Thioflavin T as a Molecular Rotor: Fluorescent Properties of Thioflavin T in Solvents with Different Viscosity

Viscosity-Based Flow Sensor on Paper for Quantitative and Label-Free Detection of α-Amylase and Its Inhibitor

α-Amylase (AMS) in human serum is a critical biomarker for the early diagnosis of pancreatic damage. In addition, the inhibition of α-amylase has long been thought to decrease the occurrence of diabetes. Thus, it is critical to construct a facile and convenient method for the determination of AMS and its inhibitor. In this study, we demonstrate a novel amylase sensor based on translating the viscosity change of the aqueous solution into the difference of the water diffusion length on a pH paper strip. AMS can be quantitatively detected by measuring the viscosity change of the amylopectin solution in the presence of AMS with different concentrations. The paper-based AMS sensor has a very high sensitivity with a detection limit of 0.017 U/mL and also shows excellent specificity. In addition, the inhibitory effect of acarbose on AMS is demonstrated with the IC₅₀ value determined to be 21.66 ± 1.13 μg/mL. Furthermore, it is also evaluated for the detection of AMS in human serum samples of healthy people and acute pancreatitis patients. The difference in amylase levels between the two groups is unambiguously distinguished. Overall, this study provides a very simple, cost-effective, equipment-free, high-throughput, and label-free method for rapid and quantitative detection of α-amylase and may have significant applications in the diagnosis of acute pancreatitis and the screening of AMS inhibitors.

Coherent Two-Dimensional and Broadband Electronic Spectroscopies

Over the past few decades, coherent broadband spectroscopy has been widely used to improve our understanding of ultrafast processes (e.g., photoinduced electron transfer, proton transfer, and proton-coupled electron transfer reactions) at femtosecond resolution. The advances in femtosecond laser technology along with the development of nonlinear multidimensional spectroscopy enabled further insights into ultrafast energy transfer and carrier relaxation processes in complex biological and material systems. New discoveries and interpretations have led to improved design principles for optimizing the photophysical properties of various artificial systems. In this review, we first provide a detailed theoretical framework of both coherent broadband and two-dimensional electronic spectroscopy (2DES). We then discuss a selection of experimental approaches and considerations of 2DES along with best practices for data processing and analysis. Finally, we review several examples where coherent broadband and 2DES were employed to reveal mechanisms of photoinitiated ultrafast processes in molecular, biological, and material systems. We end the review with a brief perspective on the future of the experimental techniques themselves and their potential to answer an even greater range of scientific questions.

Polysorbate 80 controls Morphology, structure and stability of human insulin Amyloid-Like spherulites

Amyloid protein aggregates are not only associated with neurodegenerative diseases and may also occur as unwanted by-products in protein-based therapeutics. Surfactants are often employed to stabilize protein formulations and reduce the risk of aggregation. However, surfactants alter protein-protein interactions and may thus modulate the physicochemical characteristics of any aggregates formed. Human insulin aggregation was induced at low pH in the presence of varying concentrations of the surfactant polysorbate 80. Various spectroscopic and imaging methods were used to study the aggregation kinetics, as well as structure and morphology of the formed aggregates. Molecular dynamics simulations were employed to investigate the initial interaction between the surfactant and insulin. Addition of polysorbate 80 slowed down, but did not prevent, aggregation of insulin. Amyloid spherulites formed under all conditions, with a higher content of intermolecular beta-sheets in the presence of the surfactant above its critical micelle concentration. In addition, a denser packing was observed, leading to a more stable aggregate. Molecular dynamics simulations suggested a tendency for insulin to form dimers in the presence of the surfactant, indicating a change in protein-protein interactions. It is thus shown that surfactants not only alter aggregation kinetics, but also affect physicochemical properties of any aggregates formed.

A Comparative Study of High-Contrast Fluorescence Lifetime Probes for Imaging Amyloid in Tissue

Optical imaging of protein aggregates in living and post-mortem tissue can often be impeded by unwanted fluorescence, prompting the need for novel methods to extract meaningful signal in complex biological environments. Historically, benzothiazolium derivatives, prominently Thioflavin T, have been the state-of-the-art fluorescent probes for amyloid aggregates, but their optical, structural, and binding properties typically limit them to in vitro applications. This study compares the use of novel uncharged derivative, PAP_1, with parent Thioflavin T as a fluorescence lifetime imaging probe. This is applied specifically to imaging recombinant α-synuclein aggregates doped into brain tissue. Despite the 100-fold lower brightness of PAP_1 compared to that of Thioflavin T, PAP_1 binds to α-synuclein aggregates with an affinity several orders of magnitude greater than Thioflavin T; thus, we observe a specific decrease in the fluorescence lifetime of PAP_1 bound to α-synuclein aggregates, resulting in a separation of >1.4 standard deviations between PAP_1-stained brain tissue background and α-synuclein aggregates that is not observed with Thioflavin T. This enables contrast between highly fluorescent background tissue and amyloid fibrils that is attributed to the greater affinity of PAP_1 for α-synuclein aggregates, avoiding the substantial off-target staining observed with Thioflavin T.

