Rapid Filament Supramolecular Chirality Reversal of HET-s (218-289) Prion Fibrils Driven by pH Elevation

Vibrational circular dichroism beyond solutions

Since the first vibrational circular dichroism (VCD) experiments conducted in the early 1970s, VCD spectroscopy has significantly advanced and firmly established itself in various fields of modern science and technology. For example, it became one of the preferred methods for absolute configuration determination in the pharmaceutical industry. Nevertheless, VCD development and applications have mostly focused on samples in solution, whereas applications to solid-state samples remain relatively rare. Although the first solid-state experiments were performed around the time of VCD discovery, they did not become the mainstream due to considerably more demanding methodological and theoretical challenges. In this review, we take the reader on a journey through some of the applications of VCD spectroscopy to solid-state samples. We look at the field of solid-state VCD from both a historical perspective and a methodological point of view, highlighting the diverse directions explored with this technique. We attempt to categorize all the variety of solid-state VCD experiments undertaken to date. Additionally, we briefly outline the main challenges faced by the field, and provide an overview of the theoretical methodology accompanying the experimental developments. Finally, we conclude our solid-state VCD journey with an outlook on the future prospects of the field.

Structural Insights Into Amyloid Polymorphism: The Impact of Glutamine to Norleucine Substitutions in GNNQQNY Aggregation

Polypeptides can self-assemble into highly organized amyloid structures through complex and poorly understood mechanisms. To better understand the key parameters governing amyloidogenesis, we investigated the aggregation of the Sup35 prion-derived GNNQQNY sequence alongside two rationally designed mutants, glutamine to norleucine in the 4th or 5th position, where selective removal of hydrogen bonding capacity reduces amyloid structural stability. Our findings reveal that β-sheet arrays form rapidly as an initial step, followed by π-π aromatic interactions between Tyr residues, which drive hierarchical self-assembly into 3D fibrillar structures via hydrophobic zippers and partial water exclusion. As the oligomers grow, they also acquire twist and chirality at the protofilament level, with Tyr ladders serving as key interaction surfaces that dictate the final amyloid architecture. These ladders guide protofibrils to assemble into either oppositely twisted chiral fibers or achiral nanocrystals, contributing to amyloid polymorphism. The emergence of distinct polymorphs is influenced by multiple factors, including fibril twisting, side-chain interactions, solvent exclusion, and local microenvironmental conditions. Our study provides crucial insights into the hierarchical nature of amyloid self-assembly and highlights the structural adaptability of amyloid fibrils, which is essential for designing functional amyloids and understanding the pathogenicity of disease-associated aggregates.

Environmental sensitivity of amyloidogenic motifs in fungal NOD-like receptor-mediated immunity: Molecular and structural insights into amyloid assembly

This study investigates the aggregation behavior of amyloidogenic motifs associated with fungal NOD-like receptor (NLR) proteins, focusing on their sensitivity to various environmental conditions. We aimed to develop a minimal model that explains amyloid aggregation, aligning with in vivo observations and the expected role of these motifs in amyloid-based signaling. The purpose was to understand how changes in physicochemical conditions influence amyloid formation, which is crucial for fungal immune responses and has potential applications in controlling fungal infections. To achieve this, two amyloidogenic motifs, PUASM_N and PUASM_C, derived from the fungus Colletotrichum gloeosporioides, were synthesized and subjected to different conditions that simulate their natural environment. These conditions included varying pH levels, peptide concentrations, and surface adsorption properties. The aggregation kinetics, morphology, and secondary structures of the peptides were analyzed using Thioflavin T (ThT) fluorescence assay, transmission electron microscopy (TEM), and Fourier transform infrared micro-spectroscopy (micro-FTIR). The results showed that PUASM_N aggregates rapidly without a lag phase, forming long, structured fibers. In contrast, PUASM_C aggregates more slowly, with a significant lag phase, forming shorter, irregular fibers. The aggregation of PUASM_C was highly sensitive to environmental factors, such as alkaline pH and surface hydrophobicity, which accelerated its aggregation. PUASM_N, however, displayed consistent aggregation behavior under different conditions. Our findings suggest that minor environmental changes can modulate the functional roles of PUASM peptides, potentially aiding Colletotrichum gloeosporioides in regulating its antipathogenic activity in response to environmental challenges.

