Formation Of Amyloid-like Fibrils Research Articles

Pharmacological induction of heat shock proteins ameliorates toxicity of mutant PKCγ in spinocerebellar ataxia type 14

Amyloid and amyloid-like protein aggregations are hallmarks of multiple, varied neurodegenerative disorders, including Alzheimer's and Parkinson's diseases. We previously reported that spinocerebellar ataxia type 14 (SCA14), a dominant-inherited neurodegenerative disease that affects cerebellar Purkinje cells, is characterized by the intracellular formation of neurotoxic amyloid-like aggregates of genetic variants of protein kinase Cγ (PKCγ). A number of protein chaperones, including heat shock protein 70 (Hsp70), promote the degradation and/or refolding of misfolded proteins and thereby prevent their aggregation. Here, we report that, in various SCA14-associated, aggregating PKCγ variants, endogenous Hsp70 is incorporated into aggregates and that expression of these PKCγ mutants up-regulates Hsp70 expression. We observed that PKCγ binds Hsp70 and that this interaction is enhanced in the SCA14-associated variants, mediated by the kinase domain that is involved in amyloid-like fibril formation as well as the C2 domain of PKCγ. Pharmacological up-regulation of Hsp70 by the Hsp90 inhibitors celastrol and herbimycin A attenuated the aggregation of mutant PKCγ in primary cultured Purkinje cells. Up-regulation of Hsp70 diminished net PKCγ aggregation by preventing aggregate formation, resulting in decreased levels of apoptotic cell death among primary cultured Purkinje cells expressing the PKCγ variant. Of note, herbimycin A also ameliorated abnormal dendritic development. Extending our in vitro observations, administration of celastrol to mice up-regulated cerebellar Hsp70. Our findings identify heat shock proteins as important endogenous regulators of pathophysiological PKCγ aggregation and point to Hsp90 inhibition as a potential therapeutic strategy in the treatment of SCA14.

Bacillus subtilis HelD, an RNA Polymerase Interacting Helicase, Forms Amyloid-Like Fibrils.

HelD, an RNA polymerase binding protein from Bacillus subtilis, stimulates transcription and helps in timely adaptation of cells under diverse environmental conditions. At present, no structural information is available for HelD. In the current study, we performed size exclusion chromatography coupled to small angle X-ray scattering (SEC-SAXS) which suggests that HelD is predominantly monomeric and globular in solution. Using combination of size exclusion chromatography and analytical ultracentrifugation, we also show that HelD has a tendency to form higher order oligomers in solution. CD experiments suggest that HelD has both α-helical (∼35%) and β sheet (∼26%) secondary structural elements. Thermal melting experiments suggest that even at 90°C, there is only about 30% loss in secondary structural contents with Tm of 44°C. However, with the increase in temperature, there was a gain in the β-sheet content and significant irreversible loss of α-helical content. Using a combination of X-ray fiber diffraction analysis, and dye based assays including Thioflavin-T based fluorescence and Congo red binding assays, we discovered that HelD forms amyloid-like fibrils at physiologically relevant conditions in vitro. Using confocal imaging, we further show that HelD forms amyloid inclusions in Escherichia coli. Bioinformatics-based sequence analysis performed using three independent web-based servers suggests that HelD has more than 20 hot-spots spread across the sequence that may aid the formation of amyloid-like fibrils. This discovery adds one more member to the growing list of amyloid or amyloid-like fibril forming cytosolic proteins in bacteria. Future studies aimed at resolving the function of amyloid-like fibrils or amyloid inclusions may help better understand their role, if any, in the bacterial physiology.

Inhibition of the Formation of Amyloid-Like Fibrils Using Herbal Extracts

We tested the amyloid fibril formation inhibitory effect of seven teas diluted in 55% ethanol at pH 7.0 at a protein concentration of 0.15 mg/ml α-chymotrypsin. In the experiments we investigated the formation and inhibition of amyloid fibrils by turbidity measurements, aggregation kinetics experiments and Congo red binding assay. The results suggest that the different teas effectively inhibit the formation of amyloidlike fibrils. The two most potent inhibitors were peppermint and melilot, extracts which almost completely inhibited the formation of aggregates in 5-fold dilution. The inhibitory effect on the aggregation formation of melilot and peppermint extracts was concentration dependant. The extent of inhibition was found to be proportional with the total concentration of phenolic compounds.

