A comparative study of fibrillation kinetics of two homologous proteins under identical solution condition

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.

The effect of chrysin binding on the conformational dynamics and unfolding pathway of human serum albumin

Studies on the interactions between ligands and proteins provide insights into how a possible medication alters the structures and activities of the target or carrier proteins. The natural flavonoid aglycone Chrysin (CHR) has demonstrated anti-inflammatory, antioxidant, antiapoptotic, neuroprotective, and antineoplastic effects, both in vitro and in vivo. In this work, we investigated the impact of CHR binding on the as-yet-unexplored conformation, dynamics, and unfolding mechanism of human serum albumin (HSA). We determined CHR binding to HSA domain-II with the association constant (Ka) of 2.70 ± 0.21 × 105 M-1. The urea-induced sequential unfolding mechanism of HSA was used to elucidate the debatable binding location of CHR. CHR binding induced both secondary and tertiary structural alterations in the protein as studied by far-UV circular dichroism and intrinsic fluorescence spectroscopy. Red edge excitation shift (REES) indicated a decrease in conformational dynamics of the protein on the complex formation. This suggested an ordered compact and spatial arrangement of the CHR-boundmolecule. The binding of CHR was found to significantly modulate the urea-induced unfolding pathway of HSA. Urea-induced unfolding pathway of HSA became a two-state process (N-U) from a three-state process (N-I-U). The interaction of CHR is found to increase the thermal stability of the protein by ∼4 °C. This study focuses on the fundamental sciences and demonstrates how prospective medication compounds can alter the dynamics and stability of protein structure.

Inhibition of protein misfolding and aggregation by steroidal quinoxalin-2(1H)-one and their molecular docking studies

A series of D-ring fused 16-substituted steroidal quinoxalin-2(1H)-one attached to an electron-releasing (ER) or electron-withdrawing (EW) groups via steroidal oxoacetate intermediate were synthesized to investigate their protein aggregation inhibition potential using human lysozyme (HLZ). The influence of the type of substituent at the C-6 positions of the quinoxalin-2(1H)-one ring on the protein aggregation inhibition potential was observed, showing that the EW moiety improved the protein aggregation inhibition potency. Of all the evaluated compounds, NO2-substituted quinoxalin-2(1H)-one derivative 13 was the most active compound and had a maximum protein aggregation inhibition effect. Significant stabilization effects strongly support the binding of the most biologically active steroidal quinoxalin-2(1H)-one with docking studies. The predicted physicochemical and ADME properties lie within a drug-like space which shows no violation of Lipinski's rule of five except compounds 12 and 13. Combined, our results suggest that D-ring fused 16-substituted steroidal quinoxalin-2(1H)-one has the potential to modulate the protein aggregation inhibition effect.

Redesigning the kinetics of lysozyme amyloid aggregation by cephalosporin molecules

In lysozyme amyloidosis, fibrillar aggregates of lysozyme are associated with severe renal, hepatic, and gastrointestinal manifestations, with no definite therapy. Current drugs are now being tested in amyloidosis clinical trials as aggregation inhibitors to mitigate disease progression. The tetracycline group among antimicrobials in use is in phase II of clinical trials, whereas some macrolides and cephalosporins have shown neuroprotection. In the present study, two cephalosporins, ceftazidime (CZD) and cefotaxime (CXM), and a glycopeptide, vancomycin (VNC), are evaluated for inhibition of amyloid aggregation of hen egg white lysozyme (HEWL) under two conditions (i) 4 M guanidine hydrochloride (GuHCl) at pH 6.5 and 37° C, (ii) At pH 1.5 and 65 °C. Fluorescence quench titration and molecular docking methods report that CZD, CXM, and VNC interact more strongly with the partially folded intermediates (PFI) in comparison to the protein's natural state (N). However, only CZD and CXM proficiently inhibit the aggregation. Transmission electron microscopy, tinctorial assessments, and aggregation kinetics all support oligomer-level inhibition. Transition structures in CZD-HEWL and CXM-HEWL aggregation are shown by circular dichroism (CD). On the other hand, kinetic variables and soluble fraction assays point to a localized association of monomers. Intrinsic fluorescence (IF),1-Anilino 8-naphthalene sulphonic acid, and CD demonstrate structural and conformational modifications redesigning the PFI. GuHCl-induced unfolding and differential scanning fluorimetry suggested that the PFI monomers bound to CZD and CXM exhibited partial stability. Our results present two mechanisms that function in both solution conditions, creating a novel avenue for the screening of putative inhibitors for drug repurposing. We extend our proposed mechanisms in the designing of physical inhibitors of amyloid aggregation considering shorter time frames and foolproof methods.Communicated by Ramaswamy H. Sarma.

