Binding Modes of Thioflavin T on the Surface of Amyloid Fibrils Studied by NMR

The mechanism for the interaction of thioflavin T (ThT) with amyloid fibrils at the molecular level is not known. Here, we used ¹H NMR spectroscopy to determine the binding mode of ThT on the surface of fibrils from lysozyme and insulin. Relayed rotating‐frame Overhauser enhancements in ThT were observed, indicating that the orientation of ThT is orthogonal to the fibril surface. Importantly, the assembly state of ThT on both surfaces is different. On the surface of insulin fibrils, ThT is oligomeric, as indicated by rapid ¹H spin‐lattice relaxation rate in the rotating frame (R_1ρ), presumably due to intermolecular dipole–dipole interactions between ThT molecules. In contrast, ThT on the surface of lysozyme fibrils is a monomer, as indicated by slower ¹H R_1ρ. These results shed new light into the mechanism for the enhancement of ThT fluorescence and may lead to more efficient detectors of amyloid assemblies, which have escaped detection by ThT in monomer form.     

Solvent effect on excited state potential energy surfaces of Thioflavin T. Qualitatively different results by TDDFT and SA-2-CASSCF methods

Thioflavin T (ThT) is a viscosity-sensitive fluorescent dye and its emission intensity undergoes a significant enhancement upon binding to DNA or amyloid fibrils. This fluorescence light-up feature has been attributed earlier to restriction of structural rearrangements in the excited state that are coupled to an intramolecular charge transfer (ICT) reaction. In this work TDDFT (using B3LYP and CAM-B3LYP functionals) and SA-2-CASSCF calculations were carried out to obtain relaxed excited-state potential energy surfaces (PES) along twisting φ and wagging δ angles that describe mutual orientation of benzothiazole (BTZ) and dimethylaniline (DMA) fragments in ThT. For isolated ThT molecule both methods predict that during structural rearrangements of the initially excited Franck-Condon state, besides twisting along C C bond which connects BTZ and DMA fragments, a considerable wagging motion is expected to occur. Account for solvent effect using polarized continuum model showed qualitative differences in the excited state PES features calculated by SA-2-CASSCF and TDDFT methods. Single-reference TDDFT calculations failed to describe solvation of TICT state and predicted increase of its energy in more polar media.     

硫黄素T对淀粉样β-蛋白质40聚集成核动力学的双重影响

荧光染料硫黄素T常用于淀粉样纤维聚集过程的定性定量检测。虽然有研究表明,某些抑制淀粉样蛋白质聚集的小分子抑制剂会与硫黄素T相互作用,影响其测试结果。但硫黄素T如何影响淀粉样蛋白质的聚集成核动力学尚不清晰。本文以淀粉样β-蛋白质40 (Aβ40)为模型,系统研究了硫黄素T对Aβ40聚集成核的影响。研究发现：硫黄素T能够显著改变Aβ40的聚集成核动力学,且影响程度与硫黄素T的浓度密切相关。即在低浓度硫黄素T存在下,Aβ40成核速率的延迟时间先随着硫黄素T浓度的升高而缩短,后随着硫黄素T浓度的升高延迟时间反而延长。但延伸的速率却随硫黄素T浓度的升高而缓慢增大。另外,硫黄素T基本不会影响Aβ40的二级结构和纤维形态。同时,等温滴定微量热实验结果表明,硫黄素T结合Aβ40之间的主要作用力为疏水相互作用。据此,本研究提出硫黄素T对Aβ40聚集成核动力学的双重影响机理。这些结果有助于进一步了解硫黄素T与淀粉样蛋白质的作用特点,为今后硫黄素T在Aβ40聚集成核动力学实验中的使用提供参考。     

Towards Ratiometric Sensing of Amyloid Fibrils In Vitro

The aggregation of amyloid‐β peptide and its accumulation in the human brain has an important role in the etiology of Alzheimer’s disease. Thioflavin T has been widely used as a fluorescent marker for these amyloid aggregates. Nevertheless, its complex photophysical behavior, with strong wavelength dependencies of all its fluorescence properties, requires searching for new fluorescent probes. The use of 2‐(2′‐hydroxyphenyl)imidazo[4,5‐b]pyridine (HPIP), which shows two emission bands and a rich excited‐state behavior due to the existence of excited‐state intramolecular processes of proton transfer and charge transfer, is proposed. These properties result in a high sensitivity of HPIP fluorescence to its microenvironment and cause a large differential fluorescence enhancement of the two bands upon binding to aggregates of the amyloid‐β peptide. Based on this behavior, a very sensitive ratiometric method is established for the detection and quantification of amyloid fibrils, which can be combined with the monitoring of fluorescence anisotropy. The binding selectivity of HPIP is discussed on the basis of the apparent binding equilibrium constants of this probe to amyloid‐β (1–42) fibrils and to the nonfibrillar protein bovine serum albumin. Finally, an exhaustive comparison between HPIP and thioflavin T is presented to discuss the sensitivity and specificity of these probes to amyloid aggregates and the significant advantages of the HPIP dye for quantitative determinations.     

