Linking folding with aggregation in Alzheimer's β-amyloid peptides

Khandogin and Brooks. 10.1073/pnas.0703832104.

Supporting Information

Files in this Data Supplement:

SI Figure 7
SI Figure 8
SI Figure 9
SI Figure 10
SI Table 1

SI Figure 7

Fig. 7. Simulation convergence. Cumulative average of helix content is computed by using the fraction of helical residues as a function of simulation time in simulations at pH 2 (red), 4 (orange), 6 (green), and 8 (blue).

SI Figure 8

Fig. 8. Strength of the electrostatic interactions, Glu²² × × ×Lys²⁸ and Asp²³ × × ×Lys²⁸ at different pH. Probability densities for the distance between Glu²²/Asp²³ and Lys²⁸ are plotted by using the last 30 ns of the simulation data for Aβ(1-28) and Aβ(10-42). The distance is defined as the minimum separation between the carboxylate oxygen atom of Glu²² or Asp²³ and the amino nitrogen atom of Lys²⁸. Data obtained from simulations at pH 4, 6, and 8 are shown in orange, green, and blue, respectively.

SI Figure 9

Fig. 9. Correlation between β-turn formation in residues 23-26 and the hydrophobic interaction between Phe¹⁹ and Leu³⁴ in Aβ(10-42). Relative free energy, ∆G, is plotted as a function of the Phe¹⁹-Leu³⁴ distance in the presence (solid lnes) and absence (dashed lines) of the β-turn at pH 8. The distance between Phe¹⁹ and Leu³⁴ is defined as the minimum separation between the side-chain heavy atoms. ∆G is defined as -RT lnP, where P is the probability density for the distance to fall into one of the 30 bins between 3 and 18 Å.

SI Figure 10

Fig. 10. Relative free energy as a function of the backbone CO× × ×NH distance between Lys¹⁶ and Phe²⁰ (x axis) and the minimum side-chain heavy-atom distance between His¹⁴ and Phe¹⁹ (y axis) in the simulation of Aβ(10-42) at pH 6.