Frequency dependence of ultrasonic effects on the kinetics of hen egg white lysozyme fibrillation

Our study aimed to investigate the effects of ultrasound on the fibrillation kinetics of HEWL (hen egg white lysozyme) and its physicochemical properties. Ultrasound, a mechanical wave, can induce conformational changes in proteins. To achieve this, we developed an ultrasound exposure system and used various biophysical techniques, including ThT fluorescence spectroscopy, ATR-FTIR, Far-UV CD spectrophotometry, Fluorescence microscopy, UV-spectroscopy, and seeding experiments. Our results revealed that higher frequencies significantly accelerated the fibrillation of lysozyme by unfolding the native protein and promoting the fibrillation process, thereby reducing the lag time. We observed a change in the secondary structure of the sonicated protein change to the β-structure, but there was no difference in the Tm of native and sonicated proteins. Furthermore, we found that higher ultrasound frequencies had a greater seeding effect. We propose that the effect of frequency can be explained by the impact of the Reynolds number, and for the Megahertz frequency range, we are almost at the transition regime of turbulence. Our results suggest that laminar flows may not induce any significant change in the fibrillation kinetics, while turbulent flows may affect the process.

Biophysical Evidence for the Amyloid Formation of a Recombinant Rab2 Isoform of Leishmania donovani

BACKGROUND

The most fatal form of Visceral leishmaniasis or kala-azar is caused by the intracellular protozoan parasite Leishmania donovani. The life cycle and the infection pathway of the parasite are regulated by the small GTPase family of Rab proteins. The involvement of Rab proteins in neurodegenerative amyloidosis is implicated in protein misfolding, secretion abnormalities and dysregulation. The inter and intra-cellular shuttlings of Rab proteins are proposed to be aggregation-prone. However, the biophysical unfolding and aggregation of protozoan Rab proteins is limited. Understanding the aggregation mechanisms of Rab protein will determine their physical impact on the disease pathogenesis and individual health.

OBJECTIVE

This work investigates the acidic pH-induced unfolding and aggregation of a recombinant Rab2 protein from L. donovani (rLdRab2) using multi-spectroscopic probes.

METHODS

The acidic unfolding of rLdRab2 is characterised by intrinsic fluorescence and ANS assay, while aggregation is determined by Thioflavin-T and 90⁰ light scattering assay. Circular dichroism determined the secondary structure of monomers and aggregates. The aggregate morphology was imaged by transmission electron microscopy.

RESULTS

rLdRab2 was modelled to be a Rab2 isoform with loose globular packing. The acidinduced unfolding of the protein is a plausible non-two-state process. At pH 2.0, a partially folded intermediate (PFI) state characterised by ~ 30% structural loss and exposed hydrophobic core was found to accumulate. The PFI state slowly converted into well-developed protofibrils at high protein concentrations demonstrating its amyloidogenic nature. The native state of the protein was also observed to be aggregation-prone at high protein concentrations. However, it formed amorphous aggregation instead of fibrils.

CONCLUSION

To our knowledge, this is the first study to report in vitro amyloid-like behaviour of Rab proteins in L donovani. This study provides a novel opportunity to understand the complete biophysical characteristics of Rab2 protein of the lower eukaryote, L. donovani.