Polarity-active NIR probes with strong two-photon absorption and ultrahigh binding affinity of insulin amyloid fibrils

Amyloid fibrils are associated with many neurodegenerative diseases. In situ and in vivo visualization of amyloid fibrils is important for medical diagnostics and requires fluorescent probes with both excitation and emission wavelengths in the far-red and NIR region, and simultaneously with high binding-affinity to amyloid fibrils and the ability to cross the blood–brain barrier, which, however, remain a challenge. Here, we rationally design and synthesize an excellent polarity-sensitive two-photon excited NIR fluorophore (TZPI) based on a donor (D)–acceptor (A)-ion compound. The electron-rich carbazole group and the ionic pyridinium bromide group, linked by an electron-poor π-conjugated benzothiadiazole group, ensure strong near infrared (NIR) emission. Furthermore, the lipophilic carbazole together with the benzothiadiazole group facilitates docking of the probe in the hydrophobic domains of amyloid aggregates with the dissociation constant K_d = 20 nM and 13.5-fold higher binding affinity to insulin fibrils than the commercial probe ThT. On association with the amyloid fibrils, the tiny decrease in polarity leads to a large increase in its NIR emission intensity with an on–off ratio > 10; meanwhile, the TZPI probe exhibits a quantum yield of up to 30% and two-photon absorption cross-section values of up to 467.6 GM at 890 nm. Moreover, the application of TZPI in two-photon imaging is investigated. The ultrahigh binding affinity, the strong NIR emission, the good two-photon absorption properties, the high photo-stability, the appropriate molecular mass of 569 Da and the lipophilicity with log P = 1.66 ± 0.1 to cross the BBB make TZPI promising as an ideal candidate for detecting amyloid plaques in vivo.

A polarity-active NIR probe based on the transformation from the CT state to the LE state for two-photon imaging of amyloid fibrils.     

AFM and fluorescence spectrascopy investigation for disaggregation of existing Aβ fibrils by baicalein

The wavelength for the peak of fluorescence emission of thioflavin T（ThT） was changed from 445 nm to 481 nm when ThT was added in Aβ solution which indicating theβ-sheet structure of Aβ fibril.The significant decrease in the intensity of fluorescence at 481 nm was observed when the baicalein was added in mixed solution of Aβ and ThT,suggesting that the depolymerization of Aβ fibrils happened and there were Aβfibrils left to react with ThT to keep the initial fluorescence intensity.And the existing Aβfibrils are disaggregated by baicalein in a time- and dose-dependent manner.AFM images of the morphologies of the Aβ_1-42 fibrils obviously changed smaller and more dispersive when baicalein added indicating also the depolymerization of Aβ.The results demonstrate a basis for development of a potential herb drug candidate for the treatment of Alzheimer’s disease（AD）.     

Thioflavin T forms a non-fluorescent complex with α-helical poly-L-glutamic acid

Thioflavin T (ThT) is a molecular-rotor-type fluorophore reputed for the selective binding to amyloid fibrils. Using induced circular dichroism, here we show that ThT binds in an orderly manner to α-helical poly-L-glutamic acid (PLGA) implying that neither stacked β-sheets nor π-π stacking interactions are necessary for the binding between the dye and proteins.     

Cold Denaturation of α‐Synuclein Amyloid Fibrils

Although amyloid fibrils are associated with numerous pathologies, their conformational stability remains largely unclear. Herein, we probe the thermal stability of various amyloid fibrils. α‐Synuclein fibrils cold‐denatured to monomers at 0–20 °C and heat‐denatured at 60–110 °C. Meanwhile, the fibrils of β2‐microglobulin, Alzheimer’s Aβ1‐40/Aβ1‐42 peptides, and insulin exhibited only heat denaturation, although they showed a decrease in stability at low temperature. A comparison of structural parameters with positive enthalpy and heat capacity changes which showed opposite signs to protein folding suggested that the burial of charged residues in fibril cores contributed to the cold denaturation of α‐synuclein fibrils. We propose that although cold‐denaturation is common to both native proteins and misfolded fibrillar states, the main‐chain dominated amyloid structures may explain amyloid‐specific cold denaturation arising from the unfavorable burial of charged side‐chains in fibril cores.     

