Calcium enhances binding of Aβ monomer to DMPC lipid bilayer

Abstract

Using isobaric-isothermal replica-exchange molecular dynamics and the all-atom explicit-solvent model, we studied the equilibrium binding of Aβ monomers to a zwitterionic dimyristoylphosphatidylcholine (DMPC) bilayer coincubated with calcium ions. Using our previous replica-exchange molecular dynamics calcium-free simulations as a control, we reached three conclusions. First, calcium ions change the tertiary structure of the bound Aβ monomer by destabilizing several long-range intrapeptide interactions, particularly the salt bridge Asp(23)-Lys(28). Second, calcium strengthens Aβ peptide binding to the DMPC bilayer by enhancing electrostatic interactions between charged amino acids and lipid polar headgroups. As a result, Aβ monomer penetrates deeper into the bilayer, making disorder in proximal lipids and bilayer thinning more pronounced. Third, because calcium ions demonstrate strong affinity to negatively charged amino acids, a considerable influx of calcium into the area proximal to the bound Aβ monomer is observed. Consequently, the localizations of negatively charged amino acids and calcium ions in the Aβ binding footprint overlap. Based on our data, we propose a mechanism by which calcium ions strengthen Aβ-bilayer interactions. This mechanism involves two factors: 1) calcium ions make the DMPC bilayer partially cationic and thus attractive to the anionic Aβ peptide; and 2) destabilization of the Asp(23)-Lys(28) salt bridge makes Lys(28) available for interactions with the bilayer. Finally, we conclude that a single Aβ monomer does not promote permeation of calcium ions through the zwitterionic bilayer.

Figure 1

(a) Sequence of Aβ10–40 monomer with color-coded regions S1–S4. (b) DMPC lipid molecule divided into atom groups of choline (G1), phosphate (G2), glycerol (G3), and two fatty acid tails (G4 and G5). (c) Simulation system including the DMPC bilayer (orange), two Aβ monomers (gray), Ca²⁺ ions (green), and water (thin blue lines). Cl⁻ ions are excluded, for clarity. Phosphorus atoms with their centers of mass located at ≈±z_P are purple. Most of the calcium ions near the peptide (proximal region) are bound to negatively charged amino acids, with only a few bound to G2. In the distant region, calcium ions typically coordinate G2 groups. To see this figure in color, go online.

Figure 2

Distribution of helical structure, <H(i)>, in Aβ monomer with respect to sequence position i. Data for Aβ+BL+Ca system are in black, whereas data for the calcium-free Aβ+BL and the Aβ+water systems are in red and blue, respectively. Simulation errors are given by vertical bars. Color codes for regions S1–S4 are as in Fig. 1a. The plot shows that calcium ions have a fairly small impact on the formation of helix in the bilayer-bound Aβ monomer. To see this figure in color, go online.

Figure 3

(a) Difference contact map, $<\text{Δ}C\left(i,j\right)>$, showing changes in the probabilities of contacts being formed between amino acids i and j in systems Aβ+BL+Ca and Aβ+BL. $<\text{Δ}C\left(i,j\right)>$ is defined as <ΔC(i,j)>₁ − <ΔC(i,j)>₂, where indices 1 and 2 stand for Aβ+BL+Ca and Aβ+BL, respectively. Color codes for the regions S1–S4 are as in Fig. 1a. (b) Probability distributions, $P\left(r_{\text{DK}}\right)$, for the distance between the centers of mass of Asp²³ and Lys²⁸ side chains, $r_{\text{DK}}$. Data for the Aβ+BL+Ca and Aβ+BL systems are in black and red, respectively. The figure demonstrates destabilization of the Asp²³-Lys²⁸ salt bridge by calcium. To see this figure in color, go online.

Figure 4

Probabilities, $P\left(z;i\right)$, of occurrence of amino acids i at distance z from the bilayer midplane (z = 0 Å). Black and red lines show the average positions of amino acids i along the z axis, $<z\left(i\right)>$, for the Aβ+BL+Ca and Aβ+BL systems, respectively. Color codes for regions S1–S4 are as in Fig. 1a. The dashed line marks the average position of the center of mass of phosphorus atoms, z_P. The plot reveals that calcium promotes deeper insertion of Aβ monomer into the DMPC bilayer. To see this figure in color, go online.

Figure 5

Difference contact map, <ΔC_l(i,k)>, displaying changes in the probability of contacts forming between amino acids i and lipid groups k. <ΔC_l(i,k)> is defined as <ΔC_l(i,k)>₁ − <ΔC_l(i,k)>₂, where indices 1 and 2 stand for Aβ+BL+Ca and Aβ+BL, respectively. Color codes for the regions S1–S4 are as in Fig. 1a. The plot implicates calcium ions in promoting stronger binding of polar segments S1 and S3 (particularly charged amino acids Glu¹¹, Glu²², Asp²³, and Lys²⁸) to lipid headgroups. To see this figure in color, go online.

Figure 6

Number density of lipid heavy atoms, n_l(r,z), computed as a function of distance r from the peptide center of mass and distance z from the bilayer midplane at z = 0 Å. Black and red lines mark the boundaries of the lipid bilayer, z_l(r), for the Aβ+BL+Ca and Aβ+BL systems, respectively. The boundaries of the proximal region are represented by dashed vertical lines. The figure shows that calcium enhances thinning of the DMPC bilayer caused by bound Aβ monomer. To see this figure in color, go online.

Figure 7

The lipid carbon-deuterium order parameter, −<S_CD(i)>, computed for carbon atoms i in the fatty acid chains, $sn-2$. Solid and dashed lines represent proximal and distant lipids, respectively, whereas data represented in black and red are for the Aβ+BL+Ca and Aβ+BL systems, respectively. Errors are shown by vertical bars. The plot reveals that calcium ions slightly enhance the disorder in proximal lipid tails. To see this figure in color, go online.

Figure 8

Average numbers of Ca²⁺ ions interacting with amino acids i, <C_i(i)>, (black). Light green and orange lines represent <C_i(i)> computed with the Asp²³-Lys²⁸ salt bridge formed and disrupted, respectively. Color codes for regions S1–S4 are as in Fig. 1a. Errors are shown by vertical bars. The plot underscores the strong affinity of calcium ions for negatively charged amino acids and the effect of salt bridge disruption on Ca²⁺ binding to Glu²² and Asp²³. To see this figure in color, go online.

Figure 9

Number density of calcium ions in the DMPC bilayer, n_i(r,z), computed as a function of distance r from the peptide center of mass and distance z from the bilayer midplane at z = 0 Å. The boundaries of the proximal region are represented by dashed vertical lines. The figure illustrates the influx of calcium into the Aβ binding footprint driven by the affinity of the ions for negatively charged amino acids. To see this figure in color, go online.

Figure 10

Probability distributions, P(C_n), for the number of phosphate groups coordinated by a calcium ion, C_n. Gray and dashed bars correspond to P(C_n) values computed for distant ions and for proximal ions bound to Aβ negatively charged amino acids. It follows from the plot that binding to Aβ compromises the ability of Ca²⁺ to coordinate phosphate groups.