Efficient Hydro- and Organogelation by Minimalistic Diketopiperazines Containing a Highly Insoluble Aggregation-Induced, Blue-Shifted Emission Luminophore*

We report the synthesis, gelation abilities and aggregation-induced, blue-shifted emission (AIBSE) properties of two minimalistic diketopiperazine-based gelators. Despite containing a highly insoluble luminophore that makes up more than half of their respective molecular masses, efficient hydrogelation by multiple stimuli for one and efficient organogelation for the other compound are reported. Insights into the aggregation and gelation properties were gained through examination of the photophysical and material properties of selected gels, which are representative of the different modes of gelation. The synthesis of the gelators is highly modular and based on readily available amino acid building blocks, allowing the efficient and rapid diversification of these core structures and fine-tuning of gel properties.

Exploring the Effect of Aliphatic Substituents on Aryl Cyano Amides on Enhancement of Fluorescence upon Binding to Amyloid-β Aggregates

The self-assembly of amyloid-β (Aβ) peptides into amyloid aggregates is a pathological hallmark of Alzheimer's Disease. We previously reported a fluorescent Aryl Cyano Amide (ARCAM) probe that exhibits an increase in fluorescence emission upon binding to Aβ aggregates in solution and in neuronal tissue. Here, we investigate the effect of introducing small aliphatic substituents on the spectroscopic properties of ARCAM both free in solution and when bound to aggregated Aβ. We found that introducing substituents designed to hinder the rotation of bonds between the electron donor and acceptor on these fluorophores can affect the overall brightness of fluorescence emission of the probes in amyloid-free solutions, but the relative fluorescence enhancement of these probes in amyloid-containing solutions is dependent on the location of the substituents on the ARCAM scaffold. We also observed the capability to tune the excitation or emission wavelength of these probes by introducing electron-donating or -withdrawing substituents that putatively affect either the energy required for photoexcitation or the stability of the photoexcited state. These studies reveal new design principles for developing ARCAM-based fluorescent Aβ-binding probes with an enhanced fluorescence signal compared to background and tunable spectroscopic properties, which may lead to improved chemical tools for aiding in the diagnosis of amyloid-associated neurodegenerative diseases.

A tale of two tails: Self-assembling properties of A- and B-chain parts of insulin's highly amyloidogenic H-fragment

Due to the spontaneous transition of native insulin into therapeutically inactive amyloid, prolonged storage decreases effectiveness of the hormone in treatment of diabetes. Various regions of the amino acid sequence have been implicated in insulin aggregation. Here, we focus on smaller fragments of the highly amyloidogenic H-peptide comprising disulfide-bonded N-terminal sections of insulin's A-chain (13 residues) and B-chain (11 residues). Aggregation patterns of N-terminal fragments of A-chain (ACC_1-13, ACC_1-11, ACC_6-13, ACC_6-11, all retaining Cys6A-Cys11A disulfide bond) and B-chain (B_1-11(7A)) are examined at acidic and neutral pH. ACC_1-11 is the smallest fragment found to be amyloidogenic at either pH; removal of the N-terminal GIVEQ section renders this fragment entirely non-amyloidogenic. The self-assembling properties of ACC_1-11 contrast with aggregation-resistant behavior of B_1-11(7A) and its disulfide-linked homodimer, (B_1-11)₂ aggregating only at neutral pH. Fibrillar ACC_1-11 is similar to insulin amyloid in terms of morphology and infrared features. Secondary nucleation is likely to account for the detected shortening of insulin aggregation lag phase at neutral pH upon cross-seeding with pre-formed fibrils of ACC_1-11 or (B_1-11)₂. An aggregation-enhancing effect of monomeric ACC_1-11 on co-dissolved native insulin is also observed. Our findings are discussed in the context of mechanisms of insulin aggregation.

Identification of Thioflavin T Binding Modes to DNA: A Structure-Specific Molecular Probe for Lasing Applications

The binding mechanism of thioflavin T (ThT) to DNA was studied using polarized light spectroscopy and fluorescence-based techniques in solutions and in solid films. Linear dichroism measurements showed that ThT binds to DNA duplex by intercalation. Time-resolved fluorescence studies revealed a second binding mode which is the external binding to the DNA phosphate groups. Both binding modes represent the nonspecific type of interactions. The studies were complemented with the analysis of short oligonucleotides having DNA cavities. The results indicate that the interplay between three binding modes-intercalation, external binding, and binding inside DNA cavities-determines the effective fluorescence quantum yield of the dye in the DNA structures. External binding was found to be responsible for fluorescence quenching because of energy transfer between intercalated and externally bound molecules. Finally, amplified spontaneous emission (ASE) was successfully generated in the ThT-stained films and used for detecting different DNA structures. ASE measurements show that ThT-stained DNA structures can be used for designing bioderived microlasers.

