scholarly journals Sequence-independent recognition of the amyloid structural motif by GFP protein family

2020 ◽  
Vol 117 (36) ◽  
pp. 22122-22127 ◽  
Author(s):  
Sherry C. S. Xu ◽  
Josephine G. LoRicco ◽  
Anthony C. Bishop ◽  
Nathan A. James ◽  
Welby H. Huynh ◽  
...  
Keyword(s):  
Amyloid Fibrils ◽  
Amyloid Fibril ◽  
Fluorescent Protein ◽  
Protein Localization ◽  
Fibril Formation ◽  
Structural Motif ◽  
Diagnostic Tools ◽  
Lag Phase ◽  
Dependent Manner ◽  
Amyloid Fibril Formation

Cnidarian fluorescent protein (FP) derivatives such as GFP, mCherry, and mEOS2 have been widely used to monitor gene expression and protein localization through biological imaging because they are considered functionally inert. We demonstrate that FPs specifically bind amyloid fibrils formed from many natural peptides and proteins. FPs do not bind other nonamyloid fibrillar structures such as microtubules or actin filaments and do not bind to amorphous aggregates. FPs can also bind small aggregates formed during the lag phase and early elongation phase of fibril formation and can inhibit amyloid fibril formation in a dose-dependent manner. These findings suggest caution should be taken in interpreting FP-fusion protein localization data when amyloid structures may be present. Given the pathological significance of amyloid-related species in some diseases, detection and inhibition of amyloid fibril formation using FPs can provide insights on developing diagnostic tools.

scholarly journals Tannic Acid Inhibits α-Synuclein Amyloid Fibril Formation via Binding to the Monomer N-terminal Domain

2021 ◽  
Author(s):  
Jonathan Stoeber ◽  
Jonathan K Williams ◽  
Prabhas V. Moghe ◽  
Jean Baum
Keyword(s):  
Tannic Acid ◽  
Amyloid Fibrils ◽  
Amyloid Fibril ◽  
Critical Role ◽  
Intrinsically Disordered Protein ◽  
Fibril Formation ◽  
Dependent Manner ◽  
Intrinsically Disordered ◽  
Terminal Domain ◽  
Amyloid Fibril Formation

α-Synuclein (αS) is an intrinsically disordered protein (IDP) that aggregates into amyloid fibrils during the progression of Parkinson's Disease and other synucleinopathies. The N-terminal domain (residues 1-60) is now understood to play a critical role in the initial nucleation of aggregation, as well as a pivotal role in the monomer-fibril interaction underlying amyloid seeding. Here we report on the interaction between αS and the polyphenol tannic acid (TA), where a combination of solution NMR, atomic force microscopy (AFM), and ThT assays have identified that TA targets the αS N-terminal domain to inhibit amyloid fibril formation in a pH dependent manner. This work highlights the importance of targeting the N-terminus of αS to arrest fibril formation, and suggests the importance of including polyphenolic moieties in future amyloid inhibitors.

scholarly journals The amphibian antimicrobial peptide uperin 3.5 is a cross-α/cross-β chameleon functional amyloid

2021 ◽  
Vol 118 (3) ◽  
pp. e2014442118
Author(s):  
Nir Salinas ◽  
Einav Tayeb-Fligelman ◽  
Massimo D. Sammito ◽  
Daniel Bloch ◽  
Raz Jelinek ◽  
...  
Keyword(s):  
Antimicrobial Peptide ◽  
Amyloid Fibrils ◽  
Amyloid Fibril ◽  
Membrane Damage ◽  
Fibril Formation ◽  
Regulation Mechanism ◽  
Bacterial Cells ◽  
Amyloid Fibril Formation ◽  
Β Amyloid ◽  
Β Sheets

Antimicrobial activity is being increasingly linked to amyloid fibril formation, suggesting physiological roles for some human amyloids, which have historically been viewed as strictly pathological agents. This work reports on formation of functional cross-α amyloid fibrils of the amphibian antimicrobial peptide uperin 3.5 at atomic resolution, an architecture initially discovered in the bacterial PSMα3 cytotoxin. The fibrils of uperin 3.5 and PSMα3 comprised antiparallel and parallel helical sheets, respectively, recapitulating properties of β-sheets. Uperin 3.5 demonstrated chameleon properties of a secondary structure switch, forming mostly cross-β fibrils in the absence of lipids. Uperin 3.5 helical fibril formation was largely induced by, and formed on, bacterial cells or membrane mimetics, and led to membrane damage and cell death. These findings suggest a regulation mechanism, which includes storage of inactive peptides as well as environmentally induced activation of uperin 3.5, via chameleon cross-α/β amyloid fibrils.

