Unraveling the novel effects of aroma from small molecules in preventing hen egg white lysozyme amyloid fibril formation

Analysis of the enzymatic degradation of lysozyme fibrils using a combination method of non-denaturing gel electrophoresis and double staining with Coomassie Brilliant Blue G-250 and R-250 dyes

The Amyloid fibrils of proteins are involved in various diseases, such as Alzheimer's disease. To suppress such amyloid fibrils, it is essential to develop methods to elucidate their enzymatic degradation process. Lysozyme in egg white has been well studied as a model protein of amyloid fibrils. Here, we establish a method for separating and evaluating both lysozyme fibrils and their enzymatic degradation products by combining non-denaturing gel electrophoresis and anionic dye staining with Congo red and two Coomassie brilliant blue (CBB) dyes. By combining non-denaturing gel electrophoresis and amyloid-specific Congo red staining, the separation site of lysozyme fibril was stained explicitly by Congo red and identified on the gel, and the amount of lysozyme fibrils decreased following the enzymatic degradation of lysozyme fibrils. Both lysozyme fibrils and their enzymatic degradation products were separated and examined by combining non-denaturing gel electrophoresis and double staining with CBB G-250 and R-250 dyes. Protein stained with negatively charged colloidal CBB G-250 could migrate to the anode side of electrophoresis. Following gel electrophoresis, noncolloidal CBB R-250 was used to detect lysozyme fibrils and the enzymatic degradation products. This method can be applied to investigate the enzymatic degradation process of amyloid fibrils.

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.

Amyloid fibril reduction through covalently modified lysine in HEWL and insulin

Proteins possess a variety of nucleophiles, which can carry out different reactions in the functioning cells. Proteins endogenously and synthetically can be modified through their nucleophilic sites. The roles of these chemical modifications have not been completely revealed. These modifications can alter the protein folding process. Protein folding directly affects the function of proteins. If an error in protein folding occurs, it may cause protein malfunction leading to several neurodegenerative disorders such as Alzheimer's and Parkinson's. In this study, Hen Egg White Lysozyme (HEWL) and bovine insulin, as model proteins for studying the amyloid formation, were covalently attached with 5(6)-thiophenolfluorescein. The amyloid formation of the covalently labeled lysozyme and insulin were compared with the native proteins. Interestingly, the results indicated that the covalent attachment of fluorescein slowed down the amyloid formation of HEWL and insulin significantly. The amyloid formation was examined using Thioflavin T (ThT) fluorescence assay, circular dichroism, FTIR, and gel electrophoresis. Tandem mass spectrometry was employed to identify the sites of covalent modifications in HEWL. It turned out that two surface lysine residues (K97 and K 116) in HEWL were modified. Computational studies, including docking and molecular simulations, revealed that 5(6)-thiophenolfluorescein makes several non-covalent interactions with HEWL residues, including Lys 97, leading to the reduction of the β-sheet in the protein. Additionally, AFM analysis confirmed the amyloid fibril reduction of lysine-modified bovine insulin and HEWL. Altogether, our results expand mechanistic insights into preventing amyloid formation by providing an approach for reducing amyloid formation by modifying specific lysine residues in the proteins.

Unravelling the Novel Effects of Three Volatile Compounds in Preventing Fibril Formation of Disease Related Tau and α-Synuclein Proteins- Towards Identifying Candidate Aromatic Substances for Treating Neurodegenerative Diseases

Background: The aggregation of tau and α-synuclein into fibrillary assemblies in nerve cells is the molecular hallmark of Alzheimer’s and Parkinson’s diseases, respectively. In our previous studies, we investigated the anti-amyloidogenic effects of three different aroma-producing (volatile) compounds including cinnamaldehyde, phenyl ethyl alcohol, and TEMED on the fibrillation process of HEWL, as a model protein. Our previous results showed that while TEMED was able to completely stop the process of fibril formation, cinnamaldehyde and phenyl ethyl alcohol gave rise to oligomeric/protofibrillar forms and were involved in the entrapment of intermediate species of HEWL. In this study, we investigated the anti-amyloidogenic effect of the same three volatile compounds on recombinantly produced tau and α-synuclein proteins.

Methods: The thioflavin T fluorescence assay, circular dichroism, SDS-PAGE/native-PAGE, dynamic light scattering, and atomic force microscopy were used, where necessary, to further our understanding of the inhibitory effects of the three volatile compounds on the fibril formation of tau and α-synuclein proteins and allow for a comparison with previous data obtained for HEWL.

Results: Our results revealed that contrary to the results obtained for HEWL (a globular protein), the volatile compound TEMED was no longer able to prevent fibril formation in either of the natively unstructured tau or α-synuclein proteins, and instead, cinnamaldehye and phenyl ethyl alcohol, in particular, had the role of preventing fibril formation of tau or α-synuclein.

