Suppression of lysozyme aggregation at alkaline pH by tri-N-acetylchitotriose

Molecular insights into the phase transition of lysozyme into amyloid nanostructures: Implications of therapeutic strategies in diverse pathological conditions

Lysozyme, a well-known bacteriolytic enzyme, exhibits a fascinating yet complex behavior when it comes to protein aggregation. Under certain conditions, this enzyme undergoes flexible transformation, transitioning from partially unfolded intermediate units of native conformers into complex cross-β-rich nano fibrillar amyloid architectures. Formation of such lysozyme amyloids has been implicated in a multitude of pathological and medical severities, like hepatic dysfunction, hepatomegaly, splenic rupture as well as spleen dysfunction, nephropathy, sicca syndrome, renal dysfunction, renal amyloidosis, and systemic amyloidosis. In this comprehensive review, we have attempted to provide in-depth insights into the aggregating behavior of lysozyme across a spectrum of variables, including concentrations, temperatures, pH levels, and mutations. Our objective is to elucidate the underlying mechanisms that govern lysozyme's aggregation process and to unravel the complex interplay between its structural attributes. Moreover, this work has critically examined the latest advancements in the field, focusing specifically on novel strategies and systems, that have been implemented to delay or inhibit the lysozyme amyloidogenesis. Apart from this, we have tried to explore and advance our fundamental understanding of the complex processes involved in lysozyme aggregation. This will help the research community to lay a robust foundation for screening, designing, and formulating targeted anti-amyloid therapeutics offering improved treatment modalities and interventions not only for lysozyme-linked amyloidopathy but for a wide range of amyloid-related disorders.

Hen lysozyme fibrillogenesis, molten globule intermediate and effect of copper salts

The amyloid fibres have been related to many diseases. The molten globule intermediate has been proposed to form part of the folding pathway of many proteins. In the present study, we investigated the mechanism of amyloid-fibres formation of hen egg-white lysozyme (HEWL) incubated in a potassium phosphate buffer, pH 11.8, 100 mM, at 37 °C for 30 h, and evaluated the influence of Cu(II) present in two salts (CuSO₄ and CuCl₂) during fibrillogenesis. Co-incubation and post-incubation of lysozyme with copper salts reduced the fluorescence signal of thioflavin T with an increment in the intrinsic fluorescence of the protein. The ANS fluorescence test showed that incubation of HEWL for 6 h generated a molten globule intermediate state that formed amyloid fibres when incubation was carried out for a 30-h timespan. Dynamic light scattering showed a heterogeneous population of states in samples incubated in the absence or the presence of salts during the fibrillation process. The existence of a reducing potential was verified during the formation of HEWL amyloid fibres with the bathocuproine disulphonate test. Transmission electron microscopy confirmed the presence and absence of fibres in solutions incubated with and without Cu(II). This work demonstrated that lysozyme formed amyloid fibres at 37 °C and copper inhibited its formation.Communicated by Ramaswamy H. Sarma.

Insights on Aggregation of Hen Egg-White Lysozyme from Raman Spectroscopy and MD Simulations

Protein misfolding and aggregation play a significant role in several neurodegenerative diseases. In the present work, the spontaneous aggregation of hen egg-white lysozyme (HEWL) in an alkaline pH 12.2 at an ambient temperature was studied to obtain molecular insights. The time-dependent changes in spectral peaks indicated the formation of β sheets and their effects on the backbone and amino acids during the aggregation process. Introducing iodoacetamide revealed the crucial role of intermolecular disulphide bonds amidst monomers in the aggregation process. These findings were corroborated by Molecular Dynamics (MD) simulations and protein-docking studies. MD simulations helped establish and visualize the unfolding of the proteins when exposed to an alkaline pH. Protein docking revealed a preferential dimer formation between the HEWL monomers at pH 12.2 compared with the neutral pH. The combination of Raman spectroscopy and MD simulations is a powerful tool to study protein aggregation mechanisms.

Estimating near-wall diffusion coefficients of arbitrarily shaped rigid macromolecules

We developed a computationally efficient approach to approximate near-wall diffusion coefficients of arbitrarily shaped rigid macromolecules. The proposed method relies on extremum principles for Stokes flows produced by the motion of rigid bodies. In the presence of the wall, the rate of energy dissipation is decreased relative to the unbounded fluid. In our approach, the position- and orientation-dependent mobility matrix of a body suspended near a no-slip plane is calculated numerically using a coarse-grained molecular model and the Rotne-Prager-Yamakawa description of hydrodynamics. Effects of the boundary are accounted for via Blake's image construction. The matrix components are scaled using ratios of the corresponding bulk values evaluated for the detailed representation of the molecule and its coarse-grained model, leading to accurate values of the near-wall diffusion coefficients. We assess the performance of the approach for two biomolecules at different levels of coarse-graining.

