Designed α-sheet peptides inhibit amyloid formation by targeting toxic oligomers
- University of Washington, United States
- Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, United States
Figures
Figure 1
α-sheet conversion, conformational properties and peptide designs.
(A) β- to α-sheet conversion of transthyretin (as reported by Armen et al., 2004a, 2004b). The protein backbone is shown in cartoon representation with the region of interest (residues 105–121) …
Figure 2 with 4 supplements
α-Sheet designs inhibit amyloid formation and selectively bind toxic species.
(A) Peptide designs (800 μM) were co-incubated at pH 4.5 with 40 μΜ TTR (monomer) at 37°C and aggregation was monitored by Congo red binding. Error bars indicate the standard deviation. (B) Toxicity …
Figure 2—figure supplement 1
Increase in Congo red binding is not due to peptide aggregation.
Congo red binding of peptides incubated under identical aggregation conditions reveals that contributions to dye binding do not come from the designs.
Figure 2—figure supplement 2
AFM spectroscopy reveals aggregation conditions ultimately result in fibrils.
Congo red binds multiple soluble species in addition to fibrils, so presence of fibrils was confirmed visually. Application of a TTR solution aggregated for 72 hr revealed the presence of small …
Figure 2—figure supplement 3
Increase in ThT fluorescence is not due to peptide aggregation.
ThT fluorescence of peptides incubated under identical aggregation conditions indicate that the peptides do not contribute to the observed increase in fluorescence.
Figure 2—figure supplement 4
AFM spectroscopy confirms an increase in fibrillar products.
Application of an aggregated Aβ solution reveals the presences of aggregates and fibrils. Fibrils are indicated with arrows. Scale = 200 nm.
Figure 3 with 4 supplements
Immobilized designs bind toxic soluble oligomer from solution.
Peptide designs were immobilized onto agarose beads and their ability to bind TTR or Aβ from solution at various stages of aggregation was probed using dot blot analysis. The presence of TTR or Aβ …
Figure 3—figure supplement 1
Statistical analysis of data presented in Figure 3A.
Relative peak density values from dot blot analyses are given as average values from three independent experiments, with standard deviations. Statistical analysis for E1, E2 and W8 were performed …
Figure 3—figure supplement 2
Nonspecific binding of nonnative TTR to column matrix.
While the column-binding assay is not quantitative, nor was it expected to be, we can estimate the confidence in the peak densities by seeing to what extent TTR binds to the column matrix in the …
Figure 3—figure supplement 3
Statistical analysis of data presented in Figure 3B.
Relative peak density values from dot blot analyses are given as average values from three independent experiments, with standard deviations. Statistical analysis for E1, E2 and W8 were performed …
Figure 3—figure supplement 4
Immobilized α-sheet designs do not bind fibrils.
TTR (red) or Aβ (black) fibrils were applied to agarose beads coated with the α1 design. The elution profile does not show any increase in elution when guanidine is applied to the column, indicating …
Figure 4 with 3 supplements
Designed peptides display unique spectroscopic signatures expected for α-sheet.
(A) CD spectra for peptide designs reveal a random coil structure for rc and β-structure spectrum with a bit of random coil for β. In contrast, α1, α2 and α3 have largely featureless CD spectra with …
Figure 4—figure supplement 1
Distances corresponding to dNN NOEs calculated from MD simulations.
r−6 weighted distances calculated from MD simulations of α1 in α-sheet and in β-sheet conformation. α1 is not stable as a β-sheet and did not retain the structure well even in these short …
Figure 4—figure supplement 2
Distances corresponding to intraresidue dαN NOEs calculated from MD simulations.
r−6 weighted distances calculated from MD simulations of α1 in α-sheet and in β-sheet conformation. r−6 intensities, which should be proportional to the NOE intensity, were calculated for each …
Figure 4—figure supplement 3
Distances corresponding to sequential dαN (i–i+1) NOEs calculated from MD simulations.
r−6 intensities, which should be proportional to the NOE intensity, were calculated for each structure and then averaged across the pooled simulations and time points and converted back to distance …
