The F19W mutation reduces the binding affinity of the transmembrane Aβ11-40 trimer to the membrane bilayer

Abstract

Alzheimer's disease is linked to the aggregation of the amyloid-β protein (Aβ) of 40 or 42 amino acids. Lipid membranes are known to modulate the rate and mechanisms of the Aβ aggregation. Point mutations in Aβ can alter these rates and mechanisms. In particular, experiments show that F19 mutations influence the aggregation rate, but maintain the fibril structures. Here, we used molecular dynamics simulations to examine the effect of the F19W mutation in the 3Aβ_11-40 trimer immersed in DPPC lipid bilayers submerged in aqueous solution. Substituting Phe by its closest (non-polar) aromatic amino acid Trp has a dramatic reduction in binding affinity to the phospholipid membrane (measured with respect to the solvated protein) compared to the wild type: the binding free energy of the protein-DPPC lipid bilayer increases by 40-50 kcal mol^-1 over the wild-type. This is accompanied by conformational changes and loss of salt bridges, as well as a more complex free energy surface, all indicative of a more flexible and less stable mutated trimer. These results suggest that the impact of mutations can be assessed, at least partially, by evaluating the interaction of the mutated peptides with the lipid membranes.

Fig. 1. Sequence of the Aβ_11–40. Hydrophilic and hydrophobic regions are shown in blue and red, respectively.

Fig. 2. Initial conformation of the transmembrane F19W 3Aβ_11–40 trimer with highlighted mutations. Water molecules are represented in red, DPPC molecules are shown in cyan, and neutralizing Na⁺ ions are shown as black balls.

Fig. 3. REMD simulations convergence at 324 K. Probability distributions (unnormalized) of the secondary structures (a) beta, (b) coil, (c) turn, (d) alpha contents, (e) the radius gyration (R_g), (f) the RMSD, (g) the total solvent-accessible surface area, (h) the salt bridge D23–N27 of chain A of the transmembrane F19W 3Aβ_11–40. The results were calculated for two time windows 250–350 ns (black curves) and 250–400 ns (red curves).

Fig. 4. Secondary structure distributions per residue averaged for all three chains of the transmembrane F19W 3Aβ_11–40. For clarity, the distribution of each secondary structure is presented on a different scale. The average values are given in the parenthesis.

Fig. 5. Interpeptide side-chain–side-chain, SC–SC, (left (a) Chain A - Chain B, (b) Chain B - Chain C, (c) Chain A - Chain C) and backbone–backbone, BB–BB, (right (d) Chain A -Chain B, (e) Chain B - Chain C, (f) Chain A - Chain C) contacts of the transmembrane F19W 3Aβ_11–40. For clarity, the contact maps of neighbor pair – chains in the protein are presented on a different scale. The color in the figure indicates the probability of the contact between neighbor chains in the peptide. For example, in panel (a), the color varies from white to green, blue and red, indicating that the probability of the contact between chain A and chain B varies from 0% to 25%, 50% and 100%, respectively.

Fig. 6. Distance distributions between the charge groups of D23 and N27 (a) and D23 and K28 (b) in chain A (black), chain B (red), and chain C (green) of the transmembrane mutant F19W 3Aβ_11–40. The polar contacts are counted when their distance is within a 0.46 nm cutoff.

Fig. 7. Population of intermolecular contacts between phosphate atoms of DPPC lipid bilayers and heavy atoms of the truncated F19W 3Aβ_11–40. The population per residue is the sum of all populations of phosphate atoms contacts with one residue of the trimer (thus an individual value could be over 100%.).

Fig. 8. The FES of the transmembrane F19W 3Aβ_11–40 as a function of RMSD and radius gyration R_g. Twelve minima are noted from S1 to S12 with those representative structures shown in Fig. 9. For clarity, several minima very closed to each other are shown in only one line with the names of the minima are noted.

Fig. 9. Representative structures of the twelve minima shown in Fig. 8. The population of each state is calculated using FES and clustering methods and is given in parentheses. Here, the residues β-contents are represented in yellow, those of mutant F19W are shown in blue, and coil conformations are shown as grey and purple colors, respectively.