Structure and elasticity of lipid membranes with genistein and daidzein bioflavinoids using X-ray scattering and MD simulations

Abstract

This work reports the effects of the bioflavinoids genistein and daidzein on lipid bilayers as determined by volume measurements, X-ray scattering, and molecular dynamics simulations. The experimental and simulated total molecular volumes were found to be in outstanding agreement with each other before the addition of genistein and daidzein and also after their addition. Both bioflavinoids inserted into the hydrocarbon region of both DOPC and diphytanoylPC near the carbonyls of the lipids and both decreased the bilayer thicknesses. The long axes of both bioflavinoids were oriented nearly parallel to the plane of the bilayer with their carbonyl groups preferentially pointed toward the proximal surface. A difference is that daidzein had a solubility limit of ∼0.14 mol fraction in DOPC (∼0.12 mol fraction in diphytanoylPC), whereas genistein was soluble at least to 0.20 mol fraction in both lipid membranes. Measurements of bending modulus K(C) and simulation results for area compressibility modulus K(A) indicate that both bioflavinoids soften bilayers.

Figure 1

Chemical structures of the bioflavinoids, genistein and daidzein. The long (L) and short (S) axes of the bioflavinoids are shown.

Figure 2

2D CCD images of LAXS diffuse scattering, white is highest intensity. A. DOPC, B. DOPC/20% genistein, C. DOPC/20% daidzein, D. DPhyPC, E. DPhyPC/20% genistein, F. DPhyPC/20% daidzein. The dark shadows are caused by attenuators through which the beam and orders 1 and 2 can be seen.

Figure 3

Experimental form factor |F(q_z)| data for 20 mole% genistein in DOPC (grey circles) compared to the form factors resulting from three MD NPAT simulations fixed to areas A₁ of 80 Ų (green), 83 Ų (red) and 86 Ų (blue). Also shown is the model fit (black) that yielded A₁ = 82 Ų. The inset shows more detail in the second lobe.

Figure 4

Electron density profiles for DOPC with 20% genistein resulting from MD simulation at A₁=83 Ų (solid lines) and model fitting to experimental data (dashed lines). Component groups are identified by colors shown in the legend.

Figure 5

(left) |F(q_z)| data for DOPC (black), DOPC/20%genistein (red) and DOPC/14%daidzein (blue). Lobes are numbered for DOPC.

Figure 6

(right) |F(q_z)| data for DPhyPC (black), DPhyPC/20%genistein (red) and DPhyPC/12%daidzein (blue).

Figure 7

(left). Electron density profiles of DOPC with increasing concentration of genistein obtained using the SDP procedure. Component groups are phosphate (red), carbonyl-glycerol (green), methylenes and terminal methyl group (magenta), water (blue), bioflavinoid (filled grey) and total (black).

Figure 8

(right). Electron density profiles of DOPC with increasing concentration of daidzein obtained using the SDP procedure. Line colors as for Figure 7.

Figure 9

Bending modulus, K_C, vs. concentration of genistein (solid symbols) and daidzein (open symbols) in DOPC (circles) and DPhyPC (triangles).

Figure 10

Surface tension, γ, vs. A₁ for DOPC with and without 20 mole% genistein and 14 mole% daidzein from NPAT simulations except the γ=0 point for pure DOPC which was an NPT simulation.

Figure 11

Snapshots of the MD simulations for A) DOPC/20 mole% genistein at A₁ = 83 Ų, and for B) DOPC/14 mole% daidzein at A₁ = 79 Ų. Each snapshot is 1 out of 25,000 coordinate sets that comprise the ensemble; A) collected at 30 nsecs (5 nsecs before the end of the simulation) and B) 35 nsecs. Color coding is: hydrocarbon chains (grey), bioflavinoids (gold and with yellow oxygen atoms), lipid carbonyl oxygens (red), phosphate group (green), choline group (purple) and water (blue). The scale bar marks 20 Å.

Figure 12

Probability histograms of bioflavinoids in DOPC membranes from the MD simulations for (A) the angle α of the short axis about the long axis and (B) the angle β of the long axis with respect to the bilayer normal. Colors are 20 mole% genistein (red) and 14 mole % daidzein (blue). The insets show α and β with respect to the long (L) and short (S) axes of the bioflavinoids, depicted in Figure 1.

Figure 12

Probability histograms of bioflavinoids in DOPC membranes from the MD simulations for (A) the angle α of the short axis about the long axis and (B) the angle β of the long axis with respect to the bilayer normal. Colors are 20 mole% genistein (red) and 14 mole % daidzein (blue). The insets show α and β with respect to the long (L) and short (S) axes of the bioflavinoids, depicted in Figure 1.