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1. Long-term, super-resolution imaging of amyloid structures using transient amyloid binding microscopy

   https://doi.org/10.1117/12.2507656  

   Ding, Tianben; Spehar, Kevin; Bieschke, Jan; Lew, Matthew D. (February 2019, Proc. SPIE 10884, Single Molecule Spectroscopy and Superresolution Imaging XII)

   Amyloid fibrils and tangles are signatures of Alzheimer disease, but nanometer-sized aggregation intermediates are hypothesized to be the structures most toxic to neurons. The structures of these oligomers are too small to be resolved by conventional light microscopy. We have developed a simple and versatile method, called transient amyloid binding (TAB), to image amyloid structures with nanoscale resolution using amyloidophilic dyes, such as Thioflavin T, without the need for covalent labeling or immunostaining of the amyloid protein. Transient binding of ThT molecules to amyloid structures over time generates photon bursts that are used to localize single fluorophores with nanometer precision. Continuous replenishment of fluorophores from the surrounding solution minimizes photobleaching, allowing us to visualize a single amyloid structure for hours to days. We show that TAB microscopy can image both the oligomeric and fibrillar stages of amyloid-β aggregation. We also demonstrate that TAB microscopy can image the structural remodeling of amyloid fibrils by epi-gallocatechin gallate. Finally, we utilize TAB imaging to observe the non-linear growth of amyloid fibrils. 

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2. Time-resolved β-lactam cleavage by L1 metallo-β-lactamase

   https://doi.org/10.1038/s41467-022-35029-3  

   Wilamowski, M.; Sherrell, D. A.; Kim, Y.; Lavens, A.; Henning, R. W.; Lazarski, K.; Shigemoto, A.; Endres, M.; Maltseva, N.; Babnigg, G.; et al (December 2022, Nature Communications)

   Abstract Serial x-ray crystallography can uncover binding events, and subsequent chemical conversions occurring during enzymatic reaction. Here, we reveal the structure, binding and cleavage of moxalactam antibiotic bound to L1 metallo-β-lactamase (MBL) from Stenotrophomonas maltophilia . Using time-resolved serial synchrotron crystallography, we show the time course of β-lactam hydrolysis and determine ten snapshots (20, 40, 60, 80, 100, 150, 300, 500, 2000 and 4000 ms) at 2.20 Å resolution. The reaction is initiated by laser pulse releasing Zn 2+ ions from a UV-labile photocage. Two metal ions bind to the active site, followed by binding of moxalactam and the intact β-lactam ring is observed for 100 ms after photolysis. Cleavage of β-lactam is detected at 150 ms and the ligand is significantly displaced. The reaction product adjusts its conformation reaching steady state at 2000 ms corresponding to the relaxed state of the enzyme. Only small changes are observed in the positions of Zn 2+ ions and the active site residues. Mechanistic details captured here can be generalized to other MBLs. 

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3. Multi-target amyloid probing and inhibition using basic orange fluorescence

   https://doi.org/10.1039/D3SD00124E  

   Tang, Yijing; Zhang, Dong; Gong, Xiong; Zheng, Jie (November 2023, Sensors & Diagnostics)

   Misfolding and aggregation of amyloid peptides are critical pathological events in numerous protein misfolding diseases (PMDs), such as Alzheimer's disease (AD), type II diabetes (T2D), and medullary thyroid carcinoma (MTC). While developing effective amyloid detectors and inhibitors to probe and prevent amyloid aggregation is a crucial diagnostic and therapeutic strategy for treating debilitating diseases, it is important to recognize that amyloid detection and amyloid prevention are two distinct strategies for developing pharmaceutical drugs. Here, we reported novel fluorescent BO21 as a versatile “dual-function, multi-target” amyloid probe and inhibitor for detecting and preventing amyloid aggregates of different sequences (Aβ, hIAPP, or hCT) and sizes (monomers, oligomers, or fibrils). As an amyloid probe, BO21 demonstrated a higher sensitivity and binding affinity to oligomeric and fibrillar amyloids compared to ThT, resulting in up to 18–39 fold fluorescence enhancements. As an amyloid inhibitor, BO21 also demonstrated its strong amyloid inhibition property by effectively preventing amyloid aggregation, disaggregating preformed amyloid fibrils, and reducing amyloid-induced cytotoxicity. The findings of this study offer a new perspective for the discovery of dual-functional amyloid probes and inhibitors, which have the potential to greatly expand the diagnostic and therapeutic treatments available for PMDs. 

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4. Michler’s hydrol blue elucidates structural differences in prion strains

   https://doi.org/10.1073/pnas.2001732117  

   Xiao, Yiling; Rocha, Sandra; Kitts, Catherine C.; Reymer, Anna; Beke-Somfai, Tamás; Frederick, Kendra K.; Nordén, Bengt (November 2020, Proceedings of the National Academy of Sciences)

   null (Ed.)

   Yeast prions provide self-templating protein-based mechanisms of inheritance whose conformational changes lead to the acquisition of diverse new phenotypes. The best studied of these is the prion domain (NM) of Sup35, which forms an amyloid that can adopt several distinct conformations (strains) that confer distinct phenotypes when introduced into cells that do not carry the prion. Classic dyes, such as thioflavin T and Congo red, exhibit large increases in fluorescence when bound to amyloids, but these dyes are not sensitive to local structural differences that distinguish amyloid strains. Here we describe the use of Michler’s hydrol blue (MHB) to investigate fibrils formed by the weak and strong prion fibrils of Sup35NM and find that MHB differentiates between these two polymorphs. Quantum mechanical time-dependent density functional theory (TDDFT) calculations indicate that the fluorescence properties of amyloid-bound MHB can be correlated to the change of binding site polarity and that a tyrosine to phenylalanine substitution at a binding site could be detected. Through the use of site-specific mutants, we demonstrate that MHB is a site-specific environmentally sensitive probe that can provide structural details about amyloid fibrils and their polymorphs. 

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5. Self-Assembly of Amyloid Fibrils into 3D Gel Clusters versus 2D Sheets

   https://doi.org/10.3390/biom13020230  

   Karunarathne, Kanchana; Bushra, Nabila; Williams, Olivia; Raza, Imad; Tirado, Laura; Fakhre, Diane; Fakhre, Fadia; Muschol, Martin (February 2023, Biomolecules)

   The deposition of dense fibril plaques represents the pathological hallmark for a multitude of human disorders, including many neurodegenerative diseases. Fibril plaques are predominately composed of amyloid fibrils, characterized by their underlying cross beta-sheet architecture. Research into the mechanisms of amyloid formation has mostly focused on characterizing and modeling the growth of individual fibrils and associated oligomers from their monomeric precursors. Much less is known about the mechanisms causing individual fibrils to assemble into ordered fibrillar suprastructures. Elucidating the mechanisms regulating this “secondary” self-assembly into distinct suprastructures is important for understanding how individual protein fibrils form the prominent macroscopic plaques observed in disease. Whether and how amyloid fibrils assemble into either 2D or 3D supramolecular structures also relates to ongoing efforts on using amyloid fibrils as substrates or scaffolds for self-assembling functional biomaterials. Here, we investigated the conditions under which preformed amyloid fibrils of a lysozyme assemble into larger superstructures as a function of charge screening or pH. Fibrils either assembled into three-dimensional gel clusters or two-dimensional fibril sheets. The latter displayed optical birefringence, diagnostic of amyloid plaques. We presume that pH and salt modulate fibril charge repulsion, which allows anisotropic fibril–fibril attraction to emerge and drive the transition from 3D to 2D fibril self-assembly. 

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