The Phenomenon of Vibrational Circular Dichroism Enhancement: A Systematic Survey of Literature Data

While the intensity of vibrational circular dichroism (VCD) signals is commonly 104-105 times smaller than that of corresponding IR signals, several kinds of systems display enhanced VCD spectra with g-values (VCD/IR intensity ratio) above 10-3 and even reaching 5 × 10-2 in some exceptional cases. These systems include transition metal and lanthanide complexes, protein and peptide fibrils, short oligopeptide gels, crystalline compounds, gels and solution aggregates of organic compounds. We review the literature on VCD enhancement, focusing on collecting and analyzing data on enhanced g-values. Special attention is given to the mechanisms proposed to produce these effects.

Under Heparin-Free Conditions Unsaturated Phospholipids Inhibit the Aggregation of 1N4R and 2N4R Tau

A progressive aggregation of Tau proteins in the brain is linked to both Alzheimer's disease (AD) and various Tauopathies. This pathological process can be enhanced by several substances, including heparin. However, very little if anything is known about molecules that can inhibit the aggregation of Tau isoforms. In this study, we examined the effect of phosphatidylserines (PSs) with various lengths and saturations of fatty acids (FAs) on the aggregation properties of Tau isoforms with one (1N4R) and two (2N4R) N-terminal inserts that enhance binding of Tau to tubulin. We found that PS with unsaturated and short-length FAs inhibited Tau aggregation and drastically lowered the toxicity of Tau oligomers that were formed in the presence of such phospholipids. Such an effect was not observed for PS with fully saturated long-chain FAs. These results suggest that a short-chain irreversible disbalance between saturated and unsaturated lipids in the brain could be the trigger of Tau aggregation.

Vibrational Optical Activity of Amyloid Fibrils

Amyloid fibrils are supramolecular systems showing distinct chirality at different levels of their complex multilayered architectures. Due to the regular long-range chiral organization, amyloid fibrils exhibit the most intense Vibrational Optical Activity (VOA) signal observed up to now, making VOA techniques: Vibrational Circular Dichroism (VCD) and Raman Optical Activity (ROA) very promising tools to explore their structures, handedness and intricate polymorphism. This concept article reviews up-to-date experimental studies on VOA applications to investigate amyloid fibrils highlighting its future potential in analyzing of these unique supramolecular systems, in particular in the context of biomedicine and nanotechnology.

Tubulin-binding region alters tau-lipid interactions and changes toxicity of tau fibrils formed in the presence of phosphatidylserine lipids

Alzheimer's disease is the fastest-growing neurodegenerative disease that affects over six million Americans. The abnormal aggregation of amyloid β peptide and Tau protein is the expected molecular cause of the loss of neurons in brains of AD patients. A growing body of evidence indicates that lipids can alter the aggregation rate of amyloid β peptide and modify the toxicity of amyloid β aggregates. However, the role of lipids in Tau aggregation remains unclear. In this study, we utilized a set of biophysical methods to determine the extent to which phospatidylserine (PS) altered the aggregation properties of Tau isoforms with one (1N4R) and two (2N4R) N terminal inserts that enhance the binding of Tau to tubulin. We found that the length and saturation of fatty acids (FAs) in PS altered the aggregation rate of 2N4R isoform, while no changes in the aggregation rate of 1N4R were observed. These results indicate that N terminal inserts play an important role in protein-lipid interactions. We also found that PS could change the toxicity of 1N4R and 2N4R Tau fibrils, as well as alter molecular mechanisms by which these aggregates exert cytotoxicity to neurons. Finally, we found that although Tau fibrils formed in the presence and absence of PS endocytosed by cells, only fibril species that were formed in the presence of PS exert strong impairment of the cell mitochondria.