Inhibiting and Reversing Amyloid‐β Peptide (1–40) Fibril Formation with Gramicidin S and Engineered Analogues

In Alzheimer’s disease, amyloid‐β (Aβ) peptides aggregate into extracellular fibrillar deposits. Although these deposits may not be the prime cause of the neurodegeneration that characterizes this disease, inhibition or dissolution of amyloid fibril formation by Aβ peptides is likely to affect its development. ThT fluorescence measurements and AFM images showed that the natural antibiotic gramicidin S significantly inhibited Aβ amyloid formation in vitro and could dissolve amyloids that had formed in the absence of the antibiotic. In silico docking suggested that gramicidin S, a cyclic decapeptide that adopts a β‐sheet conformation, binds to the Aβ peptide hairpin‐stacked fibril through β‐sheet interactions. This may explain why gramicidin S reduces fibril formation. Analogues of gramicidin S were also tested. An analogue with a potency that was four‐times higher than that of the natural product was identified.     

β-酪蛋白淀粉样纤维沉淀的形成及影响因素

利用硫磺素T(ThT)荧光分析法和透射电子显微镜检测β-酪蛋白形成淀粉样纤维沉淀(Fibril)的动力学过程, 研究了磷脂和硫酸肝素对其Fibril形成的影响. 实验结果表明, β-酪蛋白在65 ℃下, pH值为5.4~9.0的范围内, 加热252 h以上, 并未形成Fibril, 说明β-酪蛋白是一种很好的分子伴侣, 在高温、 弱酸和弱碱条件下均不形成淀粉样纤维沉淀. 甘油磷酸胆碱D6PC和D9PC可以显著地促进β-酪蛋白的Fibril的形成, 说明一定条件下蛋白质可能与细胞膜之间存在相互作用而导致其二级构象的转变. 硫酸肝素对β-酪蛋白形成Fibril具有促进作用, 在炎症组织中, 硫酸肝素表达量的增加有可能促进β-酪蛋白形成Fibril, 说明乳腺炎与乳腺中的Corpora Amylacea的形成存在一定的联系.     

Identifying the Bond Responsible for the Fluorescence Modulation in an Amyloid Fibril Sensor

An ultrafast intramolecular bond twisting process is known to be the responsible mechanism for the sensing activity of the extensively used amyloid fibril sensor thioflavin T (ThT). However, it is not yet known which one of the two possible single bonds in ThT is actually involved in the twisting process. To resolve this fundamental issue, two derivatives of ThT have been designed and synthesized and subsequently their photophysical properties have been studied in different solvents. It is understood from the present study that the rotation around the central C? C single bond, and not that around the C? N single bond, is primarily responsible for the sensor activity of ThT. Detailed viscosity‐dependent fluorescence studies revealed that the ThT derivative with restricted C? N bond rotation acts as a better sensor than the derivative with free C? N bond rotation. The better sensory activity is directly correlated with a shorter excited‐state lifetime. Results obtained from the photophysical studies of the ThT derivatives have also been supported by the results obtained from quantum chemical calculations.     

Microtubule‐Binding R3 Fragment from Tau Self‐Assembles into Giant Multistranded Amyloid Ribbons

Tau protein and its fragments self‐assemble into amyloid fibrils in the presence of polyanions, such as heparin. By combining microscopy, scattering, and spectroscopy techniques, we studied the aggregation of the 26‐mer Tau‐derived peptide alone, Tau_306–327, the third repeat fragment (R3) of the microtubule‐binding domain. We show that: i) the sole Tau_306–327 can self‐assemble into amyloid fibrils without the need of aggregation‐promoting polyanions; ii) the resulting structures consist of surprisingly large, well‐ordered 2D laminated flat ribbons, with a log‐normal distribution of the lateral width, reaching the unprecedented lateral size of 350 nm and/or 45 individual protofilaments, that is, the largest amyloid laminated structures ever observed for Tau or any other amyloidogenic sequence. Our results provide insight into the molecular determinants of Tau aggregation and open new perspectives in the understanding of the assembly of amyloid fibrils and β‐sheet‐based biomaterials.     

