Modulation of Surface-Catalyzed Secondary Nucleation during Amyloid Fibrillation of Hen Egg White Lysozyme by Two Common Surfactants

Investigation of self-assembly mechanism of gluten protein amyloid fibrils and molecular characterization of structure units

The mechanism of peptides self-assembly into gluten amyloid fibrils was explored through bond-breaking experiments and molecular dynamics (MD) simulations, verified through fibrillation experiments using synthetic peptides. The disruption of hydrogen bonds reduced thioflavin T fluorescence intensity and average particle size of gluten amyloid fibrils by 24 % and 81 %, respectively, causing a breakdown of internal structure. Disruption of electrostatic and hydrophobic forces induced further aggregation of fibrils. MD simulation revealed that peptides transitioned from a dispersed state to aggregation, followed by changes in secondary structure, culminating in the formation of stacked β-sheets structure units. Hydrogen bonding emerged as the primary driver of self-assembly with contributions from hydrophobic and electrostatic interactions. The synthetic single or hybrid peptide systems selected by MD formed ribbon- or fiber-like amyloid fibrils with inter-strand distance of 4.7 Å and respective inter-sheet distances of 10.2 Å and 10.8 Å, suggesting that the structure and morphology of eventual amyloid fibrils were affected by the peptide sequence and cross β-sheet structure units.

Protease-Mediated Synthesis of Zein Nanofibrils: From Structural Elucidation to Functional Application

The fibrillization of plant-based proteins enhances their functionality, enabling potential applications in food and sustainable materials. Zein, a highly hydrophobic protein from corn, is a versatile industrial ingredient, but its functionality is limited to environments containing high levels of organic solvents. This study aims to develop a protease-assisted approach for synthesizing zein nanofibrils as functional building blocks, eliminating the need for organic solvents in the conventional process. Through proteomics, microscopy, and spectroscopy, the bioprocess and structural features of these novel nanofibrils are characterized. The results reveal that over 50% of α-zein sequence is prone to fibrillization, with pepsin demonstrating a clear advantage in efficiently releasing fibrillization-prone peptide segments (bioconversion > 70%) and producing a peptide mixture suitable for self-assembly. The fibrillization process is significantly enhanced by increasing peptide concentration and adding the anionic surfactant sodium dodecyl sulfate, which can lead to the formation of semiflexible fibrils with amyloid-like β-sheet structures. These nanofibrils outperformed native zein as emulsifiers in high internal phase emulsions and are able to form fibrous hydrogels. The protease-assisted fibrillization process achieved in this study provides an effective solution for expanding applications of zein or corn proteins in a purely aqueous environment.

Mechanistic Insight into the Amyloid Fibrillation Inhibition of Hen Egg White Lysozyme by Three Different Bile Acids

Amyloid aggregation of protein is linked to many neurodegenerative diseases. Identification of small molecules capable of targeting amyloidogenic proteins has gained significant importance. Introduction of hydrophobic and hydrogen bonding interactions through site-specific binding of small molecular ligand to protein can effectively modulate the protein aggregation pathway. Here, we investigate the possible roles of three different bile acids, cholic acid (CA), taurocholic acid (TCA), and lithocholic acid (LCA) with varying hydrophobic and hydrogen bonding properties in inhibiting protein fibrillation. Bile acids are an important class of steroid compounds that are synthesized in the liver from cholesterol. Increasing evidence suggests that altered taurine transport, cholesterol metabolism, and bile acid synthesis have strong implications in Alzheimer's disease. We find that the hydrophilic bile acids, CA and TCA (taurine conjugated form of CA), are substantially more efficient inhibitors of lysozyme fibrillation than the most hydrophobic secondary bile acid LCA. Although LCA binds more strongly with the protein and masks the Trp residues more prominently through hydrophobic interactions, the lesser extent of hydrogen bonding interactions at the active site has made LCA a relatively weaker inhibitor of HEWL aggregation than CA and TCA. The introduction of a greater number of hydrogen bonding channels by CA and TCA with several key amino acid residues which are prone to form oligomers and fibrils has weakened the protein's internal hydrogen bonding capabilities for undergoing amyloid aggregation.