Amyloid Fibrils of Pisum sativum L. Vicilin Inhibit Pathological Aggregation of Mammalian Proteins

Although incurable pathologies associated with the formation of highly ordered fibrillar protein aggregates called amyloids have been known for about two centuries, functional roles of amyloids have been studied for only two decades. Recently, we identified functional amyloids in plants. These amyloids formed using garden pea Pisum sativum L. storage globulin and vicilin, accumulated during the seed maturation and resisted treatment with gastric enzymes and canning. Thus, vicilin amyloids ingested with food could interact with mammalian proteins. In this work, we analyzed the effects of vicilin amyloids on the fibril formation of proteins that form pathological amyloids. We found that vicilin amyloids inhibit the fibrillogenesis of these proteins. In particular, vicilin amyloids decrease the number and length of lysozyme amyloid fibrils; the length and width of β-2-microglobulin fibrils; the number, length and the degree of clustering of β-amyloid fibrils; and, finally, they change the structure and decrease the length of insulin fibrils. Such drastic influences of vicilin amyloids on the pathological amyloids' formation cause the alteration of their toxicity for mammalian cells, which decreases for all tested amyloids with the exception of insulin. Taken together, our study, for the first time, demonstrates the anti-amyloid effect of vicilin fibrils and suggests the mechanisms underlying this phenomenon.

The effect of novel antihypertensive drug valsartan on lysozyme aggregation: A combined in situ and in silico study

Protein misfolding can result in amyloid fiber aggregation, which is associated with various types of diseases. Therefore, preventing or treating abnormally folded proteins may provide therapeutic intervention for these diseases. Valsartan (VAL) is an angiotensin II receptor blocker (ARB) that is used to treat hypertension. In this study, we examine the anti-aggregating effect of VAL against hen egg-white lysozyme (HEWL) amyloid fibrils through spectroscopy, docking, and microscopic analysis. In vitro formation of HEWL amyloid fibrils was indicated by increased turbidity, RLS (Rayleigh light scattering), and ThT fluorescence intensity. 10 μM VAL, amyloid/aggregation was inhibited up to 83% and 72% as measured by ThT and RLS respectively. In contrast, 100 μM VAL significantly increases the fibril aggregation of HEWL. CD spectroscopy results show a stabilization of HEWL α-helical structures in the presence of 10 μM VAL while the increase in β-sheet was detected at 100 μM concentration of VAL. The hydrophobicity of HEWL was increased at 100 μM VAL, suggesting the promotion of aggregation via its self-association. Steady-state quenching revealed that VAL and HEWL interact spontaneously via hydrogen bonds and van der Waals forces. Transmission electron microscopy (TEM) images illustrate that the needle-like fibers of HEWL amyloid were reduced at 10 μM VAL, while at 100 μM the fibrils of amyloid were increased. Additionally, our computational studies showed that VAL could bind to two binding sites within HEWL. In the BS-1 domain of HEWL, VAL binds to ASN⁵⁹, ILE⁹⁸, ILE⁵⁸, TRP¹⁰⁸, VAL¹⁰⁹, SER⁵⁰, ASP⁵², ASN⁵⁹, ALA¹⁰⁷, and TRP¹⁰⁸ residues with a binding energy of -9.72 kcal mol^-1. Also, it binds to GLU⁷, ALA¹⁰, ALA¹¹, CYS⁶, ARG¹²⁸, and ARG¹⁴ in the BS-2 domain with a binding energy of -5.89 kcal mol^-1. VAL, therefore, appears to have dual effect against HEWL aggregation. We suggest that VAL stabilizes HEWL's aggregation-prone region (APR) at 10 μM, preventing aggregation. Also, we assume that at 100 μM, VAL occupies BS-2 beside BS-1 and destabilizes the folding structure of HEWL, resulting in aggregation. Further studies are needed to investigate the mechanism of action and determine its potential side effects.