Torsional Dynamics of Thioflavin T in Room‐Temperature Ionic Liquids: An Effect of Heterogeneity of the Medium

The ultrafast excited‐state dynamics of a fibril binding dye, thioflavin T (ThT), has been studied in two room‐temperature ionic liquids (RTILs): 1‐Butyl‐1‐methylpyrrolidinium bis(trifluoromethylsulfonyl)imide and methyltrioctylammonium bis(trifluoromethylsulfonyl)imide. Previously, in most studies, it was observed that the excited‐state dynamics of the ThT dye were dependent on the viscosity of the medium. In our study, by using RTILs, we have demonstrated that the excited‐state dynamics of ThT are not only viscosity dependent, but also dependent on the heterogeneous nature of the medium. The effect of structural heterogeneity present in neat RTILs on the excited‐state dynamics of ThT was observed. For both RTILs, excitation wavelength dependency on the emission properties of ThT was observed.     

Thioflavin T: Electronic Circular Dichroism and Circularly Polarized Luminescence Induced by Amyloid Fibrils

The circularly polarized luminescence (CPL) spectrum of thioflavin T (ThT) bound to insulin amyloid fibrils has been measured for the first time. It has been found that the samples exhibiting induced circular dichroism (CD) retain the optical activity in the CPL spectra, with the same sign of the rotatory strength. The fluorescence dissymmetry factor is substantial (of the order of magnitude 10^?2). Unlike in the corresponding CD and absorption spectra, there is no shift of the CPL band with respect to the fluorescence band. It has been verified that the measured CPL spectra are free from artifacts from circularly polarized scattering of emitted light by conducting additional measurements in a medium with a refractive index similar to insulin (methylsalicylate). The CD and CPL spectra have been interpreted by means of density functional calculations carried out for ThT in its ground and first excited states in different dielectric environments and for ThT interacting with an aromatic ring. It has been found that the presence of an aromatic ring close to the ThT molecule induces Cotton effects of the same order of magnitude as the stabilization of one enantiomeric conformer. Thus, it is expected that both mechanisms contribute to the induced CD and CPL effect to a similar degree.     

Thioflavin T hydroxylation at basic pH and its effect on amyloid fibril detection

The fluorescent dye thioflavin T (ThT) is commonly used for in situ amyloid fibril detection. In this work, we focused on the spectroscopic properties and chemical stability of ThT in aqueous solution as a function of pH, temperature, and dye concentration. A reversible hydroxylation process occurs in alkaline solutions, which was characterized using a combination of UV-vis absorption spectroscopy, proton NMR, and density functional theory (DFT). On the basis of these studies, we propose a chemical structure for the hydroxylated form. Finally, by means of fluorescence spectroscopy, ThT hydroxylation effects on in situ amyloid detection have been investigated, providing new insights on the efficiency of the ThT assay for quantitative fibril evaluation at basic pH.     

End Capping Alters the Structural Characteristics and Mechanical Properties of Transthyretin (105–115) Amyloid Protofibrils

Pathological amyloid proteins are associated with degenerative and neurodegenerative diseases. These amyloid proteins develop as oligomer, fibrillar, and plaque forms, due to the denatured and unstable status of the amyloid monomers. Specifically, the development of fibrillar amyloid proteins has been investigated through several experimental studies. To understand the generation of amyloid fibrils, environmental factors such as point mutations, pH, and polymorphic characteristics have been considered. Recently, amyloid fibril studies related to end‐capping effects have been conducted to understand amyloid fibril development. However, atomic‐level studies to determine the stability and mechanical properties of amyloid fibrils based on end capping have not been undertaken. In this study, we show that end capping alters the structural characteristics and conformations of transthyretin (TTR) amyloid fibrils by using molecular dynamics (MD) simulations. Variation in the structural conformations and characteristics of the TTR fibrils through end capping are observed, due to the resulting electrostatic energies and hydrophobicity characteristics. Moreover, the end capping changes the mechanical properties of TTR fibrils. Our results shed light on amyloid fibril formation under end‐capping conditions.     

Influence of Aromatic Residues on the Material Characteristics of Aβ Amyloid Protofibrils at the Atomic Scale

Amyloid fibrils, which cause a number of degenerative diseases, are insoluble under physiological conditions and are supported by native contacts. Recently, the effects of the aromatic residues on the Aβ amyloid protofibril were investigated in a ThT fluorescence study. However, the relationship between the material characteristics of the Aβ protofibril and its aromatic residues has not yet been investigated on the atomic scale. Here, we successfully constructed wild‐type (WT) and mutated types of Aβ protofibrils by using molecular dynamics simulations. Through principle component analysis, we established the structural stability and vibrational characteristics of F20L Aβ protofibrils and compared them with WT and other mutated models such as F19L and F19LF20L. In addition, structural stability was assessed by calculating the elastic modulus, which showed that the F20L model has higher values than the other models studied. From our results, it is shown that aromatic residues influence the structural and material characteristics of Aβ protofibrils.     