SERS probing of fungal HET-s fibrils formed at neutral and acidic pH conditions

Advances in precision medical diagnostics require accurate and sensitive characterization of pathogens. In particular, health conditions associated with protein misfolding require an identification of proteinaceous amyloid fibrils or their precursors. These pathogenic entities express specific molecular structures, which require ultra-sensitive, molecular-level detection methods. A potentially transformative technique termed nanoplasmonics employs electro-optical phenomena in the vicinity of specially engineered metal nanostructures. A signature application of nanoplasmonics exploits enhancement of inelastic scattering of light in specific locations near metallic nanostructures, known as surface-enhanced Raman scattering (SERS). We applied SERS complemented with confocal microscopy imaging for ultra-sensitive, non-invasive, and label-free characterization of the fungal prion HET-s (218-289) as a model for β-sheet rich amyloid structures. This characterization employed Au-coated dielectric supports as plasmonic substrates. After confirming the formation of HET-s fibrils at both pH 7.5 and 2.8 using negative staining transmission electron microscopy, we subjected the fibril-containing solutions to multimodal analysis using confocal microscopy and SERS. The SERS spectral fingerprints from all HET-s samples expressed vibrational markers for β-structure, unstructured backbone, and aromatic side-chains. However, relative intensities of major SERS bands were pronouncedly different for the two pH levels. We have analyzed potential origins of the most pronounced SERS bands and proposed hypothetical mechanistic models that could explain the observed SERS fingerprints from HET-s fibrils grown at pH 7.5 and 2.8.

Uncovering supramolecular chirality codes for the design of tunable biomaterials

In neurodegenerative diseases, polymorphism and supramolecular assembly of β-sheet amyloids are implicated in many different etiologies and may adopt either a left- or right-handed supramolecular chirality. Yet, the underlying principles of how sequence regulates supramolecular chirality remains unknown. Here, we characterize the sequence specificity of the central core of amyloid-β 42 and design derivatives which enable chirality inversion at biologically relevant temperatures. We further find that C-terminal modifications can tune the energy barrier of a left-to-right chiral inversion. Leveraging this design principle, we demonstrate how temperature-triggered chiral inversion of peptides hosting therapeutic payloads modulates the dosed release of an anticancer drug. These results suggest a generalizable approach for fine-tuning supramolecular chirality that can be applied in developing treatments to regulate amyloid morphology in neurodegeneration as well as in other disease states.

Lipids reverse supramolecular chirality and reduce toxicity of amyloid fibrils

Abrupt aggregation of misfolded proteins is a hallmark of many medical pathologies including diabetes type 2, Alzheimer and Parkinson diseases. This results in the formation of amyloid fibrils, protein aggregates with distinct supramolecular chirality. A growing body of evidence suggests that lipids can alter rates of protein aggregation. In this study, we investigated whether lipids could alter the supramolecular chirality of amyloid fibrils. We found that if present at the stage of protein aggregation, phospho- and sphingolipids uniquely reversed supramolecular chirality of insulin and lysozyme fibrils. Furthermore, amyloid fibrils with opposite supramolecular chirality exerted distinctly different cell toxicity. Specifically, insulin and lysozyme fibrils with reversed supramolecular chirality were less toxic to cells than the aggregates with normal supramolecular chirality. These findings point on the important role of lipids and supramolecular chirality of amyloid fibrils in the onset and progression of amyloid diseases.