scholarly journals Identification of Novel 1,3,5-Triphenylbenzene Derivative Compounds as Inhibitors of Hen Lysozyme Amyloid Fibril Formation

2019 ◽  
Vol 20 (22) ◽  
pp. 5558
Author(s):  
Hassan Ramshini ◽  
Reza Tayebee ◽  
Alessandra Bigi ◽  
Francesco Bemporad ◽  
Cristina Cecchi ◽  
...  
Keyword(s):  
Amyloid Fibrils ◽  
Amyloid Fibril ◽  
Inhibitory Effect ◽  
Fibril Formation ◽  
Amyloid Formation ◽  
Binding Assays ◽  
Egg White Lysozyme ◽  
Amyloid Fibril Formation ◽  
Activity Measurements ◽  
Model Protein

Deposition of soluble proteins as insoluble amyloid fibrils is associated with a number of pathological states. There is a growing interest in the identification of small molecules that can prevent proteins from undergoing amyloid fibril formation. In the present study, a series of small aromatic compounds with different substitutions of 1,3,5-triphenylbenzene have been synthesized and their possible effects on amyloid fibril formation by hen egg white lysozyme (HEWL), a model protein for amyloid formation, and of their resulting toxicity were examined. The inhibitory effect of the compounds against HEWL amyloid formation was analyzed using thioflavin T and Congo red binding assays, atomic force microscopy, Fourier-transform infrared spectroscopy, and cytotoxicity assays, such as the 3-(4,5-Dimethylthiazol)-2,5-Diphenyltetrazolium Bromide (MTT) reduction assay and caspase-3 activity measurements. We found that all compounds in our screen were efficient inhibitors of HEWL fibril formation and their associated toxicity. We showed that electron-withdrawing substituents such as –F and –NO2 potentiated the inhibitory potential of 1,3,5-triphenylbenzene, whereas electron-donating groups such as –OH, –OCH3, and –CH3 lowered it. These results may ultimately find applications in the development of potential inhibitors against amyloid fibril formation and its biologically adverse effects.

scholarly journals The Role of Buffers in Wild-Type HEWL Amyloid Fibril Formation Mechanism

Biomolecules ◽  
2019 ◽  
Vol 9 (2) ◽  
pp. 65 ◽  
Author(s):  
Sandi Brudar ◽  
Barbara Hribar-Lee
Keyword(s):  
Amyloid Fibrils ◽  
Amyloid Fibril ◽  
Cd Spectroscopy ◽  
Fibril Formation ◽  
Acetate Solution ◽  
Solution Ph ◽  
Egg White Lysozyme ◽  
Fluorescence Measurements ◽  
Amyloid Fibril Formation ◽  
Vis Spectroscopy

Amyloid fibrils, highly ordered protein aggregates, play an important role in the onset of several neurological disorders. Many studies have assessed amyloid fibril formation under specific solution conditions, but they all lack an important phenomena in biological solutions—buffer specific effects. We have focused on the formation of hen egg-white lysozyme (HEWL) fibrils in aqueous solutions of different buffers in both acidic and basic pH range. By means of UV-Vis spectroscopy, fluorescence measurements and CD spectroscopy, we have managed to show that fibrillization of HEWL is affected by buffer identity (glycine, TRIS, phosphate, KCl-HCl, cacodylate, HEPES, acetate), solution pH, sample incubation (agitated vs. static) and added excipients (NaCl and PEG). HEWL only forms amyloid fibrils at pH = 2.0 under agitated conditions in glycine and KCl-HCl buffers of high enough ionic strength. Phosphate buffer on the other hand stabilizes the HEWL molecules. Similar stabilization effect was achieved by addition of PEG12000 molecules to the solution.

