Structure and dynamics of amyloid-β segmental polymorphisms

Abstract

It is believed that amyloid-beta (Aβ) aggregates play a role in the pathogenesis of Alzheimer's disease. Aβ molecules form β-sheet structures with multiple interaction sites. This polymorphism gives rise to differences in morphology, physico-chemical property and level of cellular toxicity. We have investigated the conformational stability of various segmental polymorphisms using molecular dynamics simulations and find that the segmental polymorphic models of Aβ retain a U-shaped architecture. Our results demonstrate the importance of inter-sheet side chain-side chain contacts, hydrophobic contacts among the strands (β1 and β2) and of salt bridges in stabilizing the aggregates. Residues in β-sheet regions have smaller fluctuation while those at the edge and loop region are more mobile. The inter-peptide salt bridges between Asp23 and Lys28 are strong compared to intra-chain salt bridge and there is an exchange of the inter-chain salt-bridge with intra-chain salt bridge. As our results suggest that Aβ exists under physiological conditions as an ensemble of distinct segmental polymorphs, it may be necessary to account in the development of therapeutics for Alzheimer's disease the differences in structural stability and aggregation behavior of the various Aβ polymorphic forms.

Figure 1. Structural models of double-layer Aβ segmental polymorphism proposed by Eisenberg group.

(A) Schematic representation of the U turn structure of Aβ single layer based on ss-NMR. The first beta sheet (green) and the second beta sheet (yellow) are represented by a thick line. The thin (black) line represents the loop region that connects the two sheets. The crystal structure of Aβ₁₆₋₂₁ form II (blue) serves as an interface for model 16–21P (Figure B) and model 16–21AP (Figure C) of Aβ₁₆₋₂₁. The model 16–21AP displays antiparallel β sheet. In the model 27–32 (Figure D) interactions between double-layer Aβ is through the crystal structure of Aβ₂₇₋₃₂. The model 35–42 in Figure 1 E is based on the crystal structures of Aβ₃₅₋₄₂ form II as the interface between double-layer Aβ. The fifth model (Figure 1F) is based on the long steric zipper interfaces consisting of Aβ₃₀₋₃₅ and Aβ₃₅₋₄₂ microcrystal structure. The blue color is used here to indicate the interfacial hydrophobic interactions based on the microcrystal structures.

Figure 2. Root Mean Square Deviation (RMSD) and Radius gyration (Rg) for the Aβ segmental polymorphism models.

Variation of the C_α atom root mean square deviation (RMSD) with respect the energy minimized structure of the five segmental polymorphic models of Aβ. The <RMSD> of each model was calculated using two independent trajectories (A). Radius of gyration as a function of time for each structures during the 50 ns MD simulations (B). Red, 16–21P; pink, 16–21AP; blue, 27–32; green, 35–42; yellow, 30–42.

Figure 3. Comparison of all-atom root-mean-square deviation and solvent accessible surface areas of Aβ segmental polymorphism models.

Backbone C_α atom-positional root-mean-square fluctuations, RMSF, along the amino acid sequence for the five models (A). The results are the average of two independent salutation of each system. The variation of average per residue solvent accessible surface area for each models (B). Red, 16–21P; pink, 16–21AP; blue, 27–32; green, 35–42; yellow, 30–42.

Figure 4. Time evolution of sheet-to-sheet distances.

The inter-sheet distances for the models 16–21, 27–32, 30–42 and 35–42 were calculated by averaging the mass center distance between backbone residues of 16–21, 27–32, 30–42 and 35–42 respectively. The results are the average of two independent simulation of each system. Red, 16–21P; green, 16–21AP; blue, 27–32; pink, 35–42; cyano, 30–42.

Figure 5. The structure of the starting configuration of of the interactions of Asp²³/Lys²⁸ and Lys¹⁶/Glu²² for the double layer 16–21P model.

The positions of the residues originally involved in the formation of the salt bridge are represented in sphere visualization to emphasize their location.

Figure 6. Average intra-chain salt bridge distance (Asp_n ²³/Lys_n ²³) along the 50 ns simulation for Aβ segmental polymorphs.

The results are the average of two independent simulations and it is the average of the two layers of each system. A) 16–21P B) 16–21AP C) 27–32 D) 35–42 and E) 30–40. Red, ₁D²³-₁K²⁸; pink, ₂D²³-₂K²⁸; blue, ₃D²³-₃K²⁸; green_{, 4}D²³-₄K²⁸; yellow, ₅D²³-₅K²⁸.

Figure 7. Average inter-chain salt–bridges (Asp_n ²³/Lys_n−1 ²³) along simulation for 16–21P, 27–32, 30–40 and 35–42.

The results are the average of two independent simulations and it is the average of the two layers of each system. A) 1621P B) 27–32 C) 35–42 and D) 30–30. Red, ₁D²³-₂K²⁸; pink, ₂D²³-₃K²⁸; blue, ₃D²³-₄K²⁸; green_{, 4}D²³-₅K²⁸.

Figure 8. Average inter-sheets salt–bridge distance (Lys_n ¹⁶/Glu_n ²²) along simulation for 16–21P and 16–21AP.

A) 16–21P and (B) 16–21AP. The results are the average of two independent simulation of each system. Red, ₁K¹⁶-₁E²²; pink, ₂K¹⁶-₂E²²; blue, ₃K¹⁶-₃E²²; green_{, 4}K¹⁶-₄E²²; yellow, ₅K¹⁶-₅E²². Red, 16–21P; green, 16–21AP; blue, 27–32; pink, 35–42; cyano, 30–42.

Figure 9. Percentage of hydrogen bonds as a function time with respect to the energy minimized structure of Aβ segmental polymorphic models.

Red, 16–21P; green, 16–21AP; blue, 27–32; pink, 35–42; cyano, 30–42.

Figure 10. Secondary structure variation plot for each of the Aβ segmental polymorphism models.

(A) Aβ₁₆₋₂₁P, (B) Aβ₁₆₋₂₁AP (C) Aβ₂₇₋₃₂, (D) Aβ₃₅₋₄₂ and (E) Aβ₁₃₀₋₄₂ interfaces. The secondary structure color codes: red-β-sheet, green-bend, yellow-turn, blue -α-helix, coil-white. Where L stands for the peptide layers number and C stands for the peptide chain number.

Figure 11. Snapshots from MD simulations for double-layered Aβ segmental polymorphism models with the steric zipper interfaces.

(A) Aβ₁₆₋₂₁P, (B) Aβ₁₆₋₂₁AP (C) Aβ₂₇₋₃₂, (D) Aβ₃₅₋₄₂ and (E) Aβ₁₃₀₋₄₂ interfaces at 0ns, 25ns and 50 ns.