Beyond amyloid proteins: Thioflavin T in nucleic acid recognition

Thioflavin T (ThT) is a commercially available fluorescent dye that is commonly used in biomedical research for over five decades. It was first reported as an extrinsic fluorescent probe for the detection of amyloid fibrils and related processes and it has also been used extensively for assessing protein binding in fluorescence-based assays. Although the nucleic acid binding of ThT was reported half of a century ago in the 1970s, it was not widely explored until the start of this decade. In recent years, Thioflavin T has become a major tool in the recognition of many types of non-canonical nucleic acid conformations including duplexes, triplexes, and G-quadruplexes. The propensity of ThT binding is more towards base aberrations, bulges, and mismatches highlighting its importance in serving as a diagnostic tool in a variety of ailments/disease conditions. In this review, we cover major advancements in nucleic acid detection/binding by ThT to a variety of nucleic acid structures.

Real-time observation of structure and dynamics during the liquid-to-solid transition of FUS LC

A subset of the proteins found in pathological protein fibrils also exhibit tendencies for liquid-liquid phase separation (LLPS) both in vitro and in cells. The mechanisms underlying the connection between these phase transitions have been challenging to study due to the heterogeneous and dynamic nature of the states formed during the maturation of LLPS protein droplets into gels and solid aggregates. Here, we interrogate the liquid-to-solid transition of the low-complexity domain of the RNA-binding protein FUS (FUS LC), which has been shown to adopt LLPS, gel-like, and amyloid states. We employ magic-angle-spinning NMR spectroscopy, which has allowed us to follow these transitions in real time and with residue-specific resolution. We observe the development of β-sheet structure through the maturation process and show that the final state of FUS LC fibrils produced after LLPS is distinct from that grown from fibrillar seeds. We also apply our methodology to FUS LC G156E, a clinically relevant FUS mutant that exhibits accelerated fibrillization rates. We observe significant changes in dynamics during the transformation of the FUS LC G156E construct and begin to unravel the sequence specific contributions to this phenomenon with computational studies of the phase-separated state of FUS LC and FUS LC G156E.

Conformational Transitions upon Maturation Rule Surface and pH-Responsiveness of α-Lactalbumin Microparticulates

De novo designed protein supramolecular structures are nowadays attracting much interest as highly performing biomaterials. While a clear advantage is provided by the intrinsic biocompatibility and biodegradability of protein and peptide building blocks, developing sustainable and green bottom up approaches for finely tuning the material properties still remains a challenge. Here, we present an experimental study on the formation of protein microparticles in the form of particulates from the protein α-lactalbumin using bulk mixing in water solution and high temperature. Once formed, the structure and stability of these spherical protein condensates change upon further thermal incubation while the size of aggregates does not significantly increase. Combining advanced microscopy and spectroscopy methods, we prove that this process, named maturation, is characterized by a gradual increase of amyloid-like structure in protein particulates, an enhancement in surface roughness and in molecular compactness, providing a higher stability and resistance of the structure in acidic environments. When dissolved at pH 2, early stage particulates disassemble into a homogeneous population of small oligomers, while the late stage particulates remain unaffected. Particulates at the intermediate stage of maturation partially disassemble into a heterogeneous population of fragments. Importantly, differently matured microparticles show different features when loading a model lipophilic molecule. Our findings suggest conformational transitions localized at the interface as a key step in the maturation of amyloid protein condensates, promoting this phenomenon as an intrinsic knob to tailor the properties of protein microparticles formed via bulk mixing in aqueous solution. This provides a simple and sustainable platform for the design and realization of protein microparticles for tailored applications.

Visualising G-quadruplex DNA dynamics in live cells by fluorescence lifetime imaging microscopy

Guanine rich regions of oligonucleotides fold into quadruple-stranded structures called G-quadruplexes (G4s). Increasing evidence suggests that these G4 structures form in vivo and play a crucial role in cellular processes. However, their direct observation in live cells remains a challenge. Here we demonstrate that a fluorescent probe (DAOTA-M2) in conjunction with fluorescence lifetime imaging microscopy (FLIM) can identify G4s within nuclei of live and fixed cells. We present a FLIM-based cellular assay to study the interaction of non-fluorescent small molecules with G4s and apply it to a wide range of drug candidates. We also demonstrate that DAOTA-M2 can be used to study G4 stability in live cells. Reduction of FancJ and RTEL1 expression in mammalian cells increases the DAOTA-M2 lifetime and therefore suggests an increased number of G4s in these cells, implying that FancJ and RTEL1 play a role in resolving G4 structures in cellulo.

Direct observation of G-quadruplexes (G4s) in live cells is challenging. Here the authors report a method to identify G4s within the nuclei of live and fixed cells using a fluorescent probe combined with fluorescence lifetime imaging microscopy.

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 General Strategy to Control Viscosity Sensitivity of Molecular Rotor-Based Fluorophores

Molecular rotor-based fluorophores (RBFs) have been widely used in many fields. However, the lack of control of their viscosity sensitivity limits their application. Herein, this problem is resolved by chemically installing extended π-rich alternating carbon-carbon linkages between the rotational electron donors and acceptors of RBFs. The data reveal that the length of the linkage strongly influences the viscosity sensitivity, likely resulting from varying height of the energy barriers between the fluorescent planar and the dark twisted configurations. Three RBF derivatives that span a wide range of viscosity sensitivities were designed. These RBFs demonstrated, through a dual-color imaging strategy, that they can differentiate misfolded protein oligomers and insoluble aggregates, both in test tubes and live cells. Beyond RBFs, it is envisioned that this chemical mechanism might be generally applicable to a wide range of photoisomerizable and aggregation-induced emission fluorophores.