Effect of Antihypertensive Drug (Chlorothiazide) on Fibrillation of Lysozyme: A Combined Spectroscopy, Microscopy, and Computational Study

Amyloid fibrils abnormally accumulate together in the human body under certain conditions, which can result in lethal conditions. Thus, blocking this aggregation may prevent or treat this disease. Chlorothiazide (CTZ) is a diuretic and is used to treat hypertension. Several previous studies suggest that diuretics prevent amyloid-related diseases and reduce amyloid aggregation. Thus, in this study we examine the effects of CTZ on hen egg white lysozyme (HEWL) aggregation using spectroscopic, docking, and microscopic approaches. Our results showed that under protein misfolding conditions of 55 °C, pH 2.0, and 600 rpm agitation, HEWL aggregated as evidenced by the increased turbidity and Rayleigh light scattering (RLS). Furthermore, thioflavin-T, as well as trans electron microscope (TEM) analysis confirmed the formation of amyloid structures. An anti-aggregation effect of CTZ is observed on HEWL aggregations. Circular dichroism (CD), TEM, and Thioflavin-T fluorescence show that both CTZ concentrations reduce the formation of amyloid fibrils as compared to fibrillated. The turbidity, RLS, and ANS fluorescence increase with CTZ increasing. This increase is attributed to the formation of a soluble aggregation. As evidenced by CD analysis, there was no significant difference in α-helix content and β-sheet content between at 10 µM CTZ and 100 µM. A TEM analysis of HEWL coincubated with CTZ at different concentrations validated all the above-mentioned results. The TEM results show that CTZ induces morphological changes in the typical structure of amyloid fibrils. The steady-state quenching study demonstrated that CTZ and HEWL bind spontaneously via hydrophobic interactions. HEWL-CTZ also interacts dynamically with changes in the environment surrounding tryptophan. Computational results revealed the binding of CTZ to ILE⁹⁸, GLN⁵⁷, ASP⁵², TRP¹⁰⁸, TRP⁶³, TRP⁶³, ILE⁵⁸, and ALA¹⁰⁷ residues in HEWL via hydrophobic interactions and hydrogen bonds with a binding energy of -6.58 kcal mol^-1. We suggest that at 10 µM and 100 μM, CTZ binds to the aggregation-prone region (APR) of HEWL and stabilizes it, thus preventing aggregation. Based on these findings, we can conclude that CTZ has antiamyloidogenic activity and can prevent fibril aggregation.

Mechanistic insights into monomer level prevention of amyloid aggregation of lysozyme by glycyrrhizic acid

As the primary bioactive compound of glycyrrhiza rhizome, the triterpene glycoside conjugate Glycyrrhizic acid (GA) has demonstrated neuroprotective effects in vivo. This study evaluates the effectiveness of GA as an inhibitor of GuHCl-induced amyloid aggregation of hen egg white lysozyme (HEWL). Fibril formation as measured by Thioflavin-T fluorescence, 90⁰ light scattering, and 8-Anilinonaphthalene-1-sulfonic acid (ANS) fluorescence illustrated ∼90 % prevention of fibrils at [GA]/[HEWL] ≥2:1. Images of Transmission electron microscopy evidence for the absence of any fibril or amorphous aggregation products. The spectral characteristics of soluble HEWL were in close resemblance to unfolded monomer. Computational and fluorescence investigations performed to analyse GA-HEWL interactions demonstrated slightly higher affinity of GA to unfolded HEWL and aggregation-prone regions. The likely mechanism of monomer level aggregation prevention by GA as dermined by computational, stability, and ANS experiments illustrated that GA modulated the compactness, solvent-accessible surface, and solvent-exposed hydrophobic surfaces of aggregation-prone state of HEWL. Our findings corroborate GA as an effective inhibitor of HEWL amyloid formation. To our knowledge, GA interaction-induced inhibition of aggregation-prone states has not been previously discussed. GA's modulation of aggregation-prone states of disease-related proteins will successfully develop GA as an amyloid inhibitor for clinical trials of amyloidosis and neurodegenerative illnesses.

Influence of stabilizing osmolytes on hen egg white lysozyme fibrillation

Communicated by Ramaswamy H. Sarma.

