Cysteine inhibits amyloid fibrillation of lysozyme and directs the formation of small worm-like aggregates through non-covalent interactions

Furosemide Derails Human Lysozyme Fibrillation by Interacting with Aggregation Hot Spots: A Biophysical Comprehension

Kidney-associated human lysozyme amyloidosis leads to renal impairments;thus, patients are often prescribed furosemide. Based on this fact, the effect of furosemide on induced human lysozyme fibrillation, in vitro, is evaluated by spectroscopic, calorimetric, computational, and cellular-based assays/methods. Results show that furosemide increases the lag phase and decreases the apparent rate of aggregation of human lysozyme, thereby decelerating the nucleation phase and amyloid fibril formation, as confirmed by the decrease in the level of Thioflavin-T fluorescence. Fewer entities of hydrodynamic radii of ∼171 nm instead of amyloid fibrils (∼412 nm) are detected in human lysozyme in the presence of furosemide by dynamic light scattering. Moreover, furosemide decreases the extent of conversion of the α/β structure of human lysozyme into a predominant β-sheet. The isothermal titration calorimetry established that furosemide forms a complex with human lysozyme, which was also confirmed through fluorescence quenching and computational studies. Also, human lysozyme lytic activity is inhibited competitively by furosemide due to the involvement of amino acid residues of the active site in catalysis, as well as complex formation. Conclusively, furosemide interacts with Gln58, Ile59, Asn60, Ala108, and Trp109 of aggregation-prone regions 2 and 4 of human lysozyme, thereby masking its sites of aggregation and generating only lower-order entities that are less toxic to red blood cells than the fibrils. Thus, furosemide slows the progression of amyloid fibrillation in human lysozyme.

The NCIWEB Server: A Novel Implementation of the Noncovalent Interactions Index for Biomolecular Systems

It is well-known that the activity and function of proteins is strictly correlated with their secondary, tertiary, and quaternary structures. Their biological role is regulated by their conformational flexibility and global fold, which, in turn, is largely governed by complex noncovalent interaction networks. Because of the large size of proteins, the analysis of their noncovalent interaction networks is challenging, but can provide insights into the energetics of conformational changes or protein-protein and protein-ligand interactions. The noncovalent interaction (NCI) index, based on the reduced density gradient, is a well-established tool for the detection of weak contacts in biological systems. In this work, we present a web-based application to expand the use of this index to proteins, which only requires a molecular structure as input and provides a mapping of the number, type, and strength of noncovalent interactions. Structure preparation is automated and allows direct importing from the PDB database, making this server (https://nciweb.dsi.upmc.fr) accessible to scientists with limited experience in bioinformatics. A quick overview of this tool and concise instructions are presented, together with an illustrative application.

Influence of stabilizing osmolytes on hen egg white lysozyme fibrillation

Communicated by Ramaswamy H. Sarma.

Attenuation of Human Lysozyme Amyloid Fibrillation by ACE Inhibitor Captopril: A Combined Spectroscopy, Microscopy, Cytotoxicity, and Docking Study

Misfolding proteins could form oligomers or amyloid fibers, which can cause a variety of amyloid-associated diseases. Thus, the inhibition of protein misfolding and fibrillation is a promising way to prevent and treat these diseases. Captopril (CAP) is an angiotensin-converting enzyme inhibitor (ACEI) that is widely used to treat diseases such as hypertension and heart failure. In this study, we found that CAP inhibits human lysozyme (HL) fibrillation through the combination techniques of biophysics and biochemistry. The data obtained by thioflavin-T (ThT) and Congo red (CR) assays showed that CAP hindered the aggregation of HL amyloid fibrils by reducing the β-sheet structure of HL amyloid, with an IC₅₀ value of 34.75 ± 1.23 μM. Meanwhile, the particle size of HL amyloid decreased sharply in a concentration-dependent approach after CAP treatment. According to the visualization of atomic force microscopy (AFM) and transmission electron microscopy (TEM), we verified that in the presence of CAP, the needle-like fibers of HL amyloid were significantly reduced. In addition, CAP incubation dramatically improved the cell survival rate exposed to HL fibers. Our studies also revealed that CAP could form hydrogen bonds with amino acid residues of Glu 35 and Ala 108 in the binding pocket of HL, which help in maintaining the α-helical structure of HL and then prevent the formation of amyloid fibrillation. It can be concluded that CAP has antiamyloidogenic activity and a protective effect on HL amyloid cytotoxicity.