Amyloid‐Like Fibrillogenesis through Supramolecular Helix‐Mediated Self‐Assembly of Tetrapeptides Containing Non‐Coded α‐Aminoisobutyric Acid (Aib) and 3‐Aminobenzoic Acid (m‐ABA)

Single‐crystal X‐ray diffraction studies of two terminally protected tetrapeptides Boc‐Ile‐Aib‐Val‐m‐ABA‐OMe ( I ) and Boc‐Ile‐Aib‐Phe‐m‐ABA‐OMe ( II ) (Aib=α‐aminoisobutyric acid; m‐ABA=meta‐aminobenzoic acid) reveal that they form continuous H‐bonded helices through the association of double‐bend (type III and I) building blocks. NMR Studies support the existence of the double‐bend (type III and I) structures of the peptides in solution also. Field emission scanning electron‐microscopic (FE‐SEM) and high‐resolution transmission electron‐microscopic (HR‐TEM) images of the peptides exhibit amyloid‐like fibrils in the solid state. The Congo red‐stained fibrils of peptide I and II , observed between crossed polarizers, show green‐gold birefringence, a characteristic of amyloid fibrils.     

Self-assembly of tissue transglutaminase into amyloid-like fibrils using physiological concentration of Ca2+

Tissue transglutaminase (tTG or TG2) is a member of the transglutaminase family that catalyzes calcium dependent formation of isopeptide bonds. It has been shown that the expression of TG2 is elevated in neurodegenerative diseases such as Parkinson's, Huntington's, and Alzheimer's. We have investigated the self-assembly of TG2 in vitro. First, using software, hot spots, which are prone for aggregation, were identified in domain 2 of the enzyme. Next we expressed and purified recombinant TG2 and its truncated version that contains only the catalytic domain, and examined their amyloidogenic behavior in various conditions including different temperatures and pHs, in the presence of metal ions and Guanosine triphosphate (GTP). To analyze various stages leading to TG2 fibrillation, we employed various techniques including Thioflavin T (ThT) binding assay, Congo-Red, birefringence, Circular Dichroism (CD), 8-anilino-1-naphthalene sulfonic acid (ANS) binding, Transmission Electron Microscopy (TEM) and Atomic Force Microscopy (AFM). Our results indicated that using low concentrations of Ca(2+), TG2 self-assembled into amyloid-like fibrils; this self-assembly occurred at the physiological temperature (37 °C) and at a higher temperature (57 °C). The truncated version of TG2 (domain 2) also forms amyloid-like fibrils only in the presence of Ca(2+). Because amyloid formation has occurred with domain 2 alone where no enzymatic activity was shown, self-cross-linking by the enzyme was ruled out as a mechanism of amyloid induction. The self-assembly of TG2 was not significant with magnesium and zinc ions, indicating specificity of the self-assembly for calcium ions. The calcium role in self-assembly of TG2 into amyloid may be extended to other proteins with similar biophysical properties to produce novel biomaterials.     

Naphthoquinone–Dopamine Hybrids Inhibit α-Synuclein Aggregation,Disrupt Preformed Fibrils,and Attenuate Aggregate-Induced Toxicity

Accumulation and aggregation of the intrinsically disordered protein α-synuclein (α-Syn) into amyloid fibrils are hallmarks of a series of heterogeneous neurodegenerative disorders, known as synucleinopathies and most notably Parkinson's disease (PD). The crucial role of α-Syn aggregation in PD makes it an attractive target for the development of disease-modifying therapeutics that would inhibit α-Syn aggregation or disrupt its preformed fibrillar assemblies. To this end, we have designed and synthesized two naphthoquinone–dopamine-based hybrid small molecules, NQDA and Cl-NQDA, and demonstrated their ability to inhibit in vitro amyloid formation by α-Syn using ThT assay, CD, TEM, and Congo red birefringence. Moreover, these hybrid molecules efficiently disassembled preformed fibrils of α-Syn into nontoxic species, as evident from LUV leakage assay. NQDA and Cl-NQDA were found to have low cytotoxicity and they attenuated the toxicity induced by α-Syn towards SH-SY5Y neuroblastoma cells. NQDA was found to efficiently cross an in vitro human blood–brain barrier model. These naphthoquinone–dopamine based derivatives can be an attractive scaffold for therapeutic design towards PD.