Figure 1.
Structure and sequence of the simulated proteins.
(a) Structure of an ACD monomer in cartoon and of the ACD dimer in surface representation colored according to residue type. Color scheme used: red - acidic, blue - basic, green - polar, and white - hydrophobic. (b) Cartoon and surface representations of the human lysozyme protein colored according to the residue type. (c) Sequence and the secondary structure assignment of human α-crystallin domain (ACD, residues 66–150) and of human lysozyme using the secondary structure assignment program DSSP [97]. Yellow arrows indicate β-strands, purple indicates turn, blue indicates bend, red spirals indicate the alpha- helix, light pink spirals indicate the 310 helix, and black indicates coils. Sequence of the Aβ17–42 peptide is also shown. (d) System set up with one ACD dimer (black cartoon) placed in the center of a cubic box of water (shown in red) that also contains 10 Aβ17–42 peptides (green spheres, only backbone is shown). Sodium and Chloride ions are shown as cyan and yellow spheres, respectively.
Figure 2.
Effect of amyloid inhibitor proteins on Aβ assembly.
2D potential of mean force PMF plots as a function of the number of contacts between a peptide and the inhibitor protein (x axis) and the number of inter-peptide contacts for a peptide (y axis): (a) ACD and (b) lysozyme. Each contour level represents 0.5 kcal/mol free energy difference. The color scale for the free energy (kcal/mol) is shown at the bottom. Presence of ACD-bound oligomers is apparent. A snapshot of a crystallin-bound oligomer is shown, in which one Aβ dimer (yellow and orange) is attached to one α-crystallin domain and one Aβ trimer (green, cyan, and violet) is complexed with another α-crystallin domain. Crystallin domains are shown in gray. In contrast, lysozyme-bound monomers are primarily populated. A snapshot of lysozyme (in gray) is shown, in which three Aβ monomers (green, cyan, and violet) are found complexed. (c) Evolution of number of different sized Aβ species averaged over at least five different runs for each system. (a): control system (no inhibitor); (b): ACD-bound peptides; (c): lysozyme-bound peptides. Data is averaged over every 50 ns. Colored bars represent: yellow: uncomplexed ACD or lysozyme; red: Aβ monomer; blue: small Aβ oligomer (n = 2–5); green: larger Aβ oligomer (n>5).
Figure 3.
Binding and lifetime of inhibitor-peptide complexes.
(a) Probability distributions of the number of heavy atom contacts formed between two Aβ peptides (black) in the control system (no inhibitor), between ACD and an Aβ monomer (red), between ACD and an Aβ oligomer (green), and between lysozyme and an Aβ monomer (blue). Lysozyme-bound Aβ oligomers were excluded from the analysis due to their minor population. At least five different ∼200 ns runs were used, in which multiple binding/unbinding events were observed. (b) Mean survival time correlation function, S(t), of peptides in the vicinity of the inhibitor: ACD-bound monomer (black), ACD-bound oligomer (red) and lysozyme-bound monomer (green). Each curve shows average of five independent runs. S(t = 0) measures the average number of peptide molecules bound with inhibitor, and S(t) gives the average number of peptide molecules that remain bound after a period of time, t, given that they were present at t = 0. A short escape of 1 ns was allowed during the calculation.
Figure 4.
Probability of inhibitor-peptide contact formation.
Ensemble-averaged pairwise contact maps (a) between ACD and Aβ and (c) between lysozyme and Aβ. Data shown is averaged over all ∼200 ns runs. X and Y axes show residues from the inhibitor protein and Aβ17–42, respectively. A contact between residue i from the inhibitor and residue j from Aβ is considered, if any heavy atom from residue i is within 5 Å of any heavy atom from residue j. The contacts are color-coded according to the color scale shown in right. The secondary structure assignment of the inhibitor is shown on top. The molecular surfaces of the inhibitor proteins ((b) ACD and (d) lysozyme) are also shown, which is color-coded red to blue (low to high) according to the probability of contact formation with Aβ. (e) Contact probabilities for each residue type of ACD (red) and lysozyme (blue). (d) Residue-based contact probabilities of the Aβ17–42 peptide with ACD (red) and with lysozyme (blue).
Figure 5.
Probability of peptide-peptide contact formation.
Ensemble-averaged probabilities of (a) tertiary contact and (b) quaternary contact formation of Aβ peptides in the control system (left), ACD-bound (middle), or lysozyme-bound (right) obtained from an ensemble generated from at least five ∼200 ns runs. The size of the ensemble is>10000 conformations. The peptide is considered complexed, if it forms more than five contacts with ACD/lysozyme. Only the non-sequential tertiary contacts (that are not formed between neighboring residues (i+1, and i+2) in sequence) are shown. The contacts are color-coded according to the color scale shown on the right. Snapshots of the oligomeric conformations with prevalent inter-monomer contacts are shown at bottom. Peptides are colored in green, pink, or tan, whereas ACD/lysozyme is colored in white. The N– and C-termini of the peptides are colored in red and blue, respectively. For the ACD-bound oligomer, only the inter-peptide contacts that form with higher probability compared to the free oligomer are shown for clarity.