The Inhibitory Effect of Panax Ginseng Extract on Amyloid-like Fibril Formation of Trypsin in Aqueous Ethanol.

In case of several chronic diseases, prevention is could be more effective than treatment. Functional foods that contain significant amounts of bioactive components gained considerable attention not only in traditional but in modern medicine as well. We have investigated how P. ginseng extract inhibits the in vitro formation of amyloid-like fibrils of phenylmethylsulfonyl- trypsin (PMS-trypsin) in 60% ethanol at pH 7.0. The model system used is non-physiological, but it is capable of detecting the anti-amyloidogenic effect of the various agents. The main objective of this study was to examine the possible inhibitory effect of ginseng extract on amyloid-like fibril formation of trypsin in aqueous ethanol. The amyloid formation and aggregation kinetics of PMS-trypsin was studied by turbidity measurements, Congo Red (CR) binding assays, size exclusion chromatography and Electronic Circular Dichroism (ECD) measurements and the shapes of amyloid fibrils became visible by Transmission Electron Microscopy (TEM). In the presence of 500-fold diluted P. ginseng extract in the incubation mixture, the absorption at 350 nm decreased to 47.1% after incubation for 24 h, compared relative to the sample which contained no additives. CR binding experiments suggested that the aggregates in our samples have amyloid-like properties, and P. ginseng extract inhibits the amyloid-like fibril formation of PMS-trypsin depending on concentration. Our results show that the ginseng extract does not bind to the fibrils. In the absence of P. ginseng extracts large sized colloid aggregates were abundant. Adding P. ginseng extracts to our samples decreased the light dispersion of the solution. This is due to the decrease of the rate of the aggregation or to the smaller size of the aggregates evolved. Our results show that the presence of ginseng extract helps to maintain the native structure of the protein. In the presence of 500-fold diluted P. ginseng extract, TEM images demonstrated, that P. ginseng extract has inhibitory effect on the formation of amyloid-like fibrils of PMS-trypsin. The results indicated that P. ginseng extract significantly inhibits the formation of amyloid-like fibrils of PMS-trypsin in aqueous ethanol, and helps to maintain the native structure of the protein. The rate of inhibition depends on concentration. P. ginseng extract is an efficient antiamyloidogenic agent.

Reciprocal Interactions between Membrane Bilayers and S. aureus PSMα3 Cross-α Amyloid Fibrils Account for Species-Specific Cytotoxicity

Phenol-soluble modulin α3 (PSMα3) is a functional amyloid secreted by the pathogenic bacterium Staphylococcus aureus. This 22-residue peptide serves as a key virulence determinant, toxic to human cells via the formation of unique cross-α amyloid-like fibrils. We demonstrate that bilayer vesicles accelerated PSMα3 fibril formation, and the fibrils, in turn, inserted deeply into bilayers mimicking mammalian cell membranes, accounting for PSMα3 cellular toxicity. Importantly, a mere amphipathic helical conformation was not a sufficient determinant for membrane-activity of PSMα3, pointing to the functional role of cross-α fibrils. In contrast to deep insertion of PSMα3 into mammalian membrane bilayers, the peptide only interacted with the surface of bilayers mimicking bacterial membranes, which might be related to its lack of antibacterial activity. Together, our data provide mechanistic insight into species-specific toxicity of a key bacterial amyloid virulence factor via reciprocal interactions with membranes, and open new perspectives into amyloid-related cytotoxicity mediated by helical fibril structures.