Michler's hydrol blue elucidates structural differences in prion strains

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.

Reduction of a disulfide-constrained oligo-glutamate peptide triggers self-assembly of β2-type amyloid fibrils with the chiroptical properties determined by supramolecular chirality

Disulfide bonds prevent aggregation of globular proteins by stabilizing the native state. However, a disulfide bond within a disordered state may accelerate amyloidogenic nucleation by navigating fluctuating polypeptide chains towards an orderly assembly of β-sheets. Here, the self-assembly behavior of Glu-Cys-(Glu)₄-Cys-Glu peptide (E₆C₂), in which an intrachain disulfide bond is engineered into an amyloidogenic homopolypeptide motif, is investigated. To this end, the Thioflavin T (ThT) fluorescence kinetic assay is combined with infrared spectroscopy, circular dichroism (CD), atomic force microscopy (AFM) and Raman scattering measurements. Regardless of whether the disulfide bond is intact or reduced, E₆C₂ monomers remain disordered within a broad range of pH. On the other hand, only reduced E₆C₂ self-assembles into amyloid fibrils with the unique infrared traits indicative of three-center hydrogen bonds involving main-chain carbonyl as a bifurcating acceptor and main-chain NH and side-chain -COOH groups as hydrogen donors: the bonding pattern observed in so-called β₂-fibrils. AFM analysis of β₂-E₆C₂ reveals tightly packed rectangular superstructures whose presence coincides with strong chiroptical properties. Our findings suggest that formation of chiral amyloid superstructures may be a generic process accessible to various substrates, and that the fully extended conformation of a poly-Glu chain is a condition sine qua non for self-assembly of β₂-fibrils.

A Comparative Photophysical Study of Structural Modifications of Thioflavin T-Inspired Fluorophores

The benzothiazolium salt, Thioflavin T (ThT), has been widely adopted as the "gold-standard" fluorescent reporter of amyloid in vitro. Its properties as a molecular rotor result in a large-scale (∼1000-fold) fluorescence turn-on upon binding to β-sheets in amyloidogenic proteins. However, the complex photophysics of ThT combined with the intricate and varied nature of the amyloid binding motif means these interactions are poorly understood. To study this important class of fluorophores, we present a detailed photophysical characterization and comparison of a novel library of 12 ThT-inspired fluorescent probes for amyloid protein (PAPs), where both the charge and donor capacity of the heterocyclic and aminobenzene components have been interrogated, respectively. This enables direct photophysical juxtaposition of two structural groups: the neutral "PAP" (class 1) and the charged "mPAP" fluorophores (class 2). We quantify binding and optical properties at both the bulk and single-aggregate levels with some derivatives showing higher aggregate affinity and brightness than ThT. Finally, we demonstrate their abilities to perform super-resolution imaging of α-synuclein fibrils with localization precisions of ∼16 nm. The properties of the derivatives provide new insights into the relationship between chemical structure and function of benzothiazole probes.

Fluorescence Lifetime and Intensity of Thioflavin T as Reporters of Different Fibrillation Stages: Insights Obtained from Fluorescence Up-Conversion and Particle Size Distribution Measurements

Thioflavin T (ThT) assay is extensively used for studying fibrillation kinetics in vitro. However, the differences in the time course of ThT fluorescence intensity and lifetime and other physical parameters of the system, such as particle size distribution, raise questions about the correct interpretation of the aggregation kinetics. In this work, we focused on the investigation of the mechanisms, which underlay the difference in sensitivity of ThT fluorescence intensity and lifetime to the formation of protein aggregates during fibrillation by the example of insulin and during binding to globular proteins. The assessment of aggregate sizes and heterogeneity was performed using dynamic light scattering (DLS) and nanoparticle tracking analysis (NTA). Using the sub-nanosecond resolution measurements, it was shown that the ThT lifetime is sensitive to the appearance of as much as a few percent of ThT bound to the high-affinity sites that occur simultaneously with an abrupt increase of the average particle size, particles concentration, and size heterogeneity. The discrepancy between ThT fluorescence intensity and a lifetime can be explained as the consequence of a ThT molecule fraction with ultrafast decay and weak fluorescence. These ThT molecules can only be detected using time-resolved fluorescence measurements in the sub-picosecond time domain. The presence of a bound ThT subpopulation with similar photophysical properties was also demonstrated for globular proteins that were attributed to non-specifically bound ThT molecules with a non-rigid microenvironment.

