In silico study of amyloid β-protein folding and oligomerization

Urbanc et al. 10.1073/pnas.0408153101.

Supporting Information

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Supporting Figure 5
Supporting Table 1
Supporting Table 2
Supporting Figure 6
Supporting Text
Supporting Figure 7
Supporting Figure 8

Supporting Figure 5

Fig. 5. (a) The strong angular dependence of the hydrogen bond between the N_i atom and the C'_j atom (dashed black line) is implemented through four constraints (red solid lines). (b) The potential U(r) associated with the four constraints is determined by four interatom distances r_min, r₀, r₁, and r_max.

Table 1. The interatom distances r_min, r₀, r₁, and r_max as defined in the Fig. 5 legend, associated with the four constraints of the hydrogen-bond formation between the N_i atom and the C'_j atom

Pairs	r_min, Å	r₀, Å	r₁, Å	r_max, Å
Ni-Ca j	4.43	4.87	4.96	5.34
N_i-N_j+1	4.19	4.43	4.65	5.03
Ca _i+1-C'_j	4.33	4.67	4.77	5.17
C'_i-C'_j	4.38	4.60	4.66	4.98

Supporting Figure 6

Fig. 6. Time dependence of monomer and oligomer numbers.

Supporting Figure 7

Fig. 7. Secondary structure analysis for different assembly states averaged over 9 million, 9.5 million, and 10 million simulation steps. Per-residue propensities are shown for two secondary structure elements, a turn (Left) and a b-strand (Right) per residue for Ab40 (black curve) and Ab 42 (red curve). The secondary structure analysis is done for each assembly state separately: monomers (n = 1), dimers (n = 2), trimers (n = 3), tetramers (n = 4), and pentamers (n = 5). The secondary structure is calculated by using STRIDE (1, 2) within the VMD visualization software (3). The error bars represent the SEM values.

1. Frishman, D. & Argos, P. (1995) Proteins Struct. Funct. Genet. 23, 566–579.

2. Heinig, M. & Frishman, D. (2004) Nucleic Acids Res. 32, W500–W502.

3. Humphrey, W., Dalke, A. & Schulten, K. (1996) J. Mol. Graphics 14, 33–38.

Supporting Figure 8

Fig. 8. Intramolecular and intermolecular contact maps averaged over 9 million, 9.5 million, and 10 million simulation steps for each assembly state: monomers (n = 1), dimers (n = 2), trimers (n = 3), tetramers (n = 4), and pentamers (n = 5). The contact maps are averages over 24/21 monomers, 111/43 dimers, 64/58 trimers, 36/17 tetramers, and 11/34 pentamers of Ab 40/Ab42. Columns 1 and 3 correspond to Ab40, and columns 2 and 4 correspond to Ab42. (Asp-1, Asp-1) is at the upper-left corner of the contact maps, and (Val-40, Val-40) for Ab40 or (Ala-42, Ala-42) for Ab42 is at the lower-right corner. The strength of contacts is color-coded as described for Fig. 2. In columns 1 and 2, the black and red squares mark the centers of the Turn A and Turn B regions, respectively. In columns 3 and 4, the black rectangles mark the contacts of the N-terminal region with the central hydrophobic cluster, midhydrophobic region, and C-terminal region. In column 3, the red squares mark the contacts between pairs of central hydrophobic clusters. In column 4, the red rectangles mark the contacts of the C-terminal region with the central hydrophobic cluster and the midhydrophobic region.