Cholesterol Promotes Protein Binding by Affecting Membrane Electrostatics and Solvation Properties

Abstract

Binding of the retroviral structural protein Gag to the cellular plasma membrane is mediated by the protein's matrix (MA) domain. Prominent among MA-PM interactions is electrostatic attraction between the positively charged MA domain and the negatively charged plasma membrane inner leaflet. Previously, we reported that membrane association of HIV-1 Gag, as well as purified Rous sarcoma virus (RSV) MA and Gag, depends strongly on the presence of acidic lipids and is enhanced by cholesterol (Chol). The mechanism underlying this enhancement was unclear. Here, using a broad set of in vitro and in silico techniques we addressed molecular mechanisms of association between RSV MA and model membranes, and investigated how Chol enhances this association. In neutron scattering experiments with liposomes in the presence or absence of Chol, MA preferentially interacted with preexisting POPS-rich clusters formed by nonideal lipid mixing, binding peripherally to the lipid headgroups with minimal perturbation to the bilayer structure. Molecular dynamics simulations showed a stronger MA-bilayer interaction in the presence of Chol, and a large Chol-driven increase in lipid packing and membrane surface charge density. Although in vitro MA-liposome association is influenced by disparate variables, including ionic strength and concentrations of Chol and charged lipids, continuum electrostatic theory revealed an underlying dependence on membrane surface potential. Together, these results conclusively show that Chol affects RSV MA-membrane association by making the electrostatic potential at the membrane surface more negative, while decreasing the penalty for lipid headgroup desolvation. The presented approach can be applied to other viral and nonviral proteins.

Figure 1

MA binds peripherally to lipid bilayers with minimal structural perturbation. (A) An MD simulation snapshot showing the different lipid and protein components modeled in the SANS analysis: inner leaflet headgroups (yellow) and chains (orange), outer leaflet chains (red) and headgroups (green), protein (purple), and water (blue). Below the cross-sectional view, the volume probability profiles obtained from experimental SANS data are displayed (thick lines surrounding the volume probability profiles reflect uncertainties): POPC/POPS 70:30 mol % with bound RSV MA (B); POPC/POPS/Chol 34:30:36 mol % with bound RSV MA (C). (D−F) Structural parameters obtained from SANS analysis of POPC/POPS bilayers without and with Chol, in the absence (white bars) or presence (hatched bars) of RSV MA: average area per molecule (D); lipid hydrocarbon thickness (E); and fold-enrichment of POPS over the average composition in PS-rich clusters (F). The reported structural parameters and errors represent the mean and SD from independent fits to four different neutron contrast data sets as described in the text and Supporting Material. A complete list of structural parameters is found in Table S2.

Figure 2

Cholesterol enhances MA-membrane contacts. Given here are snapshots of MA interacting with POPC/POPS (A) and POPC/POPS/Chol (B) bilayers after 100 ns of simulation (for corresponding movies, see Movie S1, A and B). The protein is displayed in silver with specific lysine residues labeled and shown in space-fill representation (“N” and “C” denote the protein termini). Lipid tails and headgroups are shown as light and dark gray lines, respectively, and water and ions are omitted for clarity. (C) Shown is the difference in the percent time that MA lysine residues spend in contact with the bilayer in the absence and presence of Chol, where contact is defined as a distance not greater than 3 Å between any residue atom and any lipid atom. K13, K18, and K72 spend a mean 22% more time in contact with the membrane when Chol is present, whereas K82 and K95 are never in contact with either bilayer.

Figure 3

Cholesterol influences the membrane surface charge density. Charge distribution along the bilayer normal is calculated from the two simulated bilayers in the absence of MA. Addition of Chol increases the negative charge density in the headgroup region (arrow B), eliminating the peak of positive density at the water-lipid interface present in the POPC/POPS bilayer (arrow A). See Fig. S7 for the individual contributions of the membrane components.

Figure 4

Cholesterol decreases the energetic penalty for lipid desolvation. (A) Given here are contributions of MA and lipids to the total binding free energy ΔG_bind of the MA-bilayer complex estimated using the MM-GBSA method. Each energetic contribution is the sum of the interaction energy in vacuum for the respective system and the solvation penalty calculated separately for MA and the lipids. The presence of Chol results in a 5 kcal/mol reduction in the solvation penalty of the lipids relative to $\Delta E_{\text{int}}^{\text{vac}}$, resulting in a more favorable bilayer contribution to ΔG_bind compared to the PC/PS bilayer. For a detailed breakdown of the energy contributions and details of the underlying calculation, see Supporting Material. (B) A schematic illustration of the lipid headgroups (gray) on the bilayer surface in the +Chol and –Chol membranes, and the water molecules that solvate them (blue dots). Due to the area occupied by Chol itself, there are fewer lipid (PC or PS) headgroups in a bilayer patch of given size. Thus, even though Chol increases the number of bound waters per headgroup, it decreases the SASA per unit area of the bilayer (see text). Note that the spacing between the lipid headgroups in the +Chol schematic has been exaggerated to emphasize the lower packing density in this region.

Figure 5

RSV MA membrane association is quantitatively explained by membrane surface potential. (A) Coomassie-stained gel of pelleted MA associated with LUVs with increasing Chol concentration (0–50 mol %, lanes 2–7). “Back” (lane 8) represents the amount of MA pelleted in the absence of LUVs and “Total” (lane 9) represents the total MA in each binding reaction. (B) Calculated membrane surface charge density (right axis, red) and average area per molecule (left axis, black) for POPC/POPS/Chol bilayers plotted versus Chol concentration. (C) Percent of LUV-bound MA plotted against POPS concentration for membranes without (light blue triangles) and with (purple squares) 36 mol % Chol. (D) Given here is binding data from (C) plotted versus calculated ψ. (E) Percent of MA bound to LUVs at 30 mol % POPS with increasing Chol and decreasing POPC concentration at different NaCl concentrations: 50 mM (green), 100 mM (orange), and 150 mM (blue). (F) Binding data from (E) is plotted versus calculated ψ. Legend in (A) corresponds to (A, E, and F); legend in (C) corresponds to (C and D). All data points are the average, and error bars are the SD, of no fewer than four independent replicate samples.

Figure 6

Cellular plasma membrane model. (A) Asymmetric distribution of PM lipids between the inner (Chol/PE/PC/PS/PI/PIP, 40:28:5:18:8:2 mol %) and outer (Chol/PE/PC/sphingomyelin, 40:7:27:26 mol %) leaflets (see Table S4). (B) Contour plots of electrostatic surface potential (left) and protein binding (right) as a function of average area and charge per molecule. Electrostatic potential was calculated from nonlinear Poisson-Boltzmann theory assuming physiological ionic strength (150 mM NaCl) and temperature (37°C). Protein binding was calculated from a sigmoidal function that maps the binding data displayed in Fig 5F to surface potential (Fig. S10; Supporting Material). The dashed line traces the corresponding contour of half-max binding, and the white star denotes the approximate molecular area (48.9 Å²) and charge (0.32 e^–) of the PM’s inner leaflet estimated from the composition given above.