The inhibitory effect of Sunset Yellow on thermally induced Human Serum Albumin aggregates: Possible role in naturopathy

Intensive research in the field of protein aggregation confirmed that the deposition of amyloid fibrils of proteins are the major cause for the development of various neurotoxic and neurodegenerative diseases, which could be controlled by ensuring the efficient inhibition of aggregation using anti aggregation strategies. Herein, we elaborated the anti amyloidogenic potential of Sunset Yellow (SY) dye against Human Serum Albumin (HSA) fibrillogenesis utilising different biophysical, computational and microscopic techniques. The inhibitory effect of sunset yellow was confirmed by Rayleigh Light Scattering (RLS) measurements along with different dye binding assays (ANS, ThT and CR) by showing concentration dependent reduction in scattering intensity and fluorescence intensity respectively. Further, destabilization and anti fibrillation activity of HSA aggregates were characterized through spectroscopic techniques like Circular Dichroism (CD) and other microscopic techniques like Transmission Electron Microscopy (TEM) for elucidating the structural properties. The SDS-PAGE was also carried out that render the disaggregation effect of the dye on the protein. Moreover, Molecular Docking studies revealed the binding parameters justifying the stable protein-dye complex. Simulation studies were also performed accordingly. Thus, this dye which is used as food additive can serve as a potential aggregation inhibiting agent that can aid in the prevention of amyloidogenic diseases.

Characterizing the Dynamic Disassembly/Reassembly Mechanisms of Encapsulin Protein Nanocages

Encapsulins, self-assembling icosahedral protein nanocages derived from prokaryotes, represent a versatile set of tools for nanobiotechnology. However, a comprehensive understanding of the mechanisms underlying encapsulin self-assembly, disassembly, and reassembly is lacking. Here, we characterize the disassembly/reassembly properties of three encapsulin nanocages that possess different structural architectures: T = 1 (24 nm), T = 3 (32 nm), and T = 4 (42 nm). Using spectroscopic techniques and electron microscopy, encapsulin architectures were found to exhibit varying sensitivities to the denaturant guanidine hydrochloride (GuHCl), extreme pH, and elevated temperature. While all three encapsulins showed the capacity to reassemble following GuHCl-induced disassembly (within 75 min), only the smallest T = 1 nanocage reassembled after disassembly in basic pH (within 15 min). Furthermore, atomic force microscopy revealed that all encapsulins showed a significant loss of structural integrity after undergoing sequential disassembly/reassembly steps. These findings provide insights into encapsulins' disassembly/reassembly dynamics, thus informing their future design, modification, and application.

Inhibition and disruption of amyloid formation by the antibiotic levofloxacin: A new direction for antibiotics in an era of multi-drug resistance

Neurodegenerative diseases are a group of debilitating maladies involving protein aggregation. To this day, all advances in neurodegenerative disease therapeutics have helped symptomatically but have not prevented the root cause of the disease, i.e., the aggregation of involved proteins. Antibiotics are becoming increasingly obsolete due to the rising multidrug resistance strains of bacteria. Thus, antibiotics, if put to different use as therapeutics against other diseases, could pave a new direction to the world of antibiotics. Hence, we studied the antibiotic levofloxacin for its potential anti-amyloidogenic behavior using human lysozyme, a protein involved in non-systemic amyloidosis, as a model system. At the sub-stoichiometric level, levofloxacin was able to inhibit amyloid formation in human lysozyme as observed by various spectroscopic and microscopic methods, with IC₅₀ values as low as 8.8 ± 0.1 μM. Levofloxacin also displayed a retarding effect on seeding phenomena by elongating the lag-phase (from 0 to 88 h) at lower concentration, and arresting lysozyme fibrillation at the lag stage in sub-stoichiometric concentrations. Structural and computational analyses provided mechanistic insight showing that levofloxacin stabilizes the lysozyme in the native state by binding to the aggregation-prone residues, and thereby inhibiting amyloid fibrillation. Levofloxacin also showed the property of disrupting amyloid fibrils into a smaller polymeric form of proteins which were less cytotoxic as confirmed by hemolytic assay. Therefore, we throw new light on levofloxacin as an amyloid inhibitor and disruptor which could pave way to utilization of levofloxacin as a potential therapeutic against non-systemic amyloidosis and neurodegenerative diseases.