Conclusion: The results of this study further emphasized the exclusion of HEWL as a model protein for fibrillation studies and highlighted the importance of studying brain-related proteins such as tau or α-synuclein and the need to assess the effects of volatile compounds such as cinnamaldehye and phenyl ethyl alcohol as potential substances in the treatment of neurodegenerative diseases.

Unraveling diverse action of triton X-100 and methimazole on lysozyme fibrillation/aggregation: Physicochemical insights

Identification of functionalities responsible for prevention of fibrillation in proteins is important to design effective drugs in addressing neurodegenerative diseases. We have used nonionic surfactant triton X-100 (TX-100) and antithyroid drug methimazole (MMI) to understand mechanistic aspects of action of these molecules having different functionalities on hen egg-white lysozyme at different stages of fibrillation. After establishing the nucleation, elongation and maturation stages of fibrillation of protein at 57 °C, energetics of interactions with these molecules have been determined by using isothermal titration calorimetry. Differential scanning calorimetry has permitted assessment of thermal stability of the protein at these stages, with or without these molecular entities. The enthalpies of interaction of TX-100 and MMI with protein fibrils suggest importance of hydrogen bonding and polar interactions in their effectiveness towards prevention of fibrils. TX-100, in spite of several polar centres, is unable to prevent fibrillation, rather it promotes. MMI is able to establish polar interactions with interacting strands of the protein and disintegrate fibrils. A rigorous comparison with inhibitors reported in literature highlights importance -OH and >CO functionalities in fibrillation prevention. Even though MMI has hydrogen bonding centres, its efficiency as inhibitor falls after the inhibited lysozyme fibrils further interact and form amorphous aggregates.

The aroma of TEMED as an activation and stabilizing signal for the antibacterial enzyme HEWL

The unpleasant smell released from dead bodies, may serve as an alarm for avoiding certain behaviour or as feeding or oviposition attractants for animals. However, little is known about their effect on the structure and function of proteins. Previously, we reported that using the aroma form of TEMED (a diamine), representative of the "smell of death", could completely inhibit the fibril formation of HEWL, as an antibacterial enzyme, and a model protein for fibrillation studies. To take this further, in this study we investigated the kinetics of TEMED using a number of techniques and in particular X-ray crystallography to identify the binding site(s) of TEMED and search for hotspot(s) necessary to inhibit fibril formation of HEWL. Structural data, coupled with other experimental data reported in this study, revealed that TEMED completely inhibited fibril formation and stabilized the structure of HEWL through enhancement of the CH-Π interaction and binding to an inhibitor hotspot comprised of residues Lys33, Phe34, Glu35 and Asn37 of HEWL. Additionally, results from this study showed that the binding of TEMED increased the activity and thermal stability of HEWL, helping to improve the function of this antibacterial enzyme. In conclusion, the role of the "smell of death”, as an important signal molecule affecting the activity and stability of HEWL was greatly highlighted, suggesting that aroma producing small molecules can be signals for structural and functional changes in proteins.

The role of Cinnamaldehyde and Phenyl ethyl alcohol as two types of precipitants affecting protein hydration levels

Release of water is the main force which drives proteins towards crystallisation (giving rise to protein crystals for crystallography) and aggregation (main cause of neurodegenerative diseases), and as such it is possible to make changes in the crystallisation/aggregation process by using compounds which are able to reduce the amount of water molecules around proteins. Cinnamaldehyde and Phenyl ethyl alcohol are the active constituents of cinnamon and rose flower, respectively. Traditional Iranian Medicine (TIM) suggests the use of cinnamon and rose flower for the reduction of excess coldness and wetness from the brain of patients suffering from Dementia. Using crystallisation as a model system and X-ray crystallography, we tested whether Cinnamaldehyde or Phenyl ethyl alcohol can mimic the role of precipitants resulting in the formation of crystals of HEWL (as a model protein) by releasing water from the surrounding protein environment. Results have revealed that both Cinnamaldehyde and Phenyl ethyl alcohol, in particular, were capable to adequately act as 'precipitants' but in the presence of NaCl (as a salt), resulting in better crystals of HEWL by changing the amount of charge and/or making water molecules unavailable in the symmetry related position, in line with the role suggested for these compounds by TIM.

Cinnamaldehyde and Phenyl Ethyl Alcohol promote the entrapment of intermediate species of HEWL, as revealed by structural, kinetics and thermal stability studies

Numerous efforts have been directed towards investigating the different stages leading to the fibrillation process in neurodegenerative diseases and finding the factors modulating it. In this study, using a wide range of molecular techniques as well as fibrillation kinetics coupled with differential scanning fluorimetry (DSF) and crystal structure determination of HEWL treated with cinnamaldehyde (Cin) and Phenyl ethyl alcohol (PEA) in their aroma form during fibrillation, we were able to identify the binding positions of Cin and PEA in HEWL. Additionally, crystal structures were used to suggest residues Thr43, Asn44, Arg45 and Arg68 as a plausible ‘hotspot’ promoting entrapment of intermediate species in the process of fibril formation in HEWL. We were also able to use DSF to show that Cin can significantly decrease the thermal stability of HEWL, promoting the formation of partially unfolded intermediate species. In conclusion, our data led us to emphasize that compounds in their ‘aroma form’ can influence the structure and stability of protein molecules and suggest reconsideration of HEWL as a model protein for fibrillation studies related to neurodegenerative diseases based on the initial structure of the proteins, whether globular (HEWL) or intrinsically disordered.

