Figure 3. Determinants of amyloid beta (Aß) nucleation.

(A) Effect of single aa mutants on nucleation for each Aß position. The wild-type (WT) aa and position are indicated on the x-axis and coloured on the basis of aa type. The horizontal line indicates the WT nucleation score (0). (B to D) Effect of each mutant aa on nucleation for the Ct (27-41) (B), the Nt (2-26) (C), and the negatively charged gatekeeper positions (D1, E3, D7, E11, and E22) (D). The three position clusters are mutually exclusive. Colour code indicates aa type. The horizontal line is set at the WT nucleation score (0). (E) Effect on nucleation for single aa mutations to proline, threonine, valine, and isoleucine. Mutations to other aa are indicated in grey. The horizontal line indicates WT nucleation score (0). Point size and shape indicate false discovery rate (FDR) and familial Alzheimer’s disease (fAD) class, respectively (see legend). (F) Nucleation scores as a function of hydrophobicity changes (Kyte and Doolittle, 1982) for single and double aa mutants in the Ct (27-41) cluster. Only double mutants with both mutations in the indicated position-range were used. Weighted Pearson correlation coefficient and p-value are indicated. (G) Nucleation score distributions arranged by the number of charged residues (y-axis) and the total net charge (x-axis) for single and double aa mutants in the full peptide (1-42). Only polar, charged, and glycine aa types were taken into account, for both WT and mutant residues. Colour gradient indicates the total number of charged residues. Numbers inside each cell indicate the number of positive and negative residues. The horizontal line indicates WT nucleation score (0). Boxplots represent median values and the lower and upper hinges correspond to the 25th and 75th percentiles, respectively. Whiskers extend from the hinge to the largest value no further than 1.5*IQR (interquartile range). Outliers are plotted individually or omitted when the boxplot is plotted together with individual data points or a violin plot.

Figure 3—figure supplement 1. Determinants of amyloid beta (Aß) nucleation.

(A and B) Nucleation scores as a function of aggregation predictors (Tango, Waltz, Zyggregator, and Camsol; Tartaglia and Vendruscolo, 2008; Fernandez-Escamilla et al., 2004; Oliveberg, 2010; Sormanni et al., 2015) for single and double aa mutants in the Ct (27-41) (A) and Nt (2-26) (B) clusters (gatekeeper positions are excluded from the N-terminal and C-terminal classes). Only double mutants with both mutations in the indicated position-range were used. Weighted Pearson correlation coefficient and p-value are indicated. (C) Percentage of yeast growth in medium lacking adenine for sup35N, supN-Aß, and supN-Aß C-terminal fragments 22-42, 24-42, and 27-42. One-way ANOVA with Dunnett’s multiple comparisons test. *p<0.05, **p<0.01, ***p<0.001, ****p<0.0001. (D) Effect of each mutant aa on nucleation for the six negatively charged positions (D1, E3, D7, E11, E22, and D23). Colour code indicates aa type (see legend). The horizontal line is set at the wild-type (WT) nucleation score (0). (E) Nucleation scores as a function of hydrophobicity changes (Kyte and Doolittle, 1982) for single and double aa mutants in the Nt (2-26) cluster. Only double mutants with both mutations in the indicated position-range were used. Weighted Pearson correlation coefficient and p-value are indicated. (F) Nucleation scores distributions arranged by the number of charged residues (y-axis) and the total net charge (x-axis) for single and double aa mutants in the Nt (2-26), Ct (27-41), and gatekeepers (D1, E3, D7, E11, L17, E22, and A42) clusters. Only double mutants with both mutations in the indicated position-range were used. Only polar, charged, and glycine aa types were taken into account, for both WT and mutant residues. Colour gradient indicates the total number of charged residues. Numbers inside each cell indicate the number of positive and negative residues. The horizontal line indicates WT nucleation score (0). (F) Nucleation score distributions arranged by the number of negatively charged residues (y-axis) and the number of positively charged (x-axis) for single and double aa mutants in the full peptide (1-42). Only polar, charged, and glycine aa types were taken into account, for both WT and mutant residues. Colour gradient indicates the total number of charged residues. Numbers inside each cell indicate the total net charge. The horizontal line indicates WT nucleation score (0). Boxplots represent median values and the lower and upper hinges correspond to the 25th and 75th percentiles, respectively. Whiskers extend from the hinge to the largest value no further than 1.5*IQR (interquartile range). Outliers are plotted individually or omitted when the boxplot is plotted together with individual data points or a violin plot.

Figure 3—figure supplement 2. Effect of mutations to each specific amino acid (aa) on amyloid beta (Aß) nucleation.

Mutations to other aa are indicated in grey. The wild-type (WT) AA is indicated with ‘*’. The horizontal line indicates WT nucleation score (0). Point size indicates false discovery rate (FDR) (big, FDR < 0.1; small, FDR > 0.1) and shape indicates familial Alzheimer’s disease (fAD) class (round, variants of uncertain significance [VUS]; triangle, dominant; rhombus, recessive). Boxplots represent median values and the lower and upper hinges correspond to the 25th and 75th percentiles, respectively. Whiskers extend from the hinge to the largest value no further than 1.5*IQR (interquartile range). Outliers are plotted individually or omitted when the boxplot is plotted together with individual data points or a violin plot.