Association thermodynamics and conformational stability of beta-sheet amyloid beta(17-42) oligomers: effects of E22Q (Dutch) mutation and charge neutralization

Abstract

Amyloid fibrils are associated with many neurodegenerative diseases. It was found that amyloidogenic oligomers, not mature fibrils, are neurotoxic agents related to these diseases. Molecular mechanisms of infectivity, pathways of aggregation, and molecular structure of these oligomers remain elusive. Here, we use all-atom molecular dynamics, molecular mechanics combined with solvation analysis by statistical-mechanical, three-dimensional molecular theory of solvation (also known as 3D-RISM-KH) in a new MM-3D-RISM-KH method to study conformational stability, and association thermodynamics of small wild-type Abeta(17-42) oligomers with different protonation states of Glu(22), as well the E22Q (Dutch) mutants. The association free energy of small beta-sheet oligomers shows near-linear trend with the dimers being thermodynamically more stable relative to the larger constructs. The linear (within statistical uncertainty) dependence of the association free energy on complex size is a consequence of the unilateral stacking of monomers in the beta-sheet oligomers. The charge reduction of the wild-type Abeta(17-42) oligomers upon protonation of the solvent-exposed Glu(22) at acidic conditions results in lowering the association free energy compared to the wild-type oligomers at neutral pH and the E22Q mutants. The neutralization of the peptides because of the E22Q mutation only marginally affects the association free energy, with the reduction of the direct electrostatic interactions mostly compensated by the unfavorable electrostatic solvation effects. For the wild-type oligomers at acidic conditions such compensation is not complete, and the electrostatic interactions, along with the gas-phase nonpolar energetic and the overall entropic effects, contribute to the lowering of the association free energy. The differences in the association thermodynamics between the wild-type Abeta(17-42) oligomers at neutral pH and the Dutch mutants, on the one hand, and the Abeta(17-42) oligomers with protonated Glu(22), on the other, may be explained by destabilization of the inter- and intrapeptide salt bridges between Asp(23) and Lys(28). Peculiarities in the conformational stability and the association thermodynamics for the different models of the Abeta(17-42) oligomers are rationalized based on the analysis of the local physical interactions and the microscopic solvation structure.

Figure 1

Root mean-square displacements of the backbone atoms from the initial structures in the production MD simulations for the wild-type Aβ_17–42 monomer, dimer, trimer, tetramer, and pentamer with the charge state corresponding to neutral pH. (Vertical lines) Dynamically metastable parts of the trajectories used for the free energy calculations. Conformational changes monitored by the RMSDs demonstrate a similar dependence on the system size for the WT pH 4 and the E22Q mutants.

Figure 2

Mean-square fluctuations (B-factors) of the α-carbon atoms on a per-residue basis for the wild-type Aβ_17–42 monomer, dimer, and tetramer at neutral pH. B-factors are normalized as follows: B_i = 8π²/3〈Δr²_i〉, where the angle brackets denote an average over MD conformations.

Figure 3

Association free energy of the wild-type Aβ_17–42 oligomers and the E22Q mutants as a function of their size.

Figure 4

Solvent entropic and interpeptide nonpolar contributions to the association free energy for the wild-type Aβ_17–42 oligomers and the E22Q mutants.

Figure 5

Size evolution of the electrostatic part of the association free energy for the wild-type Aβ_17–42 oligomers and the E22Q mutants.

Figure 6

Local electrostatic contribution to the free energy resolved on a per-residue basis for the wild-type Aβ_17–42 oligomers with the charge distributions corresponding to the solvent pH 7 (charged Glu²²) and pH 4 (protonated Glu²²) conditions, and for the E22Q mutant. (Top panel) Gas-phase electrostatic contribution. (Bottom panel) Gas-phase electrostatic energy combined with the solvation electrostatic energy. (Vertical lines) Location of Glu²² (the WT peptides) or Gln²² (the E22Q mutants), as well as the saltbridge-forming Asp²³ and Lys²⁸.

Figure 7

Same as in Fig. 6, but for the electrostatic contribution to the association free energy.

Figure 8

Effect of the Dutch mutation on the microscopic solvation structure around the Aβ_17–42 pentamer. (A) Three-dimensional solvation density map for the wild-type pentamer represented by the isosurfaces of the distribution functions for water oxygen (red color) and hydrogen (blue color). Isosurfaces correspond to the water density exceeding the bulk density value by a factor of 3. (B) Change in the solvation structure upon the Dutch (E22Q) point mutation shown by the isosurface of the differential solvation density for water oxygen. Differential density is defined as the density excess for the wild-type oligomer with respect to that of the mutant. Isosurface value is 0.3. (Red ellipse) Location of the charged Glu residues substituted by the neutral Gln upon the Dutch mutation. Data shown is for the starting conformation used in MD simulations. Image was produced with VMD (99).

Figure 9

Effect of the Dutch mutation on the local entropic contribution to the solvation free energy. Results are for (A) the wild-type and (B) the Dutch mutant Aβ_17–42 pentamers. (Left panel, red ellipse) Contribution of the internal domains to the entropic part of the solvation free energy for the wild-type oligomer. Isosurfaces correspond to the local entropic contribution to the solvation free energy of 0.6 kcal/(mol ų) for the WT pH 7 model and 0.1 kcal/(mol ų) for the Dutch mutant. Image was produced with VMD (99).