The Achilles’ Heel of “Ultrastable” Hyperthermophile Proteins: Submillimolar Concentrations of SDS Stimulate Rapid Conformational Change, Aggregation, and Amyloid Formation in Proteins Carrying Overall Positive Charge

Broken but not beaten: Challenge of reducing the amyloids pathogenicity by degradation

BACKGROUND

The accumulation of ordered protein aggregates, amyloid fibrils, accompanies various neurodegenerative diseases (such as Parkinson's, Huntington's, Alzheimer's, etc.) and causes a wide range of systemic and local amyloidoses (such as insulin, hemodialysis amyloidosis, etc.). Such pathologies are usually diagnosed when the disease is already irreversible and a large amount of amyloid plaques have accumulated. In recent years, new drugs aimed at reducing amyloid levels have been actively developed. However, although clinical trials have demonstrated a reduction in amyloid plaque size with these drugs, their effect on disease progression has been controversial and associated with significant side effects, the reasons of which are not fully understood.

AIM OF REVIEW

The purpose of this review is to summarize extensive array of data on the effect of exogenous and endogenous factors (physico-mechanical effects, chemical effects of low molecular weight compounds, macromolecules and their complexes) on the structure and pathogenicity of mature amyloids for proposing future directions of the development of effective and safe anti-amyloid therapeutics.

KEY SCIENTIFIC CONCEPTS OF REVIEW

Our analysis show that destruction of amyloids is in most cases incomplete and degradation products often retain the properties of amyloids (including high and sometimes higher than fibrils, cytotoxicity), accelerate amyloidogenesis and promote the propagation of amyloids between cells. Probably, the appearance of protein aggregates, polymorphic in structure and properties (such as amorphous aggregates, fibril fragments, amyloid oligomers, etc.), formed because of uncontrolled degradation of amyloids, may be one of the reasons for the ambiguous effectiveness and serious side effects of the anti-amyloid drugs. This means that all medications that are supposed to be used both for degradation and slow down the fibrillogenesis must first be tested on mature fibrils: the mechanism of drug action and cytotoxic, seeding, and infectious activity of the degradation products must be analyzed.

SDBS induces multiple catalase conformations in a dose-dependent manner

Amyloid fibrils have been linked to several incurable diseases. They are long and thin fibrous proteins that self-assemble into fibrils. Small molecules can stimulate amyloid fibrillation, but the mechanism by which this happens is not well understood. This study examined how a negatively charged benzene ring containing surfactant, sodium dodecylbenzene sulphonate (SDBS), affects the fibrillation of bovine liver catalase (BLC). After SDBS treatment, BLC conformational changes were examined in vitro using turbidity, RLS kinetics, intrinsic fluorescence, ThT fluorescence, far-UV CD, and TEM. BLC in the native state was alpha-helical at pH 7.4, while it was converted to a random coil structure at pH 2.0. Far-UV CD and intrinsic fluorescence data showed that at concentrations <0.1 mM of SDBS, randomly coiled BLC assumed a native-like alpha-helical structure. However, between 0.1 and 1.0 mM SDBS, BLC was aggregated. ThT fluorescence and far-UV CD measurements showed the amyloid-like structures in the aggregated BLC. At higher SDBS concentrations (>1.0 mM) at pH 2.0, BLC again attains a native-like alpha-helical structure. It is essential for therapeutic purposes to clearly understand the process underlying surfactant- or lipid-induced fibrillation.

Bovine liver catalase turns into three conformational states after exposure to an anionic surfactant

The mechanism by which anionic surfactants promote amyloid fibril is not well understood. Here, we investigated how sodium dodecyl sulfate (SDS), a negatively charged surfactant, affects the fibrillation of the partially unfolded random-coiled bovine liver catalase (BLC) at a pH of 2.0. We used several methods, including turbidity, RLS kinetics, intrinsic fluorescence, ThT fluorescence, far-UV CD, and TEM imaging, to evaluate the conformational changes of BLC in vitro in response to SDS treatment. BLC is a multimeric protein and well folded at physiological pH but forms a random coil structure at pH 2.0. Intrinsic fluorescence and far-UV CD data showed that below 0.1 mM SDS, random coiled BLC turned into a native-like structure. BLC incubated with an SDS concentration ranging from 0.1 to 2.0 mM led to the formation of aggregates. The ThT fluorescence intensity was enhanced in the aggregated BLC samples (0.1-2.0 mM SDS), and cross beta-sheeted structure was detected by the far UV CD measurements. BLC adopts a complete alpha-helical structure upon interacting with SDS at a more than 2.0 mM concentration at pH 2.0. Understanding the mechanism of surfactant- or lipid-induced fibrillation is important for therapeutic purposes.