Sensing and modulation of amyloid fibrils by photo-switchable organic dots

Nanoscale ◽  
2020 ◽  
Vol 12 (32) ◽  
pp. 16805-16818
Author(s):  
Aslam Uddin ◽  
Bibhisan Roy ◽  
Gregor P. Jose ◽  
Sk Saddam Hossain ◽  
Partha Hazra
Keyword(s):  
Amyloid Fibrils ◽  
Amyloid Fibril ◽  
Early Stage ◽  
Fibril Formation ◽  
Amyloid Formation ◽  
Amyloid Fibril Formation

Our study demonstrates that organic dots can be used for the imaging and early stage detection of amyloid fibril formation and the modulation of amyloid formation pathways.

scholarly journals Acceleration of amyloid fibril formation by multichannel sonochemical reactor

2021 ◽  
Author(s):  
Kentaro Noi ◽  
Kichitaro Nakajima ◽  
Keiichi Yamaguchi ◽  
Masatomo So ◽  
Kensuke Ikenaka ◽  
...  
Keyword(s):  
Amyloid Fibrils ◽  
Amyloid Fibril ◽  
Ultrasonic Transducer ◽  
Reaction System ◽  
Ultrasound Irradiation ◽  
Alpha Synuclein ◽  
Fibril Formation ◽  
Driving Voltage ◽  
Amyloid Fibril Formation ◽  
Beta 2 Microglobulin

Abstract Formation of amyloid fibrils of various amyloidogenic proteins is dramatically enhanced by ultrasound irradiation. For applying this phenomenon to the study of protein aggregation science and diagnosis of neurodegenerative diseases, a multichannel ultrasound irradiation system with individually adjustable ultrasound-irradiation conditions is necessary. Here, we develop a sonochemical reaction system, where an ultrasonic transducer is placed in each well of a 96-well microplate to perform ultrasonic irradiation of sample solutions under various conditions with high reproducibility, and applied it for studying amyloid-fibril formation of amyloid $\beta$, $\alpha$-synuclein, $\beta$2-microglobulin, and lysozyme. The results clearly show that our instrument is superior to conventional shaking method in terms of degree of acceleration and reproducibility of fibril formation reaction. The acceleration degree is controllable by controlling the driving voltage applied to each transducer. We have thus succeeded in developing a useful tool for the study of amyloid fibril formation in various proteins.

scholarly journals Structural development of amyloid precursors in insulin B chain and the inhibition effect by fibrinogen

2021 ◽  
Author(s):  
Naoki Yamamoto ◽  
Rintaro Inoue ◽  
Yoshiteru Makino ◽  
Naoya Shibayama ◽  
Akira Naito ◽  
...  
Keyword(s):  
Amyloid Fibrils ◽  
Amyloid Fibril ◽  
Fibril Formation ◽  
Size Exclusion ◽  
Inhibition Mechanism ◽  
Structural Development ◽  
Amyloid Fibril Formation ◽  
Transmission Electron ◽  
Exclusion Chromatography ◽  
The Stability

Amyloid fibrils are abnormal protein aggregates that relate to a large number of amyloidoses and neurodegenerative diseases. The oligomeric precursors, or prefibrillar intermediates, which emerge prior to the amyloid fibril formation, have been known to play a crucial role for the formation. Therefore, it is essential to elucidate the mechanisms of the structural development of the prefibrillar intermediates and ways to prevent its fibril formation. An insulin-derived peptide, insulin B chain, has been known for its stable accumulation of the prefibrillar intermediates. In this study, structural development of B chain prefibrillar intermediates was monitored by transmission electron microscopy and small-angle X-ray scattering combined with size exclusion chromatography and solid-state NMR spectroscopy to elucidate the stability and secondary structure. We further tracked its inhibition process by fibrinogen (Fg), which has been known to effectively prevent the amyloid fibril formation of B chain. We demonstrated that prefibrillar intermediates are wavy structures with low β-sheet content, growing in a multistep manner toward the nucleation for the amyloid fibril formation. In the presence of Fg, the formation of the prefibrillar intermediates slowed down by forming specific complexes. These observations suggest that the prefibrillar intermediates serve as reaction fields for the nucleation and its propagation for the amyloid fibril formation, whereas the inhibition of prefibrillar intermediate elongation by Fg is the significant factor to suppress the fibril formation. We propose that the obtained molecular picture could be a general inhibition mechanism of the amyloid fibril formation by the inhibitors.

