Formed by a TTR Mutant. Supporting Information

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1 Possible Existence of α-sheets in the Amyloid Fibrils Formed by a TTR Mutant Supporting Information Mary Rose Hilaire, 1, Bei Ding, 1,2, Debopreeti Mukherjee, 1, Jianxin Chen, 1,2 and Feng Gai 1,2,* 1 Department of Chemistry and 2 The Ultrafast Optical Processes Laboratory, University of Pennsylvania, Philadelphia, PA Methods and Materials Sample Preparation. The TTR (Sequence: NH 2 -YTIAALLSPYS-CONH 2 ), TTR-111D M (Sequence: NH 2 -YTIAAL-D M -SPYS-CONH 2 ), and Aβ F19K* (Sequence: KLVK*FAE, where K* represents Lys(Nvoc)) peptides were synthesized on a Liberty Blue automated microwave peptide synthesizer (CEM, Matthews, NC) using Fmoc-based solid phase peptide synthesis. Peptides were purified by reverse-phase high performance liquid chromatography (HPLC) and were identified by matrix assisted laser desorption ionization mass spectroscopy (MALDI-MS). Trifluoroacetic acid (TFA) removal and H-D exchange were achieved by multiple rounds of lyophilization against a 0.1 M DCl solution. The peptides were then monomerized by dissolving in 1,1,1,3,3,3-Hexafluoro-2-propanol (HFIP) at a concentration of 1 mm. Subsequent HFIP removal was done using N 2 gas, followed by lyophilization. Peptide aggregation and fibrilization were achieved following previous practice. 1 For the TTR peptides, first, an appropriate amount of monomerized and lyophyilized peptide solid was dissolved in a mixture of acetonitrile (10%) and D 2 O (90%) with a pd of 2.0 to yield a 4-5 mm peptide solution. Then, this solution was heated at 37 C for 6 hrs (for mutant) or 48 hrs (for wild-type), followed by incubation at 25 C in a dry box for ~1 week for wild-type or <1 day for mutant to allow fibril formation. The same aggregation protocol was followed for the Aβ F19K* peptide except for the fact that the peptide was dissolved in water and the ph was brought to 4.0 using 0.01 M HCl before the onset of aggregation. S1

2 Figure S1: Structure of the TTR protofibrils, as determined by Fitzpatrick et al., 1 showing the water density (light red) as well as the Leu111 sidechains (red circles). Figure reprinted with permission from Ref. 1. Copyright 2013, Proceedings of the National Academy Sciences. Figure S2: Schematic representation the structure of a β-sheets (left) and an α-sheet (right), showing the orientation of the backbone units as well as the respective backbone-backbone hydrogen-bonding patterns. S2

3 Figure S3. AFM image of the fibrils formed by TTR-111D M. Figure S4: 2D IR spectrum of TTR fibrils at waiting time T = 0. S3

4 0.15 Normalized Absorbance Wavenumber (cm -1 ) Figure S5: Ester carbonyl vibrational band of TTR-111D M fibrils (blue). Black line is a fit of this band to a Gaussian function with a ω 0 = cm -1 and a bandwidth (FWHM) of 7.2 cm TTR TTR TTR-111D M TTR-111D M Normalized Absorbance Normalized Absorbance Wavenumber (cm -1 ) Wavenumber (cm -1 ) Figure S6: Normalized ATR-FTIR spectra of TTR (blue) and TTR-111D M (red) fibrils as dry films in the amide I (left) and amide A (right) band regions. Besides the differences in their amide I bands, as seen in the solution case (Figure 2), there are substantial differences in the amide A band region of the spectra, indicating a change in the N-D stretching vibrations of the peptides. Additionally, the intensity difference in the ~2575 cm -1 band, which arises from D 2 O, indicates that the TTR-111D M fibrils contain more D 2 O than the TTR fibrils. S4

5 Figure S7: 2D IR spectrum in the ester carbonyl band region of TTR-111D M fibrils at waiting time T = 0. Figure S8: 2D IR spectrum in the amide I band region of TTR-111D M fibrils at waiting time T = 0 fs (left) and T = 2000 fs (right), measured with polarization configuration <XXYY>. S5

6 45000 ε (M -1 cm -1 ) Wavelength (nm) Figure S9: UV-Vis spectrum of methyl acetate, a model compound for the -D M sidechain, whose structure is shown. 10 TTR-111D M monomers [θ] (10 3 deg cm 2 dmol -1 ) Wavelength (nm) Figure S10: Far-UV CD spectrum of a monomerized TTR-111D M solution, which is characterized by a negative band at around 200 nm and hence indicates that the peptide is disordered. In addition, it shows that unaggregated TTR-111D M monomers do not give rise to an enhanced CD signal as observed with TTR-111D M fibrils (Figure 5). S6

7 Figure S11: AFM images of TTR (A) and TTR-111D M (B) fibrils with their respective 2D- FFT (B, D). Cuts along the white lines in B and D are shown in Panel E for both fibrils. The distance between the peaks in E correspond to the pitch of the fibrils. For the TTR-111D M fibrils, there is only one peak in E, which means there is no measurable twist in the fibrils. On the other hand, the TTR fibrils in E have three peaks at 15.8, 27.3, and 40.0 µm -1, which corresponds to an average pitch distance of 83 nm. S7

8 Figure S12: TEM images of TTR-111DM fibrils, showing the uniformity of the assembly. The width of the fibrils at a specific position was estimated based on the distance between the corresponding two arrows shown. S8

9 [θ] (1000 deg cm 2 dmol -1 ) (A) Normalized fluorescence intensity (B) Without peptide Fibrils With peptide Fibrils Wavelength (nm) Wavelength (nm) Figure S13: (A) ICD spectrum of ThT (500 µm) in the presence of TTR-111D M fibrils and (B) fluorescence spectra of ThT in the presence and absence of TTR-111D M fibrils. Figure S14: (A) ICD spectrum of ThT (700 µm) in the presence of Aβ F19K* fibrils and (B) a TEM image of the fibrils formed by the Aβ F19K* peptide. References (1) Fitzpatrick, A. W. P.; Debelouchina, G. T.; Bayro, M. J.; Clare, D. K.; Caporini, M. A.; Bajaj, V. S.; Jaroniec, C. P.; Wang, L.; Ladizhansky, V.; Müller, S. A.; MacPhee, C. E.; Waudby, C. A.; Mott, H. R.; De Simone, A.; Knowles, T. P. J.; Saibil, H. R.; Vendruscolo, M.; Orlova, E. V; Griffin, R. G.; Dobson, C. M. Proc. Natl. Acad. Sci. U. S. A. 2013, 110 (14), S9