Use solid-state NMR to study the molecular structures of disease-associated peptide aggregates
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Our lab uses solid-state nuclear magnetic resonance (ssNMR) to characterize the molecular structures of different types of aggregates formed by disease-associated proteins or peptides. In this thesis, we study three aggregate samples to reveal the structural information related to their molecular arrangements, aggregating mechanisms, and possible pathological pathways. First, we characterized the thermal aggregate of Fibroblast Growth Factor-1 (FGF-1) with Dr. Blaber’s lab. We found the well-structured region in aggregate comprised the folding nucleus of FGF-1, which supports a hypothetical aggregation mechanism involving a partially folded intermediate. Second, we collaborated with Dr. Rosenberry and Dr. Stagg to investigate the 150 kDa Amyloid-β(1-42) (Aβ) oligomers associated with Alzheimer’s disease. A domain-swapped four-fold symmetric structural model of the oligomer was proposed based on NMR data and cryogenic electron microscopy (cryo-EM) 2D classification. The novel structural model can explain several critical phenomena about the cytotoxicity of the oligomers. Last, with the help from Dr. Lieberman’s lab, we explored the atomic structure of an amyloid sample—the P1 peptide amyloid derived from the residue sequence of glaucoma-associated myocilin. An amyloid model of stacked U-shaped antiparallel β-sheets was successfully built by NMR-constrained molecular dynamic (MD) simulation. These structural studies demonstrate the power of ssNMR in characterizing different forms of protein aggregates. We hope ssNMR analysis can become more efficient and automatic with state-of-the-art NMR techniques.