On the Protein Fibrillation Pathway: Oligomer Intermediates Detection Using ATR-FTIR Spectroscopy

Oligomeric intermediates on the pathway of amyloid fibrillation are suspected as the main cytotoxins responsible for amyloid-related pathogenicity. As they appear to be a part of the lag phase of amyloid fibrillation when analyzed using standard methods such as Thioflavin T (ThT) fluorescence, a more sensitive method is needed for their detection. Here we apply Fourier transform infrared spectroscopy (FTIR) in attenuated total reflectance (ATR) mode for fast and cheap analysis of destabilized hen-egg-white lysozyme solution and detection of oligomer intermediates of amyloid fibrillation. Standard methods of protein aggregation analysis— Thioflavin T (ThT) fluorescence, atomic force microscopy (AFM), and 8-anilinonaphthalene-1-sulphonic acid (ANS) fluorescence were applied and compared to FTIR spectroscopy data. Results show the great potential of FTIR for both, qualitative and quantitative monitoring of oligomer formation based on the secondary structure changes. While oligomer intermediates do not induce significant changes in ThT fluorescence, their secondary structure changes were very prominent. Normalization of specific Amide I region peak intensities by using Amide II peak intensity as an internal standard provides an opportunity to use FTIR spectroscopy for both qualitative and quantitative analysis of biological samples and detection of potentially toxic oligomers, as well as for screening of efficiency of fibrillation procedures.

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.

Mechanism of lysozyme adsorption onto gold surface determined by quartz crystal microbalance and surface plasmon resonance

In this study, the physicochemical characterization of lysozyme adsorbed on gold was investigated. Through the use of MP-SPR it was possible to establish that the orientation of molecules changes from side-on to between or end-on with increasing surface coverage. The data confirms that the process of adsorption is driven primarily by electrostatic interactions but also by hydrophobic forces. MP-SPR data was compared with the Random Sequential Adsorption model for a molecule with an ellipsoidal shape. Contact angle measurements showed that higher surface coverage also translates in more hydrophilic properties of obtained lysozyme layer. Comparison of CD and PM-IRRAS spectra in solution and adsorbed state respectively showed changes in the secondary structures of lysozyme. These changes are dependent on pH, but fundamentally they go in the direction of the increase of β-turn/random content with a simultaneous decrease in β-sheet fraction, which suggests that aggregation is not occurring. The combination of MP-SPR and QCM-D measurements allowed the estimation of the number of water molecules associated with the lysozymes films. It has been observed that hydration decreases from 70% in pH = 4 to 30% in pH = 11. This data indicates that hydration is driven mainly by the degree of protonation of lysozyme molecules.

Advances in protein misfolding, amyloidosis and its correlation with human diseases

Protein aggregation, their mechanisms and trends in the field of neurodegenerative diseases is still far from completely being decoded. It is mainly attributed to the complexity surrounding the interaction between proteins which includes various regulatory mechanisms involved with the presentation of abnormal conditions. Although most proteins are functional in their soluble form, they have also been reported to convert themselves into insoluble aggregates under certain conditions naturally. Misfolded protein forms aggregates which are mostly unwanted by the cellular system and are mostly involved in various pathophysiologies including Alzheimer's, Type II Diabetes mellitus, Kurus's etc. Challenges lie in understanding the complex mechanism of protein misfolding and its correlation with clinical evidence. It is often understood that due to the slowness of the process and its association with ageing, timely intervention with drugs or preventive measures will play an essential role in lowering the rate of dementia causing diseases and associated ailments in the future. Today approximately more than 35 proteins have been identified capable of forming amyloids under defined conditions, and nearly all of them have been associated with disease outcomes. This review incorporates a major understanding from the history of diseases associated with protein misfolding, to the current state of neurodegenerative diseases globally, highlighting challenges in drug development and current state of research in a comprehensive manner in the field of protein misfolding diseases. There is increasing clinical association of protein misfolding with regards to amyloids compelling us to thread questions solved and further helping us design possible solutions by generating a pathway-based research on which future work in this field could be driven.

Barbituric Acid Based Fluorogens: Synthesis, Aggregation-Induced Emission, and Protein Fibril Detection

Fluorescent dyes, especially those emitting in the long wavelength region, are excellent candidates in the area of bioassay and bioimaging. In this work, we report a series of simple organic fluorescent dyes consisting of electron-donating aniline groups and electron-withdrawing barbituric acid groups. These dyes are very easy to construct while emitting strongly in the red region in their solid state. The photophysical properties of these dyes, such as solvatochromism and aggregation-induced emission, are systematically characterized. Afterward, the structure-property relationships of these barbituric acid based fluorogens are discussed. Finally, we demonstrate their potential applications for protein amyloid fibril detection.