SDS-induced hexameric oligomerization of myotoxin-II from Bothrops asper assessed by sedimentation velocity and nuclear magnetic resonance

We report the solution behavior, oligomerization state, and structural details of myotoxin-II purified from the venom of Bothrops asper in the presence and absence of sodium dodecyl sulfate (SDS) and multiple lipids, as examined by analytical ultracentrifugation and nuclear magnetic resonance. Molecular functional and structural details of the myotoxic mechanism of group II Lys-49 phospholipase A2 homologues have been only partially elucidated so far, and conflicting observations have been reported in the literature regarding the monomeric vs. oligomeric state of these toxins in solution. We observed the formation of a stable and discrete, hexameric form of myotoxin-II, but only in the presence of small amounts of SDS. In SDS-free medium, myotoxin-II was insensitive to mass action and remained monomeric at all concentrations examined (up to 3 mg/ml, 218.2 μM). At SDS concentrations above the critical micelle concentration, only dimers and trimers were observed, and at intermediate SDS concentrations, aggregates larger than hexamers were observed. We found that the amount of SDS required to form a stable hexamer varies with protein concentration, suggesting the need for a precise stoichiometry of free SDS molecules. The discovery of a stable hexameric species in the presence of a phospholipid mimetic suggests a possible physiological role for this oligomeric form, and may shed light on the poorly understood membrane-disrupting mechanism of this myotoxic protein class.

Role of salts and solvents on the defibrillation of food dye "sunset yellow" induced hen egg white lysozyme amyloid fibrils

Several food dyes are known to induce amyloid fibrillation when interacting with proteins. Here, we studied the role of sunset yellow (SY) in the amyloid fibrillation of hen egg white lysozyme (HEWL) and characterized the changes using spectroscopy techniques. Turbidity results showed that SY dye induces aggregation in HEWL in concentrations dependent manner. The aggregation induced by SY dye is kinetically very fast, no lag phase was detected, and the kinetics process follows an isodesmic kinetics pathway. The SY-dye induce aggregates have cross-β secondary structure confirmed by far-UV CD measurements. The effect of salts and solvents was also seen on SY-induced aggregates. Turbidity, far-UV CD, and kinetics results suggest that certain concentrations of NaCl and (NH₄)₂SO₄ solubilize the SY-induce amyloid fibrils, but (NH₄)₂SO₄ is more effective. Similarly, solvents are also solubilized the SY-induces HEWL amyloid fibrillation but the order of defibrillation is as follows: Isopropanol> ethanol > methanol which signified that isopropanol is more effective than other solvents. The salts and solvents data suggest that the electrostatic, as well as hydrophobic interaction, is responsible for SY-induced amyloid fibrillation. These conformational changes should be examined, more seriously for the purpose of food safety.

Arsenite Induced Conformational Changes and Aggregation in Human Serum Albumin (HSA) and its Prevention by Naringin

Background:

Heavy metals and metalloids like arsenic, cadmium, mercury acts as denaturing agent for biomolecules. They interfere with protein’s physiological activity by forming a complex with the protein’s side chain or removing the essential metal ions from metalloproteins and replacing them. Protein aggregation is an extensive phenomenon in a cell and is linked with various pathological conditions.

Aim:

In this study, we aim to prove that proteins are highly susceptible to arsenite toxicity by arsenite-induced protein aggregation; and that naringin reduces the aggregation effect.

Methods:

Several biophysical techniques were employed to study the protein aggregation due to arsenite and its prevention by naringin.

Results:

Through our experiments, the results showed that aggregation induced by arsenite was reduced in the presence of naringin at twice the concentration of arsenite.

Conclusion:

In conclusion, our study showed that naringin plays a protective role during HSA aggregation due to arsenite.

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

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

Denaturant effect on amyloid fibrils: Declasterization, depolymerization, denaturation and reassembly

Accumulation of amyloid fibrils in organism accompanies many serious diseases, such as Alzheimer's and Parkinson's diseases, diabetes, prion diseases, etc. It is generally accepted that amyloids are highly resistant to degradation, which complicates their elimination in vivo and is one of the reasons for their pathogenicity. However, using a wide range of physicochemical approaches and specially elaborated method for the tested samples preparation by equilibrium microdialysis technique, it is proved that the stability of amyloids is greatly exaggerated. It turned out that amyloid fibrils formed from at least two amyloidogenic proteins, one of which is a model object for fibrils studying and the second is the cause of hemodialysis amyloidosis in an acute renal failure, are less stable than monomeric proteins. A mechanism of the degradation/reassembly of amyloid fibrils was proposed. It was shown that amyloid «seed» is a factor affecting not only the rate of the fibrils formation, but also their structure. Obtained results are a step towards identifying effects that can lead to degradation of amyloids and their clearance without adverse influence on the functionally active state of the protein or to change the structure and, as a result, the pathogenicity of these protein aggregates.