Study of Nanofibrils Formation of Fibroin Protein in Specific Thermal and Acidity Conditions

Background:

Amyloid fibrils are insoluble arranged aggregates of proteins that are fibrillar in structure and related to many diseases (at least 20 types of illnesses) and also create many pathologic conditions. Therefore understanding the circumstance of fibril formation is very important

Objectives:

This study aims to work on fibrillar structure formation of fibroin (as a model protein)

Material and Methods:

In this experimental study, fibroin was extracted from bombyx mori silk cocoon, and the concentration was obtained by Bradford method. The protein was incubated in a wide range of times (0 min to 7 days) in specific acidity and thermal conditions (pH=1.6, T=70 °C). The assays of UV-vis spectroscopy with congo red, field emission scanning electron microscopy, transmission electron microscopy, atomic force microscopy and circular dichroism spectroscopy were employed to monitor the fibrillation process.

Results:

Fibroin assemblies were formed upon the process of aggregation and fibril formation with a variety of morphology ranging from nanoparticles to elongated fibrils.

Conclusion:

The results showed progressive pathway of fibril formation

7-Methoxytacrine and 2-Aminobenzothiazole Heterodimers: Structure-Mechanism Relationship of Amyloid Inhibitors Based on Rational Design

The formation and accumulation of amyloid aggregates are the phenomena that accompany amyloidoses, which are currently untreatable and include Alzheimer's and Parkinson's diseases, diabetes mellitus, non-neuropathic lysozyme systemic amyloidosis, and others. One of the very promising therapeutic approaches seems to be an inhibition of amyloid formation and/or clearance of amyloid aggregates. Small molecules have a great potential to interfere with amyloid fibrillation of peptides and polypeptides, which can be improved by connection of cyclic structures into single multicyclic molecules and their dimerization. In our study, we focused on heterodimers consisting of 7-methoxytacrine (7-MEOTA) and 2-aminobenzothiazole (BTZ) parent molecules connected by an aliphatic linker. Using in vitro and in silico methods, we investigated the ability of studied compounds to inhibit the amyloid aggregation of hen egg white lysozyme. Heterodimerization led to significant improvement of inhibitory activity compared to that of the parent molecules. The efficiency of the heterodimers varied; the most effective inhibitor contained the longest linker, eight carbons long. We suggest that binding of a heterodimer to a lysozyme blocks the interaction between the β-domain and C-helix region essential for the formation of amyloid cross-β structure. Elongation of the linker ultimately enhances the compound's ability to prevent this interaction by allowing the BTZ part of the heterodimer to bind more effectively, increasing the compound's binding affinity, and also by greater steric obstruction. This study represents an important contribution to the recent rational design of potential lead small molecules with anti-amyloid properties, and the heterodimers studied are prospective candidates for the treatment of systemic lysozyme amyloidosis and other amyloid-related diseases.

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.

Protein misfolding, aggregation and mechanism of amyloid cytotoxicity: An overview and therapeutic strategies to inhibit aggregation

Protein and peptides are converted from their soluble forms into highly ordered fibrillar aggregates under various conditions inside the cell. Such transitions confer diverse neurodegenerative diseases including Alzheimer's disease, Huntington's disease Prion's disease, Parkinson's disease, polyQ and share abnormal folding of potentially cytotoxic protein species linked with degeneration and death of precise neuronal populations. Presently, major advances are made to understand and get detailed insight into the structural basis and mechanism of amyloid formation, cytotoxicity and therapeutic approaches to combat them. Here we highlight classifies and summarizes the detailed overview of protein misfolding and aggregation at their molecular level including the factors that promote protein aggregation under in vivo and in vitro conditions. In addition, we describe the recent technologies that aid the characterization of amyloid aggregates along with several models that might be responsible for amyloid induced cytotoxicity to cells. Overview on the inhibition of amyloidosis by targeting different small molecules (both natural and synthetic origin) have been also discussed, that provides important approaches to identify novel targets and develop specific therapeutic strategies to combat protein aggregation related neurodegenerative diseases.