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 charge transfer absorption spectra: an intrinsic probe to monitor structural and oligomeric transitions in proteins

The utility of ProCharTS as an intrinsic spectral probe to track protein aggregation and monitor conformational changes is reported.

Protein fibrillation lag times during kinetic inhibition

Protein aggregation is linked to more than 30 human pathologies, including Alzheimer's and Parkinson's diseases. Since small oligomers that form at the beginning of the fibrillation process probably are the most toxic elements, therapeutic strategies involving fibril fragmentation could be detrimental. An alternative approach, named kinetic inhibition, aims to prevent fibril formation by using small ligands that stabilize the parent protein. The factors that govern fibrillation lag times during kinetic inhibition are largely unknown, notwithstanding their importance for designing effective long-term therapies. Inhibitor-bound species are not likely to be incorporated into the core of mature fibrils, although their presence could alter the kinetics of the fibrillation process. For instance, inhibitor-bound species may act as capping elements that impair the nucleation process and/or fibril growth. Here, we address this issue by studying the effect of two natural inhibitors on the fibrillation behavior of lysozyme at neutral pH. We analyzed a set of 79 fibrillation curves obtained in lysozyme alone and a set of 37 obtained in the presence of inhibitors. We calculated the concentrations of the relevant species at the beginning of the curves using the inhibitor-binding constants measured under the same experimental conditions. We found that inhibitor-bound protein species do not affect fibrillation onset times, which are mainly determined by the concentration of unbound protein species present in equilibrium. In this system, knowledge of the fibrillation kinetics and inhibitor affinities suffices to predict the effect of kinetic inhibitors on fibrillation lag times. In addition, we developed a new methodology to better estimate fibrillation lag times from experimental curves.

Enzymatic functionalization of a nanobody using protein insertion technology

Antibody-based products constitute one of the most attractive biological molecules for diagnostic, medical imagery and therapeutic purposes with very few side effects. Their development has become a major priority of biotech and pharmaceutical industries. Recently, a growing number of modified antibody-based products have emerged including fragments, multi-specific and conjugate antibodies. In this study, using protein engineering, we have functionalized the anti-hen egg-white lysozyme (HEWL) camelid VHH antibody fragment (cAb-Lys3), by insertion into a solvent-exposed loop of the Bacillus licheniformis β-lactamase BlaP. We showed that the generated hybrid protein conserved its enzymatic activity while the displayed nanobody retains its ability to inhibit HEWL with a nanomolar affinity range. Then, we successfully implemented the functionalized cAb-Lys3 in enzyme-linked immunosorbent assay, potentiometric biosensor and drug screening assays. The hybrid protein was also expressed on the surface of phage particles and, in this context, was able to interact specifically with HEWL while the β-lactamase activity was used to monitor phage interactions. Finally, using thrombin-cleavage sites surrounding the permissive insertion site in the β-lactamase, we reported an expression system in which the nanobody can be easily separated from its carrier protein. Altogether, our study shows that insertion into the BlaP β-lactamase constitutes a suitable technology to functionalize nanobodies and allows the creation of versatile tools that can be used in innovative biotechnological assays.

Preventing disulfide bond formation weakens non-covalent forces among lysozyme aggregates

Nonnative disulfide bonds have been observed among protein aggregates in several diseases like amyotrophic lateral sclerosis, cataract and so on. The molecular mechanism by which formation of such bonds promotes protein aggregation is poorly understood. Here in this work we employ previously well characterized aggregation of hen eggwhite lysozyme (HEWL) at alkaline pH to dissect the molecular role of nonnative disulfide bonds on growth of HEWL aggregates. We employed time-resolved fluorescence anisotropy, atomic force microscopy and single-molecule force spectroscopy to quantify the size, morphology and non-covalent interaction forces among the aggregates, respectively. These measurements were performed under conditions when disulfide bond formation was allowed (control) and alternatively when it was prevented by alkylation of free thiols using iodoacetamide. Blocking disulfide bond formation affected growth but not growth kinetics of aggregates which were ∼50% reduced in volume, flatter in vertical dimension and non-fibrillar in comparison to control. Interestingly, single-molecule force spectroscopy data revealed that preventing disulfide bond formation weakened the non-covalent interaction forces among monomers in the aggregate by at least ten fold, thereby stalling their growth and yielding smaller aggregates in comparison to control. We conclude that while constrained protein chain dynamics in correctly disulfide bonded amyloidogenic proteins may protect them from venturing into partial folded conformations that can trigger entry into aggregation pathways, aberrant disulfide bonds in non-amyloidogenic proteins (like HEWL) on the other hand, may strengthen non-covalent intermolecular forces among monomers and promote their aggregation.