Roles of Tryptophan and Charged Residues on the Polymorphisms of Amyloids Formed by K-Peptides of Hen Egg White Lysozyme Investigated through Molecular Dynamics Simulations

Atomistic molecular dynamics simulations of amyloid models, consisting of the previously reported STDY-K-peptides and K-peptides from the hen egg white lysozyme (HEWL), were performed to address the effects of charged residues and pH observed in an in vitro study. Simulation results showed that amyloid models with antiparallel configurations possessed greater stability and compactness than those with parallel configurations. Then, peptide chain stretching and ordering were measured through the end-to-end distance and the order parameter, for which the amyloid models consisting of K-peptides and the STDY-K-peptides at pH 2 displayed a higher level of chain stretching and ordering. After that, the molecular mechanics energy decomposition and the radial distribution function (RDF) clearly displayed the importance of Trp62 to the K-peptide and the STDY-K-peptide models at pH 2. Moreover, the results also displayed how the negatively charged Asp52 disrupted the interaction networks and prevented the amyloid formation from STDY-K-peptide at pH 7. Finally, this study provided an insight into the interplay between pH conditions and molecular interactions underlying the formation of amyloid fibrils from short peptides contained within the HEWL. This served as a basis of understanding towards the design of other amyloids for biomaterial applications.

An amphiphilic small molecule drives insulin aggregation inhibition and amyloid disintegration

The aggregation of proteins into ordered fibrillar structures called amyloids, and their disintegration represent major unsolved problems that limit the therapeutic applications of several proteins. For example, insulin, commonly used for the treatment of diabetes, is susceptible to amyloid formation upon exposure to non-physiological conditions, resulting in a loss of its biological activity. Here, we report a novel amphiphilic molecule called PAD-S, which acts as a chemical chaperone and completely inhibits fibrillation of insulin and its biosimilars. Mechanistic investigations and molecular docking lead to the conclusion that PAD-S binds to key hydrophobic regions of native insulin, thereby preventing its self-assembly. PAD-S treated insulin was biologically active as indicated by its ability to phosphorylate Akt, a protein in the insulin signalling pathway. PAD-S is non-toxic and protects cells from insulin amyloid induced cytotoxicity. The high aqueous solubility and easy synthetic accessibility of PAD-S facilitates its potential use in commercial insulin formulations. Notably, PAD-S successfully disintegrated preformed insulin fibrils to non-toxic smaller fragments. Since the structural and mechanistic features of amyloids are common to several human pathologies, the understanding of the amyloid disaggregation activity of PAD-S will inform the development of small molecule disaggregators for other amyloids.

Lysozyme amyloid fibril: Regulation, application, hazard analysis, and future perspectives

Self-assembly of misfolded proteins into ordered fibrillar aggregates known as amyloid results in various human diseases. However, more and more proteins, whether in human body or in food, have been found to be able to form amyloid fibrils with in-depth researches. As a model protein for amyloid research, lysozyme has always been the focus of research in various fields. Firstly, the formation mechanisms of amyloid fibrils are discussed concisely. Researches on the regulation of lysozyme amyloid fibrils are helpful to find suitable therapeutic drugs and unfriendly substances. And this review article summarizes a number of exogenous substances including small molecules, nanoparticles, macromolecules, and polymers. Small molecules are mainly connected to lysozyme through hydrophobic interaction, electrostatic interaction, π-π interaction, van der Waals force and hydrogen bond. Nanoparticles inhibit the formation of amyloid fibers by stabilizing lysozyme and fixing β-sheet. Besides, the applications of lysozyme amyloid fibrils in food-related fields are considered furtherly due to outstanding physical and mechanical properties. Nevertheless, the potential health threats are still worthy of our attention. Finally, we also give suggestions and opinions on the future research direction of lysozyme amyloid fibrils.

SDS modulates amyloid fibril formation and conformational change in succinyl-ConA at low pH

The anionic surfactant sodium dodecyl sulfate (SDS) is homologous to the cellular membrane lipids, and is known to stimulate amyloid fibrillation in several proteins. However, the mechanism by which SDS influences aggregation and structural changes in succinylated protein has not been determined. In this study, we observed the effects of variable SDS concentrations on succinyl-ConA aggregation at pH 3.5 and proposed a possible mechanism of SDS-induced succinyl-ConA aggregation. We used several biophysical techniques to identify the changes caused by SDS. Our results suggest that SDS stimulates succinyl-ConA aggregation in a concentration-dependent manner. From turbidity measurements, it was evident that a very low concentration (<0.1 mM) of SDS did not induce succinyl-ConA aggregation and proteins remained soluble. However, aggregations were observed at 0.1-2.5 mM SDS, which then dissipated at SDS concentrations above 2.5 mM. Far-UV CD results suggest that the β-sheet secondary structure of succinyl-ConA transformed into the cross-β-sheet structure in the presence of aggregating SDS concentrations. Notably, at SDS concentrations above 2.5 mM, the succinyl-ConA β-sheet transformed into an α-helical structure. The SDS-induced succinyl-ConA amyloid-like aggregates were confirmed by transmission electron microscopy (TEM). We propose that SDS modulates amyloid fibrillation in succinyl-ConA due to electrostatic and hydrophobic interactions and succinylation affects SDS-induced succinyl-ConA aggregation.