Structure-guided mutational evidence and postulates explaining how a glycohydrolase from Pyrococcus furiosus functions simultaneously as an amylase and as a 4-α-glucanotransferase

Pyrococcus furiosus exoamylase-cum-4-α-glucanotransferase (4-α-GTase; PF0272; PfuAmyGT) is reported to both (i) act upon starch, and (ii) catalyze 'disproportionation' of maltooligosaccharides (with glucose as the smallest product). PfuAmyGT shares ∼65% sequence identity with a homo-dimeric Thermococcus litoralis 4-α-GTase, for which structures are available in complex with a non-hydrolysable analog of maltotetraose (acarbose) bound to one subunit and maltose (of unknown origin) bound to the other subunit. We structurally transposed the maltose onto the acarbose-bound subunit and discovered that the two molecules lie juxtaposed in what could be perfect 'acceptor' and 'donor' substrate-binding sites, respectively. We also discovered that there is a loop between the two sites which could use an available aspartate to excise a glucose from the donor, and an available tryptophan to transfer the glucose to the non-reducing end of the acceptor glucan. We derived a structure for PfuAmyGT through homology-based modeling, identified the potential donor site, acceptor site, glucan-transferring loop, and catalytically important residues, and mutated these to alanine to examine effect(s) upon activity. Mutation D362A abolished creation of shorter, or longer, maltooligosaccharides. Mutation W365A abolished creation of longer oligosaccharides. Mutation H366A had no effect on activity. We propose that D362 facilitates glucose excision, and that W365 facilitates its transfer, either (a) directly into solution (allowing PfuAmyGT to act as an exoamylase), or (b) by glycoside bond formation with an acceptor (allowing PfuAmyGT to act as a 4-α-glucanotransferase), depending upon whether the acceptor site is vacant or occupied in a reaction cycle.

Complete observation of all structural, conformational, and fibrillation transitions of monomeric globular proteins at submicellar sodium dodecyl sulfate concentrations

Although considerable information is available regarding protein-sodium dodecyl sulfate (SDS) interactions, it is still unclear as to how much SDS is needed to denature proteins. The role of protein charge and micellar surfactant concentration on amyloid fibrillation is also unclear. This study reports on equilibrium measurements of SDS interaction with six model proteins and analyzes the results to obtain a general understanding of conformational breakdown, reorganization and restructuring of secondary structure, and entry into the amyloid fibrillar state. Significantly, all of these responses are entirely resolved at much lower than the critical micellar concentration (CMC) of SDS. Electrostatic interaction of the dodecyl sulfate anion (DS^- ) with positive surface potential on the protein can completely unfold both secondary and tertiary structures, which is followed by protein chain restructuration to α-helices. All SDS-denatured proteins contain more α-helices than the corresponding native state. SDS interaction stochastically drives proteins to the aggregated fibrillar state.

Monomeric Camelus dromedarius GSTM1 at low pH is structurally more thermostable than its native dimeric form

Glutathione S‒transferases (GSTs) are multifunctional enzymes that play an important role in detoxification, cellular signalling, and the stress response. Camelus dromedarius is well-adapted to survive in extreme desert climate and it has GSTs, for which limited information is available. This study investigated the structure-function and thermodynamic properties of a mu-class camel GST (CdGSTM1) at different pH. Recombinant CdGSTM1 (25.7 kDa) was expressed in E. coli and purified to homogeneity. Dimeric CdGSTM1 dissociated into stable but inactive monomeric subunits at low pH. Conformational and thermodynamic changes during the thermal unfolding pathway of dimeric and monomeric CdGSTM1 were characterised via a thermal shift assay and dynamic multimode spectroscopy (DMS). The thermal shift assay based on intrinsic tryptophan fluorescence revealed that CdGSTM1 underwent a two-state unfolding pathway at pH 1.0-10.0. Its Tm value varied with varying pH. Another orthogonal technique based on far-UV CD also exhibited two-state unfolding in the dimeric and monomeric states. Generally, proteins tend to lose structural integrity and stability at low pH; however, monomeric CdGSTM1 at pH 2.0 was thermally more stable and unfolded with lower van't Hoff enthalpy. The present findings provide essential information regarding the structural, functional, and thermodynamic properties of CdGSTM1 at pH 1.0-10.0.