The albumin-based nanoparticle formation in relation to protein aggregation

Albumin is an attractive protein for the preparation of nanoparticle with possible therapeutic applications, due to its biodegradable, nontoxic, non-immunogenic, and metabolizable properties. Many studies have investigated the formation of albumin nanoparticles, generally by the desolvation or coacervation approaches. One of the most important parameters that should be considered in the formation of nanoparticles is their morphology (size and shape). There are many proposals to control the nanoparticle size, but it remains a challenge for researchers yet. In this study, we showed that control of BSA-based nanoparticles/microparticles size could be achieved by varying the temperature and pH and therefore controlling the rate of aggregation. The aggregation behavior was monitored by UV-Vis spectroscopy, SEM, and dye-binding assay. Our results provide more options for the size and shape control of BSA-based nanoparticle in natural buffer systems. The aggregation of BSA at different temperatures within the range of 50-80 °C were studied under the effect of different pHs in the range of 4.7-6.2. In this research, we found that protein aggregation under extreme conditions of pH and temperature, or at the pH near to pI appears to be amorphous, and at the pH above the pI seems to be the amyloid fibril structure. In some instances where the aggregation is neither too fast nor too slow, in the initial phase of the aggregation process, nanoparticle structures can be identified and separated by mechanistic approaches. This observation suggests that the best condition for monitoring the formation of albumin-based nanoparticles could be pH 5.7, 70 °C. Satisfactory rationalization of all aspects of our experimental observation requires further and more detailed study.

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.

Inhibition behavior of Sennoside A and Sennoside C on amyloid fibrillation of human lysozyme and its possible mechanism

Amyloid proteins were recognized as the crucial cause of many senile diseases. In this study, the inhibitory effects of Sennoside A (SA) and Sennoside C (SC) on amyloid fibrillation were evaluated by the combination of biophysical approaches and molecular docking tool using human lysozyme (HL) as amyloid-forming model. The results of thioflavin-T (ThT), 8-anilino-1-naphthalenesulfonic acid (ANS) and congo red (CR) assays indicated that both SA and SC could inhibit the amyloid fibrillation of HL in a dose-dependent manner. The IC₅₀ value of SA and SC on HL fibrillation was 200.09 μM and 186.20 μM, respectively. These findings were further verified by transmission electron microscopy (TEM) and atomic force microscopy (AFM), which showed that the addition of SA or SC could sharply reduce the amyloid fibrillation of HL. Additionally, the interactions of HL with SA and SC were investigated by steady-state fluorescence spectra and molecular docking studies. The results suggested that both SA and SC could bind to the binding pocket of HL and form a stable complex mainly via hydrogen bonds, van-der-Waals forces and hydrophobic interactions. In conclusion, our experiments revealed that both SA and SC can significantly inhibit amyloid fibrillation of HL.

Cross-Species and Cross-Polymorph Seeding of Lysozyme Amyloid Reveals a Dominant Polymorph

The ability to self-propagate is one of the most intriguing characteristics of amyloid fibrils, and is a feature of great interest both to stopping unwanted pathological amyloid, and for engineering functional amyloid as a useful nanomaterial. The sequence and structural tolerances for amyloid seeding are not well understood, particularly concerning the propagation of distinct fibril morphologies (polymorphs) across species. This study examined the seeding and cross-seeding reactions between two unique fibril polymorphs, one long and flexible (formed at pH 2) and the other short and rigid (formed at pH 6.3), of human lysozyme and hen egg-white lysozyme. Both polymorphs could cross-seed aggregation across species, but this reaction was markedly reduced under physiological conditions. For both species, the pH 6.3 fibril polymorph was dominant, seeding fibril growth with a faster growth rate constant at pH 2 than the pH 2 polymorph. Based on fibrillation kinetics and fibril morphology, we found that the pH 2 polymorph was not able to faithfully replicate itself at pH 6.3. These results show that two distinct amyloid polymorphs are both capable of heterologous seeding across two species (human and hen) of lysozyme, but that the pH 6.3 polymorph is favored, regardless of the species, likely due to a lower energy barrier, or faster configurational diffusion, to accessing this particular misfolded form. These findings contribute to our better understanding of amyloid strain propagation across species barriers.