Conditions Governing Food Protein Amyloid Fibril Formation-Part I: Egg and Cereal Proteins

Conditions including heating mode, time, temperature, pH, moisture and protein concentration, shear, and the presence of alcohols, chaotropic/reducing agents, enzymes, and/or salt influence amyloid fibril (AF) formation as they can affect the accessibility of amino acid sequences prone to aggregate. As some conditions applied on model protein resemble conditions in food processing unit operations, we here hypothesize that food processing can lead to formation of protein AFs with a compact cross β-sheet structure. This paper reviews conditions and food constituents that affect amyloid fibrillation of egg and cereal proteins. While egg and cereal proteins often coexist in food products, their impact on each other's fibrillation remains unknown. Hen egg ovalbumin and lysozyme form AFs when subjected to moderate heating at acidic pH separately. AFs can also be formed at higher pH, especially in the presence of alcohols or chaotropic/reducing agents. Tryptic wheat gluten digests can form fibrillar structures at neutral pH and maize and rice proteins do so in aqueous ethanol or at acidic pH, respectively.

Among Commercially Available Fruit Juices, Pomegranate Is the Most Effective Inhibitor of PMS-Trypsin Amyloid-Like Fibrils Formation

The formation of amyloid fibrils is associated with many human illnesses, such as Alzheimer’s, Huntington’s, and Parkinson’s diseases, amyotrophic lateral sclerosis, spongiform encephalitis, type 2 diabetes, and primary and secondary systemic amyloidosis. Nutrition contributes to the prevention of these diseases. The aim of our work was to look for commercially available fruit juices that can inhibit the formation of amyloid fibrils. Of the fruit juices that we examined, that of pomegranate was found to be the most effective inhibitory agent using turbidity measurements and Congo red binding assay. According to our experiments, pomegranate juice reduced the amount of PMS-trypsin amyloid-like fibrils to 3.7% at 5-fold dilution compared with the sample without pomegranate. The inhibitory effect of the pomegranate juice was concentration dependent.

Avocado Juice Prevents the Formation of Trypsin Amyloid-Like Fibrils in Aqueous Ethanol

In this work fruit and vegetable juices were analyzed for their ability to prevent the aggregation of trypsin using turbidity measurement. Fruit and vegetable juices are capable of inhibiting the aggregation of PMS-trypsin in aqueous ethanol. Among the juices examined, avocado was found to be the most effective. Choline bitartrate was investigated for its ability to inhibit the fibrillation of PMS-trypsin. We have found that avocado juice and choline bitartrate have an inhibitory effect on the formation of trypsin amyloid-like fibrils using Congo red-binding assay.

Tannic Acid-Induced Surface-Catalyzed Secondary Nucleation during the Amyloid Fibrillation of Hen Egg-White Lysozyme

Amyloid fibrillation by hen egg white lysozyme under the influence of tannic acid was investigated by atomic force microscopy and fluorescence spectroscopy. Tannic acid was found to be able to induce the formation of amyloid fibrils with an interesting mixed morphology. Such morphology features with the existence of areas of thickening alternating with areas of normal height. This novel modulation effect of tannic acid on amyloid fibrillation was interpreted by the established surface-catalyzed secondary nucleation theory. We further performed a fluorescence quenching study to investigate the intermolecular interaction between tannic acid and lysozyme. The results support that lysozyme and tannic acid interact with each other mainly through hydrophobic interactions. We also discussed why hydrogen-bonding interaction is not a dominant factor in the interaction between tannic acid and lysozyme though tannic acid contains a significant amount of hydroxyl groups. Our work provides new insight into the effect of tannic acid, a well-known amyloid inhibitor, on amyloid fibrillation.

Eduscho Coffee Extract Effectively Inhibits the Formation of Amyloid-like Fibrils by Trypsin in Aqueous Ethanol

In this work we used an in vitro trypsin aggregation model to show that certain commercial coffee extracts can inhibit protein aggregation. Aggregation experiments were performed using several spectroscopic methods and a dye binding assay, such as turbidity, Congo red (CR) and electronic circular dichroism (ECD), that was further supported by transmission electron microscopy (TEM). A correlation was found between the anti-aggregation properties and the total phenolic content of the coffee extracts. The results revealed that the greatest effect was exerted by the Eduscho coffee extract. It was found that the inhibitory effect of this extract was concentration dependent. Using size exclusion chromatography, we demonstrated that the inhibitory effect of the Eduscho coffee extract on the formation of amyloid-like fibrils was due to its capacity to stabilize the oligomeric form of the protein.