Structural insights into a multifunctional inhibitor, 'AMTIN' from tubers of Alocasia macrorrhizos and its possible role in dengue protease (NS2B-NS3) inhibition

Protease inhibitors from plants play major role in defensive mechanism against various pathogenic organisms. AMTIN from the tubers of Alocasia macrorrhiza has been purified and characterized as multi-functional Kunitz type protease inhibitor. AMTIN is varied from other KTIs by having three different loops specific for binding to trypsin/amylase and subtilisin that are located approximately 30Ǻ away from one another as evidenced from crystallographic efforts. Biochemical studies on AMTIN reveal simultaneous binding of protease/amylase and have been cross validated using in-silico tools to model Amylase - AMTIN - Trypsin complex without any steric clashes. Apart from multi functionality, the remarkable structural and functional stability of AMTIN at high temperature, presence of many phosphorylation, myristoylation and glycosylation sites and molecular docking studies with dengue viral protease (NS2B-NS3) makes this protein interesting. Hence AMTIN can be considered as a template to design effective antivirals against dengue virus.

Allantoin and hydantoin as new protein aggregation suppressors

Allantoin is widely used in pharmaceutical and cosmetic products, and is composed of a hydantoin ring and a ureido group. Recent reports showed that allantoin suppresses thermal aggregation of hen egg white lysozyme (LYZ). However, structural insight into the properties of allantoin on protein aggregation and whether allantoin controls the aggregation of other proteins under different stress conditions remain unclear. Here we studied the structural properties of allantoin in terms of its effects on protein aggregation by comparing allantoin with urea and hydantoin. Furthermore, we analyzed the effects of allantoin and its derivatives on the aggregation of LYZ, carbonic anhydrase from bovine erythrocytes (BCA), albumin from chicken egg white (OVA), and immunoglobulin G (IgG) by various stresses in comparison with arginine. These four proteins are widely different in charged state and molecular size. Allantoin suppressed the aggregation and inactivation of LYZ comparing to arginine without affecting the melting temperature of proteins, and was responsible for the slightly improved formation of soluble oligomers and insoluble aggregates of IgG with thermal and acidic stresses. In contrast, hydantoin increased the solubility of aromatic amino acids more effectively than arginine and allantoin. The structural properties underlying the observed effects of allantoin as an aggregation suppressor include hydrophobic interactions between hydantoin moiety and aromatic ring on the surface of proteins, which is reflected on the difference between allantoin and arginine. These results show that the backbone of hydantoin ring may be a new category of additives for development of small aggregation suppressors.

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.

Aggregation and conformational stability evaluation of myoglobin in the presence of ionic surfactant

Sodium lauroyl sarcosinate (SLS) is frequently used for the solubilization of inclusion bodies in vitro due to its structural similarity to lipid plasma membrane. There are many factors that could influence protein aggregation propensity, including overall protein surface charge and hydrophobicity. Here, the aggregation pathway of myoglobin protein was studied under different conditions (pH 3.5 and 7.4) in the presence of varying concentrations of SLS to evaluate the underlying forces dictating protein aggregation. Data obtained from Rayleigh light scattering, ThT binding assay, and far-UV CD indicated that SLS have different effects on the protein depending on its concentration and environmental conditions. In the presence of low concentrations of SLS (0.05-0.1 mM), no aggregation was detected at both pH conditions tested. Whereas, as we reach higher SLS concentrations (0.5-10.0 mM), myoglobin started forming larger-sized aggregates at pH 3.5 and not pH 7.4. These results suggest that electrostatics interactions as well as hydrophobic forces play an important role in SLS-induced myoglobin aggregation.

pH induced single step shift of hydrophobic patches followed by formation of an MG state and an amyloidogenic intermediate in Lima Bean Trypsin Inhibitor (LBTI)

Lima Bean Trypsin Inhibitor (LBTI) is 83 residues monomeric protein of 9.0 KDa, consisting of six antiparallel β-strands and can undergo concentration dependant dimerization. We have tried to characterize folding intermediates of LBTI under equilibrium denaturation conditions. We have used various spectroscopic and microscopic techniques to understand the folding and misfolding pathways. LBTI forms molten globule structure at pH 2 and amyloidiogenic intermediate state (I^a) at pH 4. pH induced Shifting of surface exposed hydrophobic patches and that followed by withdrawal of the lone tyrosine residue (Y69) towards nonpolar environment have been reported. Denaturation profile of native and molten globule (MG) states of LBTI in presence of guanidine hydrochloride show sigmoidal curves with non-coincidental and irreversible behaviour in both states. Concentration dependent amyloid fibril formation was confirmed by Thioflavin T and Congo Red binding and its morphology was studied by transmission electron microscopy (TEM). This is the first report on biophysical characterization of folding intermediates of LBTI and its aggregation behaviour to the best of our knowledge.