Multi-component peptide hydrogels - a systematic study incorporating biomolecules for the exploration of diverse, tuneable biomaterials

Peptide-based supramolecular gels can be designed to be functional "smart" materials that have applications in drug delivery, tissue engineering, and supramolecular chemistry. Although many multi-component gel systems have been designed and reported, many of these applications still rely solely on single-component gel systems which limits the functionalities of the materials. Multi-component self-assembly leads to the formation of highly ordered and complex architectures while offering the possibility to generate hydrogels with interesting properties including functional complexity and diverse morphologies. Being able to incorporate various classes of biomolecules can allow for tailoring the materials' functionalities to specific application needs. Here, a novel peptide amphiphile, myristyl-Phe-Phe (C14-FF), was synthesized and explored for hydrogel formation. The hydrogel possesses a nanofiber matrix morphology, composed of β-sheet aggregates, a record-low gelation concentration for this class of compounds, and a unique solvent-dependent helical switch. The C14-FF hydrogel was then explored with various classes of biomolecules (carbohydrates, vitamins, proteins, building blocks of HA) to generate a multi-component library of gels that have potential to represent the complex natural extracellular matrix. Selected multi-component gels exhibit an excellent compatibility with mesenchymal stem cells showing high cell viability percentages, which holds great promise for applications in regenerative therapy.

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.

Biophysical Insights into Implications of PEG-400 on the α-Crystallin Structure: Multispectroscopic and Microscopic Approach

Aggregation and precipitation of α-crystallin play a vital role in the cataract development. This study was targeted to delineate the effect of PEG-400 on the structural integrity of α-crystallin employing a multispectroscopic and microscopic approach. Intrinsic fluorescence and UV-vis spectroscopy suggested alterations in the tertiary structure of α-crystallin, namely global transition of native α-crystallin to a non-native form in the presence of PEG-400. Circular dichroism spectroscopy suggested secondary structural transition in a native conformation of α-crystallin in the presence of PEG-400. Loss in the native conformation of α-crystallin is implicated in cataract developments, thus highlighting the clinical significance of this work. Further, a significant increase in ANS fluorescence of PEG-400-incubated α-crystallin (7 days) suggested this non-native form to be molten globule (MG)-like state. Increased Thioflavin T fluorescence (ThT) and congo red (CR) absorbance along with transmission electron microscopy (TEM) confirmed the formation of the aggregates of α-crystallin after prolonged incubation with PEG-400. Insights into PEG-400-induced structural alterations can provide a platform to search for new therapeutic molecules that can combat α-crystallin-directed eye diseases.

Of Twists and Curves: Electronics, Photophysics, and Upcoming Applications of Non-Planar Conjugated Organic Molecules

Non-planar conjugated organic molecules (NPCOMs) contain π-conjugation across their length and also exhibit asymmetry in their conformation. In other words, certain molecular fragments in NPCOMs are either twisted or curved out of planarity. This conformational asymmetry in NPCOMs leads to non-uniform charge-distribution across the molecule, with important photophysical and electronic consequences such as altered thermodynamic stability, chemical reactivity, as well as materials properties. Majorly, NPCOMs can be classified as having either Fused or Rotatable architectures. NPCOMs have been the focus of significant scientific attention in the recent past due to their exciting photophysical behavior that includes intramolecular charge-transfer (ICT), thermally activated delayed fluorescence (TADF) and long-lived charge-separated states. In addition, they also have many useful materials characteristics such as biradical character, semi-conductivity, dynamic conformations, and mechanochromism. As a result, rational design of NPCOMs and mapping their structure-property correlations has become imperative. Researchers have executed conformational changes in NPCOMs through a variety of external stimuli such as pH, temperature, anions-cations, solvent, electric potential, and mechanical force in order to tailor their photophysical, optoelectronic and magnetic properties. Converging to these points, this review highlights the lucrative electronic features, photophysical traits and upcoming applications of NPCOMs by a selective survey of the recent scientific literature.

Processing Induced Changes in Food Proteins: Amyloid Formation during Boiling of Hen Egg White

Amyloid fibrils (AFs) are highly ordered protein nanofibers composed of cross β-structure that occur in nature, but that also accumulate in age-related diseases. Amyloid propensity is a generic property of proteins revealed by conditions that destabilize the native state, suggesting that food processing conditions may promote AF formation. This had only been shown for foie gras, but not in common foodstuffs. We here extracted a dense network of fibrillar proteins from commonly consumed boiled hen egg white (EW) using chemical and/or enzymatic treatments. Conversion of EW proteins into AFs during boiling was demonstrated by thioflavin T fluorescence, Congo red staining, and X-ray fiber diffraction measurements. Our data show that cooking converts approximately 1-3% of the protein in EW into AFs, suggesting that they are a common component of the human diet.

Phasor-FLIM analysis of Thioflavin T self-quenching in Concanavalin amyloid fibrils

The formation of amyloid structures has traditionally been related to human neurodegenerative pathologies and, in recent years, the interest in these highly stable nanostructures was extended to biomaterial sciences. A common method to monitor amyloid growth is the analysis of Thioflavin T fluorescence. The use of this highly selective dye, diffused worldwide, allows mechanistic studies of supramolecular assemblies also giving back important insight on the structure of these aggregates. Here we present experimental evidence of self-quenching effect of Thioflavin T in presence of amyloid fibrils. A significant reduction of fluorescence lifetime of this dye which is not related to the properties of analyzed amyloid structures is found. This result is achieved by coupling Fluorescence Lifetime Imaging Microscopy with phasor approach as suitable model-free methods and constitute a serious warning that have to be taken in account if is dye is used for quantitative studies.

