic acid. LDs were stained with BODIPY. Representative images are shown. Scale bar, 5 μm (merge), 1 μm (inlay). (D) Correlation between binding index and a range of amphipathic helix physicochemical properties. Each data point corresponds to a different construct. Data for the full set of amphipathic helices analyzed in this paper. The list of amphipathic helices and associated binding indices can be found in Table 1.

Figure 6. Proposed Thermodynamic Cycle for the Partitioning of Amphipathic Helices at the LD Surface

The amphipathic helix sequence is initially unfolded in the cytosol. Following insertion of a large hydrophobic residue into a packing defect at the lipid droplet surface (I), the amphipathic helix folds in the interfacial region that separates the bulk aqueous phase from the hydrocarbon core (II). High surface pressure at the crowded droplet surface promotes desorption of the folded helix (III), which subsequently unfolds in the cytosol (IV).