Antibiotic hypersensitivity in MRSA induced by special protein aggregates

Emergence of multidrug-resistant bacteria is a major global concern. According to WHO, methicillin-resistant Staphylococcus aureus (MRSA) is a threatening pathogen resistant to a wide spectrum of antibiotics. Herein, to overcome drug resistance in MRSA, we successfully integrated traditional antibacterial methods but with a novel trick that included use of hen egg-white lysozyme's special aggregates generated by fibrillization. The minimum inhibitory concentration of oxacillin (Ox) for MRSA declined from 600 μM to <20 μM when using aggregates. Scanning and transition electron micrographs showed completely disrupted cells when treated with aggregated protein/Ox (20 μM). The assisting role of aggregates to induce antibiotic hypersensitivity was continuous and stable, but sub-inhibitory antibiotic concentration (20 μM) was required again after 8 h. Investigations regarding mechanism of antibiotic hypersensitivity revealed that aggregates were oligomers but not mature fibrils. Furthermore, reactive oxygen species levels rose significantly after treating bacteria with aggregated protein/Ox. Study of resistance mechanisms indicated that in response to wall structure alterations, mecA expression dropped significantly in the presence of aggregated protein/Ox (20 μM) relative to Ox (20 μM). This observation can be a breakthrough in finding alternatives where antibiotic dosage can be significantly reduced, thereby preventing emergence of new multidrug-resistant bacteria.

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.

The protein-binding N-terminal domain of human translation elongation factor 1Bβ possesses a dynamic α-helical structural organization

Translation elongation factor 1Bβ (eEF1Bβ) is a metazoan-specific protein involved into the macromolecular eEF1B complex, containing also eEF1Bα and eEF1Bγ subunits. Both eEF1Bα and eEF1Bβ ensure the guanine nucleotide exchange on eEF1A while eEF1Bγ is thought to have a structural role. The structures of the eEF1Bβ catalytic C-terminal domain and neighboring central acidic region are known while the structure of the protein-binding N-terminal domain remains unidentified which prevents clear understanding of architecture of the eEF1B complex. Here we show that the N-terminal domain comprising initial 77 amino acids of eEF1Bβ, eEF1Bβ(1-77), is a monomer in solution with increased hydrodynamic volume. This domain binds eEF1Bγ in equimolar ratio. The CD spectra reveal that the secondary structure of eEF1Bβ(1-77) consists predominantly of α-helices and a portion of disordered region. Very rapid hydrogen/deuterium exchange for all eEF1Bβ(1-77) peptides favors a flexible tertiary organization of eEF1Bβ(1-77). Computational modeling of eEF1Bβ(1-77) suggests several conformation states each composed of three α-helices connected by flexible linkers. Altogether, the data imply that the protein-binding domain of eEF1Bβ shows flexible spatial organization which may be needed for interaction with eEF1Bγ or other protein partners.