A dual-inhibitor system for the effective antifibrillation of Aβ40 peptides by biodegradable EGCG–Fe(iii)/PVP nanoparticles

By the synergistic effect of dual inhibition, EFPP NPs exhibited a significant effect on the inhibition of Aβ40 fibrillation and on the disaggregation of existing Aβ40 fibrils.

Rational Design of Amyloid-Like Fibrillary Structures for Tailoring Food Protein Techno-Functionality and Their Potential Health Implications

To control and enhance protein functionality is a major challenge for food scientists. In this context, research on food protein fibril formation, especially amyloid fibril formation, holds much promise. We here first provide a concise overview of conditions, which affect amyloid formation in food proteins. Particular attention is directed towards amyloid core regions because these sequences promote ordered aggregation. Better understanding of this process will be key to tailor the fibril formation process. Especially seeding, that is, adding preformed protein fibrils to protein solutions to accelerate fibril formation holds promise to tailor aggregation and fibril techno-functionality. Some studies have already indicated that food protein fibrillation indeed improves their techno-functionality. However, much more research is necessary to establish whether protein fibrils are useful in complex food systems and whether and to what extent they resist food processing unit operations. In this review the effect of amyloid formation on gelation, interfacial properties, foaming, and emulsification is discussed. Despite their prevalent role as functional structures, amyloids also receive a lot of attention due to their association with protein deposition diseases, prompting us to thoroughly investigate the potential health impact of amyloid-like aggregates in food. A literature review on the effect of the different stages of the human digestive process on amyloid toxicity leads us to conclude that food-derived amyloid fibrils (even those with potential pathogenic properties) very likely have minimal impact on human health. Nevertheless, prior to wide-spread application of the technology, it is highly advisable to further verify the lack of toxicity of food-derived amyloid fibrils.

Specific solubilization of impurities in culture media: Arg solution improves purification of pH-responsive tag CspB50 with Teriparatide

Protein purification using non-chromatographic methods is a simple technique that avoids costly resin. Recently, a cell surface protein B (CspB) tag has been developed for a pH-responsive tag for protein purification by solid-liquid separation. Proteins fused with the CspB tag show reversible insolubilization at acidic pH that can be used in solid-liquid separation for protein purification. However, brown-color impurities from co-precipitation hamper further analysis of the target proteins. In this study, we investigated the effect of additives on the co-precipitation of CspB-tagged Teriparatide (CspB50TEV-Teriparatide) expressed in Corynebacterium glutamicum and associated impurities. Arginine (Arg) at 1.0 M was found to be the most effective additive for removing impurities, particularly carotenoids and nucleic acids. Furthermore, all impurities detected in the fluorescence and absorbance spectra were successfully removed by the repetition of precipitation-redissolution in the Arg solution. The precipitation yield of the CspB50TEV-Teriparatide did not change with the addition of Arg and the repetition of the precipitation-redissolution process. Collectively, our findings indicate that the specific desorption of π-electron rich compounds by Arg may be useful in conjunction with the pH-responsive CspB tag for solid-liquid protein purification.