scholarly journals CryoEM reveals how the small molecule EGCG binds to Alzheimer’s brain-derived tau fibrils and initiates fibril disaggregation

2020 ◽  
Author(s):  
PM Seidler ◽  
DR Boyer ◽  
MR Sawaya ◽  
P Ge ◽  
WS Shin ◽  
...  
Keyword(s):  
Small Molecules ◽  
Green Tea ◽  
Small Molecule ◽  
Amyloid Fibrils ◽  
Amyloid Fibril ◽  
Fibril Formation ◽  
Paired Helical Filament ◽  
Amyloid Fibril Formation ◽  
Molecular Action ◽  
Tau Fibrils

AbstractEGCG, the most abundant favanol in green tea, is one of the few natural compounds known to inhibit amyloid fibril formation of proteins associated with neurodegeneration, and to disaggregate amyloid fibrils. Little is known of the mechanism of molecular action of EGCG, or how it or other small molecules interact with amyloid fibrils. Here we present a 3.9 Å resolution cryoEM structure that reveals the site of EGCG binding to Alzheimer’s disease (AD) brain-derived tau fibrils. The structure suggests that EGCG disaggregates fibrils of AD-tau by wedging into a cleft that is at the interface of two protofilaments of the paired helical filament, and by causing charge repulsions between tau layers of the fibril. In support of this, we observe separation of the protofilaments that EGCG wedges between, and accompanying displacement of the adjacent β-helix domain. By resolving the site of EGCG binding, our structure defines a pharmacophore-like cleft in the AD-tau fibril that will be of use for the discovery of surrogate compounds with more desirable drug-like properties.

scholarly journals The Aggregation Conditions Define Whether EGCG is an Inhibitor or Enhancer of α-Synuclein Amyloid Fibril Formation

2020 ◽  
Vol 21 (6) ◽  
pp. 1995 ◽  
Author(s):  
Rebecca Sternke-Hoffmann ◽  
Alessia Peduzzo ◽  
Najoua Bolakhrif ◽  
Rainer Haas ◽  
Alexander K. Buell
Keyword(s):  
Amyloid Fibrils ◽  
Amyloid Fibril ◽  
Epigallocatechin Gallate ◽  
Small Region ◽  
Fibril Formation ◽  
Oxidation Products ◽  
Relevant Parameter ◽  
Amyloid Formation ◽  
Experimental Conditions ◽  
Amyloid Fibril Formation

The amyloid fibril formation by α -synuclein is a hallmark of various neurodegenerative disorders, most notably Parkinson’s disease. Epigallocatechin gallate (EGCG) has been reported to be an efficient inhibitor of amyloid formation by numerous proteins, among them α -synuclein. Here, we show that this applies only to a small region of the relevant parameter space, in particular to solution conditions where EGCG readily oxidizes, and we find that the oxidation product is a much more potent inhibitor compared to the unmodified EGCG. In addition to its inhibitory effects, EGCG and its oxidation products can under some conditions even accelerate α -synuclein amyloid fibril formation through facilitating its heterogeneous primary nucleation. Furthermore, we show through quantitative seeding experiments that, contrary to previous reports, EGCG is not able to re-model α -synuclein amyloid fibrils into seeding-incompetent structures. Taken together, our results paint a complex picture of EGCG as a compound that can under some conditions inhibit the amyloid fibril formation of α -synuclein, but the inhibitory action is not robust against various physiologically relevant changes in experimental conditions. Our results are important for the development of strategies to identify and characterize promising amyloid inhibitors.

scholarly journals On the lag phase in amyloid fibril formation

2015 ◽  
Vol 17 (12) ◽  
pp. 7606-7618 ◽  
Author(s):  
Paolo Arosio ◽  
Tuomas P. J. Knowles ◽  
Sara Linse
Keyword(s):  
Amyloid Fibril ◽  
Fibril Formation ◽  
Lag Phase ◽  
Amyloid Fibril Formation

Rates of microscopic processes taking place during the lag phase of amyloid fibril formation for a reaction starting from an initially monomeric 4 μm solution of Aβ42.

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