ThX - a next-generation probe for the early detection of amyloid aggregates

Neurodegenerative diseases such as Alzheimer's and Parkinson's are associated with protein misfolding and aggregation. Recent studies suggest that the small, rare and heterogeneous oligomeric species, formed early on in the aggregation process, may be a source of cytotoxicity. Thioflavin T (ThT) is currently the gold-standard fluorescent probe for the study of amyloid proteins and aggregation processes. However, the poor photophysical and binding properties of ThT impairs the study of oligomers. To overcome this challenge, we have designed Thioflavin X, (ThX), a next-generation fluorescent probe which displays superior properties; including a 5-fold increase in brightness and 7-fold increase in binding affinity to amyloidogenic proteins. As an extrinsic dye, this can be used to study unique structural amyloid features both in bulk and on a single-aggregate level. Furthermore, ThX can be used as a super-resolution imaging probe in single-molecule localisation microscopy. Finally, the improved optical properties (extinction coefficient, quantum yield and brightness) of ThX can be used to monitor structural differences in oligomeric species, not observed via traditional ThT imaging.

Effect of pH on the structure and function of pyruvate dehydrogenase kinase 3: Combined spectroscopic and MD simulation studies

Pyruvate dehydrogenase kinase-3 (PDK3) plays important role in the glucose metabolism and is associated with cancer progression, and thus being considered as an attractive target for cancer therapy. In this study, we employed spectroscopic techniques to study the structural and conformational changes in the PDK3 at varying pH conditions ranging from pH 2.0 to 12.0. UV/Vis, fluorescence and circular dichroism spectroscopic measurements revealed that PDK3 maintains its native-like structure (both secondary and tertiary) in the alkaline conditions (pH 7.0-12.0). However, a significant loss in the structure was observed under acidic conditions (pH 2.0-6.0). The propensity of aggregate formation at pH 4.0 was estimated by thioflavin T fluorescence measurements. To further complement structural data, kinase activity assay was performed, and maximum activity of PDK3 was observed at pH 7.0-8.0 range; whereas, its activity was lost under acidic pH. To further see conformational changes at atomistic level we have performed all-atom molecular dynamics at different pH conditions for 150 ns. A well defined correlation was observed between experimental and computational studies. This work highlights the significance of structural dependence of pH for wide implications in protein-protein interaction, biological function and drug design procedures.

Glyoxal Induced Transition of Transferrin to Aggregates: Spectroscopic, Microscopic and Molecular Docking Insight

BACKGROUND & OBJECTIVE

The present study was aimed at characterizing the conformational alterations induced in human transferrin, the iron regulatory protein by glyoxal. Since protein aggregation is at the core of many disorders, thus interest in this domain has increased significantly during the past years.

METHODS

In our present study, the effect of glyoxal was monitored on human transferrin using multispectroscopic and multi-microscopic studies.

RESULTS

Intrinsic fluorescence spectroscopy suggested changes in native conformation of human transferrin evident by decreased fluorescence and blue shift in the presence of glyoxal. Further, extrinsic fluorescence was retorted and the results showed the formation of aggregates; apparent by increased Congo red (CR) absorbance, Thioflavin T (ThT) and ANS fluorescence and TEM of human transferrin in the presence of glyoxal. Molecular docking was also employed to see which residues are at core of human transferrin and glyoxal interaction. Reactive oxygen species (ROS) generation assays revealed enhanced ROS levels by human transferrin after treatment with glyoxal.

CONCLUSION

Thus, our study proposes that glyoxal induces the formation of aggregates in human transferrin. These aggregates further generate ROS which are key players in the complications associated with diabetes mellitus, giving our study clinical perspective.

The effect of heparan sulfate on promoting amyloid fibril formation by β-casein and their binding research with multi-spectroscopic approaches

As a molecular chaperone, β-casein is difficult to form amyloid fibrils under physiological conditions due to its chaperone activity. Heparan sulfate (HS) has drawn attention of technologists all over the word because of its relation to amyloid deposits in some amyloidosis diseases. For better understanding the relationship between the β-casein and HS, the multi-spectroscopic studies were employed. The data of thioflavin T (ThT) binding assay, transmission electron microscopy (TEM) and circular dichroism (CD) demonstrated that HS promoted fibril formation by β-casein in the amount and the growth speed. The results of steady-state UV-vis absorption spectra, fluorescence spectroscopy and fluorescence lifetime revealed that the β-casein-HS complexes were formed and HS quenched the fluorescence of β-casein by a static quenching mechanism. On the basis of fluorescence analysis, the value of binding constant was equal to 1.17 × 10⁷ L mol^-1 at 338.15 K and there was about one binding site between them. According to thermodynamic parameters obtained, it was deduced that a spontaneous reaction happened, and protein-ligand complex was stabilized by hydrogen bonds and hydrophobic interaction. Furthermore, using fluorescence resonance energy transfer (FRET) assay, the value of binding distance between HS and Trp143 of β-casein was calculated to be 0.93 nm. Finally, on the basis of synchronous fluorescence experiment, the polarity increasing and hydrophobicity decreasing around Trp143 occurred during the period of fibril formation by β-casein.