Modulating protein amyloid aggregation with nanomaterials

Direct exposure or intake of nanopaticles (NPs) to the human body can invoke a series of biological responses, some of which are deleterious, and as such the role of NPs in vivo requires thorough examination. Over the past decade, it has been established that biomolecules such as proteins can bind NPs to form a 'corona', where the structures and dynamics of NP-associated proteins can assign new functionality, systemic distribution and toxicity. However, the behavior and fate of NPs in biological systems are still far from being fully understood. Growing evidence has shown that some natural or artificial NPs could either up- or down-regulate protein amyloid aggregation, which is associated with neurodegenerative diseases like Alzheimer's and Parkinson's diseases, as well as metabolic diseases such as type 2 diabetes. These effects can be either indirect (e.g., through a crowding effect) or direct, depending on the NP composition, size, shape and surface chemistry. However, efforts to design anti-amyloid NPs for biomedical applications have been largely hindered by insufficient understanding of the complex processes, even though proof-of-concept experiments have been conducted. Therefore, exploring the general mechanisms of NP-meditated protein aggregation marks an emerging field in bio-nano research and a new stage of handling nanotechnology that not only aids in elucidating the origin of nanotoxicity, but also provides a foundation for engineering de novo anti-amyloid nanomedicines. In this review, we summarize research on NP-mediated protein amyloid aggregation, with the goal of contributing to sustained nanotechnology and safe nanomedicine against amyloid diseases.

A hypothetical hierarchical mechanism of the self-assembly of the Escherichia coli RNA polymerase σ(70) subunit

Diverse morphology of aggregates of amyloidogenic proteins has been attracting much attention in the last few years, and there is still no complete understanding of the relationships between various types of aggregates. In this work, we propose the model, which universally explains the formation of morphologically different (wormlike and rodlike) aggregates on the example of a σ(70) subunit of RNA polymerase, which has been recently shown to form amyloid fibrils. Aggregates were studied using AFM in solution and depolarized dynamic light scattering. The obtained results demonstrate comparably low Young's moduli of the wormlike structures (7.8-12.3 MPa) indicating less structured aggregation of monomeric proteins than that typical for β-sheet formation. To shed light on the molecular interaction of the protein during the aggregation, early stages of fibrillization of the σ(70) subunit were modeled using all-atom molecular dynamics. Simulations have shown that the σ(70) subunit is able to form quasi-symmetric extended dimers, which may further interact with each other and grow linearly. The proposed general model explains different pathways of σ(70) subunit aggregation and may be valid for other amyloid proteins.

Multiple function fluorescein probe performs metal chelation, disaggregation, and modulation of aggregated Aβ and Aβ-Cu complex

An exceptional probe comprising indole-3-carboxaldehyde fluorescein hydrazone (FI) performs multiple tasks, namely, disaggregating amyloid β (Aβ) aggregates in different biomarker environments such as cerebrospinal fluid (CSF), Aβ1-40 fibrils, β-amyloid lysozyme aggregates (LA), and U87 MG human astrocyte cells. Additionally, the probe FI binds with Cu(2+) ions selectively, disrupts the Aβ aggregates that vary from few nanometers to micrometers, and prevents their reaggregation, thereby performing disaggregation and modulation of amyloid-β in the presence as well as absence of Cu(2+) ion. The excellent selectivity of probe FI for Cu(2+) was effectively utilized to modulate the assembly of metal-induced Aβ aggregates by metal chelation with the "turn-on" fluorescence via spirolactam ring opening of FI as well as the metal-free Aβ fibrils by noncovalent interactions. These results confirm that FI has exceptional ability to perform multifaceted tasks such as metal chelation in intracellular conditions using Aβ lysozyme aggregates in cellular environments by the disruption of β-sheet rich Aβ fibrils into disaggregated forms. Subsequently, it was confirmed that FI had the ability to cross the blood-brain barrier and it also modulated the metal induced Aβ fibrils in cellular environments by "turn-on" fluorescence, which are the most vital properties of a probe or a therapeutic agent. Furthermore, the morphology changes were examined by atomic force microscopy (AFM), polarizable optical microscopy (POM), fluorescence microscopy, and dynamic light scattering (DLS) studies. These results provide very valuable clues on the Aβ (CSF Aβ fibrils, Aβ1-40 fibrils, β-amyloid lysozyme aggregates) disaggregation behavior via in vitro studies, which constitute the first insights into intracellular disaggregation of Aβ by "turn-on" method thereby influencing amyloidogenesis.