Steric zipper of the amyloid fibrils formed by residues 109-122 of the Syrian hamster prion protein |
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Authors: | Lee Shin-Wen Mou Yun Lin Shu-Yi Chou Fang-Chieh Tseng Wei-Hsiang Chen Chun-hsien Lu Chun-Yi David Yu Steve S-F Chan Jerry C C |
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Institution: | 1 Department of Chemistry, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan 2 Institute of Chemistry, Academia Sinica, Nankang, Taipei 115, Taiwan |
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Abstract: | We report the results of atomic force microscopy, Fourier-transform infrared spectroscopy, solid-state nuclear magnetic resonance, and molecular dynamics (MD) calculations for amyloid fibrils formed by residues 109-122 of the Syrian hamster prion protein (H1). Our data reveal that H1 fibrils contain no more than two β-sheet layers. The peptide strands of H1 fibrils are antiparallel with the A117 residues aligned to form a linear chain in the direction of the fibril axis. The molecular structure of the H1 fibrils, which adopts the motif of steric zipper, is highly uniform in the region of the palindrome sequence AGAAAAGA. The closest distance between the two adjacent β-sheet layers is found to be about 5 Å. The structural features of the molecular model of H1 fibrils obtained by MD simulations are consistent with the experimental results. Overall, our solid-state NMR and MD simulation data indicate that a steric zipper, which was first observed in the crystals of fibril-forming peptides, can be formed in H1 fibrils near the region of the palindrome sequence. |
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Keywords: | MD molecular dynamics PrPC cellular prion protein PrPSc scrapie prion protein SSNMR solid-state NMR FT-IR Fourier-transform infrared AFM atomic force microscopy CSA chemical shift anisotropy MAS magic-angle spinning REDOR rotational-echo double-resonance fpRFDR-CT constant time finite-pulse radio frequency-driven recoupling TFA trifluoroacetic acid DI deionized TMAFM tapping mode atomic force microscopy |
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