Heparan sulfates facilitate harmless amyloidogenic fibril formation interacting with elastin-like peptides

Heparan sulfates (HSs) modulate tissue elasticity in physiopathological conditions by interacting with various matrix constituents as tropoelastin and elastin-derived peptides. HSs bind also to protein moieties accelerating amyloid formation and influencing cytotoxic properties of insoluble fibrils. Interestingly, amyloidogenic polypeptides, despite their supposed pathogenic role, have been recently explored as promising bio-nanomaterials due to their unique and interesting properties. Therefore, we investigated the interactions of HSs, obtained from different sources and exhibiting various degree of sulfation, with synthetic amyloidogenic elastin-like peptides (ELPs), also looking at the effects of these interactions on cell viability and cell behavior using in vitro cultured fibroblasts, as a prototype of mesenchymal cells known to modulate the soft connective tissue environment. Results demonstrate, for the first time, that HSs, with differences depending on their sulfation pattern and chain length, interact with ELPs accelerating aggregation kinetics and amyloid-like fibril formation as well as self-association. Furthermore, these fibrils do not negatively affect fibroblasts’ cell growth and parameters of redox balance, and influence cellular adhesion properties. Data provide information for a better understanding of the interactions altering the elastic component in aging and in pathologic conditions and may pave the way for the development of composite matrix-based biomaterials.

Inhibition of lysozyme fibrillogenesis by hydroxytyrosol and dopamine: An Atomic Force Microscopy study

Protein aggregation underlies many human diseases characterized by the deposition of normally soluble proteins in both fibrillar and amorphous aggregates. Here, Atomic Force Microscopy (AFM) has been applied to investigate the ability to inhibit hen egg white lysozyme (HEWL) fibrillogenesis by hydroxytyrosol (HT), one of the main phenolic components of olive oil. In this framework, HEWL is a useful and well-studied model protein whose amyloid-like fibril formation can be induced under experimental conditions where HT is more stable. HEWL fibrils, obtained at pH 1.6 and at 65 °C, exhibited a height of about 3 nm and a fibril length on average of about 3 μm. The presence of HT reduced the HEWL fibril number and length with respect to the control sample. Interestingly, also dopamine, a compound with a chemical structure similar to HT, decreased both the fibril number and the fibril length. AFM experimental data were supported by Thioflavin T assay and Fourier transform infrared spectroscopy. Our results show that HT is an effective inhibitor of HEWL aggregation, thus suggesting possible future applications of this natural compound for potential prevention or treatment of amyloid diseases, or as a lead molecular structure for the design of improved modulators.

Triazavirine supramolecular complexes as modifiers of the peptide oligomeric structure

In this study, we present molecular dynamics simulations of the antiviral drug triazavirine, that affects formation of amyloid-like fibrils of the model peptide (SI). According to our simulations, triazavirine is able to form linear supramolecular structures which can act as shields and prevent interactions between SI monomers. This model, as validated by simulations, provides an adequate explanation of triazavirine’s mechanism of action as it pertains to SI peptide fibril formation.

Inhibition of Amyloid-like Fibril Formation of Trypsin by Red Wines

The aim of the present study was to examine the potential role and applicability of dietary supplements in reducing the risk of development of amyloid diseases associated with the gastrointestinal tract, such as type II diabetes. Trypsin, a well-known serine protease was used as a model protein in our experiments. The effect of various red wines on the formation of amyloid-like fibrils of trypsin was studied in vitro, in aqueous ethanol, at pH 7.0. Turbidity measurements, aggregation kinetics experiments, Congo red binding assays and electronic circular dichroism spectroscopic measurements were used to follow the aggregation process in the presence or absence of various red wines. The results suggest that red wines effectively inhibit the formation of amyloid-like fibrils of trypsin and the inhibitory effect is dose-dependent. The extent of inhibition was found to be proportional to the total concentration of phenolic compounds.

Sucrose modulates insulin amyloid-like fibril formation: effect on the aggregation mechanism and fibril morphology

Sucrose modifies the human insulin fibrillation pathways, affecting the fibril morphology.

Effect of lipid environment on amyloid fibril formation of human serum amyloid A

Human serum amyloid A (SAA) is a precursor protein of AA amyloidosis and a component of high-density lipoproteins (HDLs), thus it is essential to investigate the amyloid fibril formation of SAA under a lipid environment. We used synthetic fragment peptides corresponding to the N-terminal (residues 1–27) and central (residues 43–63) regions of the SAA molecule, which are known to have amyloidogenic properties. Measurements of tryptophan fluorescence in conjunction with circular dichroism showed that SAA (1–27) peptide binds to neutral and acidic lysophospholipids, whereas SAA (43–63) peptide binds only to acidic lysophospholipids. For both these SAA peptides, binding to lysophospholipids inhibited heparin-induced amyloid-like fibril formation by stabilizing the α-helical structure. However, acidic lysophospholipids implied a possibility to promote fibril formation of SAA (1–27) peptide by themselves. These results suggest that the amyloid fibril formation of SAA may be modulated by altering the lipid head group composition of HDLs during metabolism.