On the characterization of intermediates in the isodesmic aggregation pathway of hen lysozyme at alkaline pH

Protein aggregation leading to formation of amyloid fibrils is a symptom of several diseases like Alzheimer’s, type 2 diabetes and so on. Elucidating the poorly understood mechanism of such phenomena entails the difficult task of characterizing the species involved at each of the multiple steps in the aggregation pathway. It was previously shown by us that spontaneous aggregation of hen-eggwhite lysozyme (HEWL) at room temperature in pH 12.2 is a good model to study aggregation. Here in this paper we investigate the growth kinetics, structure, function and dynamics of multiple intermediate species populating the aggregation pathway of HEWL at pH 12.2. The different intermediates were isolated by varying the HEWL monomer concentration in the 300 nM—0.12 mM range. The intermediates were characterized using techniques like steady-state and nanosecond time-resolved fluorescence, atomic force microscopy and dynamic light scattering. Growth kinetics of non-fibrillar HEWL aggregates were fitted to the von Bertalanffy equation to yield a HEWL concentration independent rate constant (k = (6.6±0.6)×10⁻⁵ s⁻¹). Our results reveal stepwise changes in size, molecular packing and enzymatic activity among growing HEWL aggregates consistent with an isodesmic aggregation model. Formation of disulphide bonds that crosslink the monomers in the aggregate appear as a unique feature of this aggregation. AFM images of multiple amyloid fibrils emanating radially from amorphous aggregates directly confirmed that on-pathway fibril formation was feasible under isodesmic polymerization. The isolated HEWL aggregates are revealed as polycationic protein nanoparticles that are robust at neutral pH with ability to take up non-polar molecules like ANS.

Rottlerin dissolves pre-formed protein amyloid: a study on hen egg white lysozyme

BACKGROUND

Deposition of protein fibrillar aggregates called amyloids in the tissue, is the principal cause of several degenerative diseases. Here, we have shown the disaggregation potential of rottlerin towards hen egg white lysozyme (HEWL) fibrils formed under alkaline conditions (pH-12.2).

METHODS

Several biophysical methods like Atomic force microscopy (AFM), Fourier transform infrared spectroscopy (FTIR) and fluorescence emission spectra were used for the study.

RESULTS AND CONCLUSION

Rottlerin exhibited instantaneous disaggregation effect on HEWL fibrils as monitored by Thioflavin T assay, anisotropy study and AFM imaging. Further we have monitored the conformational changes induced by rottlerin on the fibril in terms of surface hydrophobicity and secondary structure through 8-anilino-1-naphthalene sulfonic acid (ANS) fluorescence and FTIR study respectively. We have also attempted to elucidate the type of interaction between HEWL and rottlerin at pH-12.2 employing techniques like quenching study and FTIR.

GENERAL SIGNIFICANCE

Rottlerin seems to have potential application as anti-amyloid compound.

Lysozyme: a model protein for amyloid research

Ever since lysozyme was discovered by Fleming in 1922, this protein has emerged as a model for investigations on protein structure and function. Over the years, several high-resolution structures have yielded a wealth of structural data on this protein. Extensive studies on folding of lysozyme have shown how different regions of this protein dynamically interact with one another. Data is also available from numerous biotechnological studies wherein lysozyme has been employed as a model protein for recovering active recombinant protein from inclusion bodies using small molecules like l-arginine. A variety of conditions have been developed in vitro to induce fibrillation in hen lysozyme. They include (a) acidic pH at elevated temperature, (b) concentrated solutions of ethanol, (c) moderate concentrations of guanidinium hydrochloride at moderate temperature, and (d) alkaline pH at room temperature. This review aims to bring together similarities and differences in aggregation mechanisms, morphology of aggregates, and related issues that arise using the different conditions mentioned above to improve our understanding. The alkaline pH condition (pH 12.2), discovered and studied extensively in our lab, shall receive special attention. More than a decade ago, it was revealed that mutations in human lysozyme can cause accumulation of large quantities of amyloid in liver, kidney, and other regions of gastrointestinal tract. Understanding the mechanism of lysozyme aggregation will probably have therapeutic implications for the treatment of systemic nonneuropathic amyloidosis. Numerous studies have begun to focus attention on inhibition of lysozyme aggregation using antibody or small molecules. The enzymatic activity of lysozyme presents a convenient handle to quantify the native population of lysozyme in a sample where aggregation has been inhibited. The rich information available on lysozyme coupled with the multiple conditions that have been successful in inducing/inhibiting its aggregation in vitro makes lysozyme an ideal model protein to investigate amyloidogenesis.