Photoinduced Reversible Modulation of Fluorescence of CdSe/ZnS Quantum Dots in Solutions with Diarylethenes

Steady-state absorption and fluorescence spectra, fluorescence decay kinetics of CdSe/ZnS quantum dots (QD) with photochromic diarylethenes (DAE) in toluene have been studied. Two kinds of QDs emitting at 525 and 600 nm were investigated and DAE were selected to ensure good overlap of their photoinduced absorption band with QDs emission spectra. It has been found that photochromic molecules form complexes with QD which results in partial fluorescence quenching. A reversible modulation of QDs emission intensity which correlates with magnitude of transient photoinduced absorption band of the diarylethenes during photochromic transformations has been demonstrated.

Solvent viscosity induces twisted intramolecular charge transfer state lifetime tunable of Thioflavin-T

Excited-state deactivation dynamics of Thioflavin-T (ThT) in gradual viscosity solvents were investigated. Femtosecond transient absorption spectra and dynamic decay curves both present significant distinction of ThT in different volume ratios binary mixtures solvents. Dynamics fitting lifetime of twisted intramolecular charge transfer (TICT) state is strongly dependent on solvents viscosity. Compared to rotation corresponding time of ThT in low viscosity solvent (0.6 cp) experimentally coincident well with Stokes-Einstein-Debye (SED) equation, the relation between rotation corresponding time and relatively high viscosity (5.9 cp to 1091.2 cp) is more consistent with fractional SED equation. Combined with optimized geometric structures of ThT by density functional theory and time-dependent density functional theory, further understand TICT state lifetime increases with increasing solvents viscosity. Our work provides a comprehensive understanding of fluorescence molecular rotor (FMR) deactivation process in different viscosity solvents and is helpful to design new FMR.

Supramolecular Self-Assembly To Control Structural and Biological Properties of Multicomponent Hydrogels

Self-assembled nanofibers are ubiquitous in nature and serve as inspiration for the design of supramolecular hydrogels. A multicomponent approach offers the possibility of enhancing the tunability and functionality of this class of materials. We report on the synergistic multicomponent self-assembly involving a peptide amphiphile (PA) and a 1,3:2,4-dibenzylidene-d-sorbitol (DBS) gelator to generate hydrogels with tunable nanoscale morphology, improved stiffness, enhanced self-healing, and stability to enzymatic degradation. Using induced circular dichroism of Thioflavin T (ThT), electron microscopy, small-angle neutron scattering, and molecular dynamics approaches, we confirm that the PA undergoes self-sorting, while the DBS gelator acts as an additive modifier for the PA nanofibers. The supramolecular interactions between the PA and DBS gelators result in improved bulk properties and cytocompatibility of the two-component hydrogels as compared to those of the single-component systems. The tunable mechanical properties, self-healing ability, resistance to proteolysis, and biocompatibility of the hydrogels suggest future opportunities for the hydrogels as scaffolds for tissue engineering and drug delivery vehicles.

Binding between G Quadruplexes at the Homodimer Interface of the Corn RNA Aptamer Strongly Activates Thioflavin T Fluorescence

Thioflavin T (ThT) is widely used for the detection of amyloids. Many unrelated DNAs and RNAs that contain G-quadruplex motifs also bind ThT and strongly activate its fluorescence. To elucidate the structural basis of ThT binding to G quadruplexes and its fluorescence turn-on, we determined its co-crystal structure with the homodimeric RNA Corn, which contains two G quadruplexes. We found that two ThT molecules bind in the dimer interface, constrained by a G quartet from each protomer into a maximally fluorescent planar conformation. The unliganded Corn homodimer crystal structure reveals a collapsed fluorophore-binding site. In solution, Corn must fluctuate between this and an open, binding-competent conformation. A co-crystal structure with another benzothiazole derivate, thiazole orange (TO), also shows binding at the Corn homodimer interface. As the bound ThT and TO make no interactions with the RNA backbone, their Corn co-crystal structures likely explain their fluorescence activation upon sequence-independent DNA and RNA G-quadruplex binding.

Green Fluorescent Protein Nanovessel Serves as a Nucleolus Targeting Material and Molecule Carrier in Living Cells

The nucleolus is responsible for RNA transcription, processing, and ribosome assembly, the dysfunction of which is associated with a number of diseases. In this report, a new member of fluorescent protein nanovessels (FPNs), constructed using thioflavin-T (ThT) and bovine serum albumin (BSA) as building blocks, is described. As a popular amyloid specific dye, ThT is nonfluorescent by itself, while its fluorescence can be lighted up upon interacting with amyloid proteins. Herein, ThT is coassembled with the BSA scaffold at high temperature to form T(hT)-FPNs. These green fluorescence emissive bio-abiotic hybrid materials can serve as a novel probe for real-time nucleolus imaging of living cells. Besides, T-FPNs show potential in delivering insoluble and/or impenetrable drugs into living cells, suggesting another role as a molecule carrier.