Spontaneous Refolding of Amyloid Fibrils from One Polymorph to Another Caused by Changes in Environmental Hydrophobicity

Here, we report a new phenomenon in which lysozyme fibrils formed in a solution of acetic acid spontaneously refold to a different polymorph through a disassembled intermediate upon the removal of acetic acid. The structural changes were revealed and characterized by deep-UV resonance Raman spectroscopy, nonresonance Raman spectroscopy, intrinsic tryptophan fluorescence spectroscopy, and atomic force microscopy. A PPII-like structure with highly solvent-exposed tryptophan residues predominates the intermediate aggregates before refolding to polymorph II fibrils. Furthermore, the disulfide (SS) bonds undergo significant rearrangements upon the removal of acetic acid from the lysozyme fibril environment. The main SS bond conformation changes from gauche-gauche-trans in polymorph I to gauche-gauche-gauche in polymorph II. Changing the hydrophobicity of the fibril environment was concluded to be the decisive factor causing the spontaneous refolding of lysozyme fibrils from one polymorph to another upon the removal of acetic acid. Potential biological implications of the discovered phenomenon are discussed.

Dynamic Modulation of Supramolecular Chirality Driven by Factors from Internal to External Levels

Supramolecular chirality, generated by the asymmetric assembly of chiral or achiral molecules, has attracted intense study owing to its potential to offer insights into natural biological structures and its crucial roles in advanced materials. The optical activity and stacking pathway of building molecules both greatly determine the chirality of the whole supramolecular structure. The flexibility of supramolecular structures makes their chirality easy to modulate through abundant means. Adjustment of the molecular structure or packing mode, or external stimuli that act like a finger gently pushing toy bricks, can greatly change the chirality of supramolecular assemblies. The dynamic regulation of chiral nanostructures on the intramolecular, intermolecular, and external levels could be regarded as the modulatory essence in numerous strategies, however, this perspective is ignored in most reviews in the literature. Herein, therefore, we focus on the ingenious dynamic modulation of chiral nanostructures by these factors. Through dynamic modulation with changes in chiroptical spectroscopy and electron microscopy, the mechanism of formation of supramolecular chirality is also elaborated.

Vibrational Circular Dichroism Reveals Supramolecular Chirality Inversion of α-Synuclein Peptide Assemblies upon Interactions with Anionic Membranes

Parkinson's disease is an incurable neurodegenerative disorder caused by the aggregation of α-synuclein (AS). This amyloid protein contains a 12-residue-long segment, AS_71-82, that triggers AS pathological aggregation. This peptide is then essential to better understand the polymorphism and the dynamics of formation of AS fibrillar structures. In this work, vibrational circular dichroism showed that AS_71-82 is random coil in solution and forms parallel β-sheet fibrillar aggregates in the presence of anionic vesicles. Vibrational circular dichroism, with transmission electronic microscopy, revealed that the fibrillar structures exhibit a nanoscale tape-like morphology with a preferential supramolecular helicity. Whereas the structure handedness of some other amyloid peptides has been shown to be driven by pH, that of AS_71-82 is controlled by peptide concentration and peptide-to-lipid (P:L) molar ratio. At low concentrations and low P:L molar ratios, AS_71-82 assemblies have a left-twisted handedness, whereas at high concentrations and high P:L ratios, a right-twisted handedness is adopted. Left-twisted assemblies interconvert into right-twisted ones with time, suggesting a maturation of the amyloid structures. As fibril species with two chiralities have also been reported previously in Parkinson's disease Lewy bodies and fibrils, the present results seem relevant to better understand AS amyloid assembly and fibrillization in vivo. From a diagnosis or therapeutic point of view, it becomes essential that future fibril probes, inhibitors, or breakers target pathological assemblies with specific chirality and morphology, in particular, because they may change with the stage of the disease.

Understanding amyloid fibril formation using protein fragments: structural investigations via vibrational spectroscopy and solid-state NMR