Effect of Silica Nanoparticles on the Amyloid Fibrillation of Lysozyme

Protein fibrils are regarded as undesired products as these are associated with numerous neuro- and non-neurodegenerative disorders. Increasing evidence suggests that the mechanism of fibrillation involves the formation of various oligomeric intermediates, which are known to be more toxic than mature fibrils. Here, we report the impact of synthesized silica nanoparticles (SiNPs) of diameters ∼52 nm on the aggregation behavior of hen egg white lysozyme (HEWL) under heat and acidic conditions. Congo red as well as ThT binding assays and AFM imaging studies indicate that SiNPs trigger the amyloid formation of HEWL in a dose-dependent manner. ThT kinetic studies and FTIR studies suggest that the fibrillation kinetics does not involve the formation of toxic oligomeric intermediates at higher concentrations of SiNPs. By measuring fluorescence lifetime values of the bound ThT, SiNP-induced fibrillation of HEWL can easily be realized. CD spectroscopic studies indicate that native HEWL becomes unfolded upon incubation under the experimental conditions and is rapidly converted into the β-sheet-rich fibrillar aggregates in the presence of SiNPs with increasing concentrations. It has been further revealed that fibrillar aggregates formed at higher concentrations of SiNPs preferably adopt an antiparallel β-sheet configuration. The enhanced fibrillation in the presence of SiNPs is likely because of preferential adsorption of the non-amyloidogenic regions of HEWL, resulting in the exposure of the aggregation-prone regions of HEWL toward the solvent. The study will provide deeper insights into the evolution of oligomer-free fibrillation that can be useful to demonstrate the underlying mechanism of amyloid fibrillation.

The physical basis of fabrication of amyloid-based hydrogels by lysozyme

Schematic of heating- and cooling-induced transitions between HEWL states, and the subsequent formation of the hydrogel.

Unveiling the stimulatory effects of tartrazine on human and bovine serum albumin fibrillogenesis: Spectroscopic and microscopic study

Amyloid fibrils are playing key role in the pathogenesis of various neurodegenerative diseases. Generally anionic molecules are known to induce amyloid fibril in several proteins. In this work, we have studied the effect of anionic food additive dye i.e., tartrazine (TZ) on the amyloid fibril formation of human serum albumins (HSA) and bovine serum albumin (BSA) at pHs7.4 and 3.5. We have employed various biophysical methods like, turbidity measurements, Rayleigh Light Scattering (RLS), Dynamic Light Scattering (DLS), intrinsic fluorescence, Congo red assay, far-UV CD, transmission electron microscopy (TEM) and atomic force microscopy (AFM) to decipher the mechanism of TZ-induce amyloid fibril formation in both the serum albumins at pHs7.4 and 3.5. The obtained results suggest that both the albumins forms amyloid-like aggregates in the presence of 1.0 to 15.0mM of TZ at pH3.5, but no amyloid fibril were seen at pH7.4. The possible cause of TZ-induced amyloid fibril formation is electrostatic and hydrophobic interaction because sulfate group of TZ may have interacted electrostatically with positively charged amino acids of the albumins at pH3.5 and increased protein-protein and protein-TZ interactions leading to amyloid fibril formation. The TEM, RLS and DLS results are suggesting that BSA forms bigger size amyloids compared to HSA, may be due to high surface hydrophobicity of BSA.

Glycine-rich loop encompassing active site at interface of hexameric M. tuberculosis Eis protein contributes to its structural stability and activity

RvEis is a crucial thermostable hexameric aminoglycoside acetyltransferase of Mycobacterium tuberculosis, overexpression of which confers Kanamycin resistance in clinical strains. The thermostability associated with hexameric RvEis is important for the enhanced intracellular survival of mycobacteria. However, the structural determinants responsible for its thermal stability remain unexplored. In this study, we have assessed the role of glycines of conserved glycine-rich motif (G¹²³GIYG¹²⁷) present at the oligomeric interface in the hydrophobic core of RvEis in sustenance of its structural stability, oligomerization and functional activity. Substitution of glycines to alanine (G123A/G127A) result in significant decrease in melting temperature (T_m), reduction in the oligomerization with concomitant increase in the monomeric form and higher susceptibility towards the denaturants like GdmCl and urea relative to wild type. G123A/G127A mutant displayed lower catalytic efficiency (k_cat/K_m) and is completely inactive at 60 °C. ANS binding assay and the complete dissociation of hexameric complex into monomers at lower concentration of urea in G123A/G127A relative to wtRvEis suggests that altered hydrophobic environment could be the reason for its instability. In sum, these results demonstrate the role of G¹²³GIYG¹²⁷ motif in structural stability and activity of RvEis.