Investigation on the effect of three isoflavones on the fibrillation of hen egg-white lysozyme

In this paper, the effects of three isoflavones including daidzein, genistein, and puerarin on fibrillation of hen egg-white lysozyme were investigated by various analytical methods. The results demonstrated that all isoflavones could effectively inhibit the fibrillogenesis of hen egg-white lysozyme and destabilized the preformed fibrils of hen egg-white lysozyme in a dose-dependent manner. To further understand the inhibition mechanism, molecular modeling was carried out. The docking results demonstrated that the isoflavones could bind to two key fibrogenic sites in hen egg-white lysozyme through van der Waals force, electrostatic forces, and hydrogen bonding, as well as σ-π stacking. By these means, isoflavones could not only obviously enhance the hydrophobicity of the binding sites, but also greatly stabilize the native state of HEWL, which was able to postpone the fibrosis process of hen egg-white lysozyme.

The distinct binding modes of pesticides affect the phase transitions of lysozyme

Studying the aggregation and nucleation of proteins in the presence of organic molecules is helpful for disclosing the mechanisms of protein crystallization.

Cationic gemini surfactant stimulates amyloid fibril formation in bovine liver catalase at physiological pH. A biophysical study

Surfactant molecules stimulate amyloid fibrillation and conformational switching in proteins but the mechanisms by which they accomplish these effects are unclear. A cationic gemini surfactant, C₁₆C₄C₁₆Br₂, with two positively charged heads and two-16C hydrophobic tails induces the amyloid fibrillation of bovine liver catalase (BLC) in vitro at physiological pH. The BLC transformed into amyloid aggregates in the presence of low concentrations (2–150 μM) of C₁₆C₄C₁₆Br₂ at pH 7.4, as confirmed by the use of several biophysical techniques (Rayleigh light scattering (RLS), intrinsic fluorescence, thioflavin T fluorescence (ThT), far-UV circular dichroism, and transmission electron microscopy). The secondary structure of BLC also changed according to the concentration of C₁₆C₄C₁₆Br₂: the α-helical structure of BLC decreased in the presence of 2–100 μM of C₁₆C₄C₁₆Br₂ but at concentrations above 200 μM BLC regained a α-helical structure very similar to the native BLC. In silico molecular docking between BLC and C₁₆C₄C₁₆Br₂ suggest that the positively charged heads of the surfactant interact with Asp127 through attractive electrostatic interactions. Moreover, a Pi-cation electrostatic interaction and hydrophobic interactions also take place between the tails of the surfactant and BLC. The stability of the BLC–C₁₆C₄C₁₆Br₂ complex was confirmed by performing a molecular dynamics simulation and evaluating parameters such as root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (R_g), and solvent accessible surface area (SASA). Apart from its aggregation inducing properties, the gemini surfactant itself causes toxicity to the cancerous cell (A549): which is confirmed by MTT assay. This work delivers new insight into the effect of cationic gemini surfactants in amyloid aggregation and paves the way to the rational design of new anti-amyloidogenic agents.

Surfactant molecules stimulate amyloid fibrillation and conformational switching in proteins but the mechanisms by which they accomplish these effects are unclear.

Complementary experimental and computational analysis of the effects of non-ionic detergents and phospholipids on insulin amyloid aggregation

Amphiphilic compounds, both detergents and lipids, are important tools for in vitro analysis of water-soluble and integral membrane proteins. A key question is whether these two groups of amphiphilic molecules use the same pathway to affect structural and functional integrity of proteins. In the present study, we tested the effect of non-ionic detergent dodecyl maltoside (DDM), two phospholipids, 1,2-dimyristoyl-sn-glycero-3- phosphocholine (DMPC), 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC), and the detergent-phospholipid mixtures on insulin amyloidogenesis in vitro. Amyloidogenesis of insulin is significantly affected by DDM in a time-and dose-dependent manner, but only slightly affected by either of phospholipids. Addition of DHPC or DMPC to detergent does not alter the inhibiting pattern, suggesting that DDM preferably binds to insulin. The molecular modeling revealed that DDM and the phospholipids occupy equivalent binding sites. DDM, due to the presence of maltose with several oxygen atoms (hydroxylic, glycosidic and ring) is involved in more hydrogen bonds than DHPC or DMPC. Hydrophobic interactions are important factors to stabilize both, DDM and phospholipids in their binding sites. Our results indicate that certain detergents (applying DDM as an example) and selected phospholipids are not always interchangeable in their use to investigate the effect of amphiphilic compounds on the behavior of amyloid-prone proteins.