It is well established that amyloid proteins play a primary role in neurodegenerative diseases. Alzheimer's, Parkinson's, type II diabetes, and Creutzfeldt-Jakob's diseases are part of a wider family encompassing more than 50 human pathologies related to aggregation of proteins. Although this field of research is thoroughly investigated, several aspects of fibrillization remain misunderstood, which in turn slows down, or even impedes, advances in treating and curing amyloidoses. To solve this problem, several research groups have chosen to focus on short fragments of amyloid proteins, sequences that have been found to be of great importance for the amyloid formation process. Studying short peptides allows bypassing the complexity of working with full-length proteins and may provide important information relative to critical segments of amyloid proteins. To this end, efficient biophysical tools are required. In this review, we focus on two essential types of spectroscopic techniques, i.e., vibrational spectroscopy and its derivatives (conventional Raman scattering, deep-UV resonance Raman (DUVRR), Raman optical activity (ROA), surface-enhanced Raman spectroscopy (SERS), tip-enhanced Raman spectroscopy (TERS), infrared (IR) absorption spectroscopy, vibrational circular dichroism (VCD)) and solid-state nuclear magnetic resonance (ssNMR). These techniques revealed powerful to provide a better atomic and molecular comprehension of the amyloidogenic process and fibril structure. This review aims at underlining the information that these techniques can provide and at highlighting their strengths and weaknesses when studying amyloid fragments. Meaningful examples from the literature are provided for each technique, and their complementarity is stressed for the kinetic and structural characterization of amyloid fibril formation.

Ultraviolet Resonance Raman Spectroscopic Markers for Protein Structure and Dynamics

UV resonance Raman (UVRR) spectroscopy is a powerful tool for investigating the structure of biological molecules, such as proteins. Numerous UVRR spectroscopic markers that provide information on the structure and environment of the protein backbone and of amino acid side chains have recently been discovered. Combining these UVRR markers with hydrogen-deuterium exchange and advanced statistics is a powerful tool for studying protein systems, including the structure and formation mechanism of protein aggregates and amyloid fibrils. These techniques allow crucial new insights into the structure and dynamics of proteins, such as polyglutamine peptides, which are associated with 10 different neurodegenerative diseases. Here we summarize the spectroscopic structural markers recently developed and the important insights they provide.

Advances of Vibrational Circular Dichroism (VCD) in bioanalytical chemistry. A review

Vibrational Circular Dichroism (VCD) is a unique and relatively new spectroscopic technique that is capable of determining an absolute configuration of chiral molecules. VCD can be also used to determine structure of large macromolecules. This review highlights the most recent advances of VCD in bioanalytical chemistry. It shows that VCD is capable of unraveling supramolecular organization of peptides, proteins, saccharides, glycerophospholipids, polypeptide microcrystals, as well as amyloid fibrils and DNA. This review also demonstrates how VCD can be utilized to explore molecule-molecule interactions that determine mechanisms of chiral separations in chromatography. It aims to attract attention of scientists from all different research areas demonstrating the strength and capability of this very powerful spectroscopic technique.

Chiral Supramolecular Gels with Lanthanide Ions: Correlation between Luminescence and Helical Pitch

We report the correlation between the fluorescence intensity and the helical pitch of supramolecular hydrogels with Tb(III) and Eu(III) as well as their inkjet printing patterning as an application. The luminescent gels, which exhibited three different emissions of red, green, and blue, could be prepared without and with Eu(III) and Tb(III). The luminescence intensity of supramolecular gels (gel-Tb and gel-Eu) composed of Tb(III) and Eu(III) was ca. 3-fold larger than that of the sol (1+Tb(III) or 1+Eu(III)), which was attributed to large tilting angles between molecules. By AFM observations, these gels showed well-defined right-handed helical nanofibers formed by coordination bonds in which the helical pitch lengths were strongly dependent on the concentrations of lanthanide ions. In particular, the large luminescence intensity of gel-Tb exhibited a smaller helical pitch length than that of gel-1 due to relatively weak π-π stacking with large tilting angles between molecules. The luminescence intensities were enhanced linearly with increasing concentrations of lanthanide ions. This is the first example of the correlation between the helical pitch length and the luminescence intensity of supramolecular materials. The coordination bonding in supramolecular hydrogels had a strong influence on rheological properties. We also developed a water-compatible inkjet printing system to generate luminescent supramolecular gels on A4-sized paper. The images of a logo and the text were composed of three different emissions and were well-printed on A4 sized paper coated with gel-1.