Controlling the Assembly and Properties of Low-Molecular-Weight Hydrogelators

Low-molecular-weight gels are formed by the self-assembly of small molecules into fibrous networks that can immobilize a significant amount of solvent. Here, we focus on our work with a specific class of gelator, the functionalized dipeptide. We discuss the current state of the art in the area, focusing on how these materials can be controlled. We also highlight interesting and unusual observations and unanswered questions in the field.

The role of liquid-liquid phase separation in aggregation of the TDP-43 low-complexity domain

Pathological aggregation of the transactive response DNA-binding protein of 43 kDa (TDP-43) is associated with several neurodegenerative disorders, including ALS, frontotemporal dementia, chronic traumatic encephalopathy, and Alzheimer's disease. TDP-43 aggregation appears to be largely driven by its low-complexity domain (LCD), which also has a high propensity to undergo liquid-liquid phase separation (LLPS). However, the mechanism of TDP-43 LCD pathological aggregation and, most importantly, the relationship between the aggregation process and LLPS remains largely unknown. Here, we show that amyloid formation by the LCD is controlled by electrostatic repulsion. We also demonstrate that the liquid droplet environment strongly accelerates LCD fibrillation and that its aggregation under LLPS conditions involves several distinct events, culminating in rapid assembly of fibrillar aggregates that emanate from within mature liquid droplets. These combined results strongly suggest that LLPS may play a major role in pathological TDP-43 aggregation, contributing to pathogenesis in neurodegenerative diseases.

Effect of Substituents on TICT Rate in Thioflavin T-Based Fluorescent Molecular Rotors

New fluorescent molecular rotors (FMRs) were developed by modification of the Thioflavin T (ThT) structure via introduction of methyl and methoxy groups. Effects of the substituents on fluorescence properties and twisted intramolecular charge transfer (TICT) rate in the excited state of the molecules were studied using steady-state fluorescence and time-resolved absorption spectroscopy. Quantum chemical calculations of the molecules in the ground and excited states were carried out to aid interpretation of the experimental results. Only cationic forms of ThT derivatives have FMR properties and exhibit viscosity-dependent fluorescence. The TICT rate was found to be affected by the size of the molecular fragments, which experience mutual rotation, dihedral angle [Formula: see text] between the fragments in the ground state as well as their donor/acceptor properties.

Harnessing Intramolecular Rotation To Enhance Two-photon Imaging of Aβ Plaques through Minimizing Background Fluorescence

The aggregation of amyloid beta (Aβ) proteins in senile plaques is a critical event during the development of Alzheimer's disease, and the postmortem detection of Aβ-rich proteinaceous deposits through fluorescent staining remains one of the most robust diagnostic tools. In animal models, fluorescence imaging can be employed to follow the progression of the disease, and among the different imaging methods, two-photon microscopy (TPM) has emerged as one of the most powerful. To date, several near-infrared-emissive two-photon dyes with a high affinity for Aβ fibrils have been developed, but there has often been a tradeoff between excellent two-photon cross-sections and large fluorescence signal-to-background ratios. In the current work, we introduced a twisted intramolecular charge state (TICT)-based de-excitation pathway, which results in a remarkable fluorescence increase of around 167-fold in the presence of Aβ fibrils, while maintaining an excellent two-photon cross section, thereby enabling high-contrast ex vivo and in vivo TPM imaging. Overall, the results suggest that adopting TICT de-excitation in two-photon fluorophores may represent a general method to overcome the tradeoff between probe brightness and signal-to-background ratio.

Stabilizing proteins to prevent conformational changes required for amyloid fibril formation

Amyloid fibrillation is associated with several human maladies, such as Alzheimer's, Parkinson's, Huntington's diseases, prions, amyotrophic lateral sclerosis, and type 2 diabetes diseases. Gaining insights into the mechanism of amyloid fibril formation and exploring novel approaches to fibrillation inhibition are crucial for preventing amyloid diseases. Here, we hypothesized that ligands capable of stabilizing the native state of query proteins might prevent protein unfolding, which, in turn, may reduce the propensity of proteins to form amyloid fibrils. We demonstrated the efficient inhibition of amyloid formation of the human serum albumin (HSA) (up to 85%) and human insulin (up to 80%) by a nonsteroidal anti-inflammatory drug, ibuprofen (IBFN). IBFN significantly increases the conformational stability of both HSA and insulin, as confirmed by differential scanning calorimetry (DSC). Moreover, increasing concentration of IBFN boosts its amyloid inhibitory propensity in a linear fashion by influencing the nucleation phase as assayed by thioflavin T fluorescence, transmission electron microscopy, and dynamic light scattering. Furthermore, circular dichroism analysis supported the DSC results, showing that IBFN binds to the native state of proteins and almost completely prevents their tendency to lose secondary and tertiary structures. Cell toxicity assay confirms that species formed in the presence of IBFN are less toxic to neuronal cells (SH-SY5Y). These results demonstrate the feasibility of using a small molecule to stabilize the native state of proteins, thereby preventing the amyloidogenic conformational changes, which appear to be the common link in several human amyloid diseases.