Understanding curcumin-induced modulation of protein aggregation

Curcumin, a diarylheptanoid compound, found in spice turmeric is known to alter the aggregation of proteins and reduce the toxicity of the aggregates. This review looks at the molecular basis of modulating protein aggregation and toxicity of the aggregates. Foremost, we identify the interaction of curcumin and its derivatives with proteins/peptides and the effect of their interaction on the conformational stability and unfolding/folding pathway(s). The unfolding/folding processes generate partially folded/unfolded intermediate, which serve as aggregation precursor state. Secondly, we discuss the effect of curcumin binding on the kinetics parameters of the aggregation process, which give information about the mechanism of the aggregation inhibition. We describe, in addition, that curcumin can accelerate/promote fibril formation by binding to oligomeric intermediate(s) accumulated in the aggregation pathway. Finally, we discuss the correlation of curcumin-induced monomeric and/or oligomeric precursor states with aggregate structure and toxicity. On the basis of these discussions, we propose a model describing curcumin-induced inhibition/promotion of formation of amyloid-like fibrils.

Amyloid-like Fibril Formation by Trypsin in Aqueous Ethanol. Inhibition of Fibrillation by PEG.

The formation of amyloid-like fibrils was studied by using the well-known serine protease trypsin as a model protein in the presence of ethanol as organic solvent. Trypsin forms amyloid-like fibrils in aqueous ethanol at pH = 7.0. The dye Congo red (CR) was used to detect the presence of amyloid-like fibrils in the samples. The binding of CR to fibrils led to an increase in absorption intensity and a red shift in the absorption band of CR. Thioflavin T (ThT) and 8-anilino-1- naphthalenesulfonic acid (ANS) binding assays were employed to characterize amyloid-like fibril formation. The ThT binding assay revealed that the protein exhibited maximum aggregation in 60% (v/v) ethanol after incubation for 24 h at 24 (o)C. The ANS binding results indicated that the hydrophobic residues were more exposed to the solvent in the aggregated form of the protein. The effects of polyethylene glycol (PEG) on the formation of amyloid-like fibrils was studied in vitro. The aggregation of trypsin was followed via the kinetics of aggregation, the far-UV circular dichroism (CD) and transmission electron microscopy (TEM) in the presence and absence of PEG. The CD measurements indicated that the protein aggregates have a cross-beta structure in 60% ethanol. TEM revealed that trypsin forms fibrils with a thread-like structure. The inhibitory effect of PEG on the aggregation of trypsin increased with rising PEG concentration. PEG therefore inhibits the formation of amyloid-like fibrils of trypsin in aqueous ethanol.

Insulin Fibrillization at Acidic and Physiological pH Values is Controlled by Different Molecular Mechanisms.

Formation of amyloid-like fibrils by insulin was studied at different insulin concentrations, pH and temperatures. At low pH (pH 2.5) the insulin fibrillization occurred only at high ([10 lM) peptide concentrations, whereas at physiological pH values the fibril formation is inhibited at higher insulin concentrations. The enthalpy of activation Ea of the fibril growth at pH 2.5 equals to 33 kJ/mol, which is considerably lower than 84 kJ/mol at physiological pH. The fibrillization rate of insulin decreases with increasing pH at high, 250 lM concentration, which was opposite to the pH effect observed in 2.5 lM insulin solutions. The latter effect indicates that protonation of histidine residues seems to be important for the fibrillization of monomeric insulin, whereas the pH effect at high concentration may result from off-pathway oligomerization propensity. Together, the different effect of environmental factors on the insulin fibrillization suggest that the reaction rate is controlled by different molecular events in acidic conditions and at physiological pH values.

Looking for a generic inhibitor of amyloid-like fibril formation among flavone derivatives.

A range of diseases is associated with amyloid fibril formation. Despite different proteins being responsible for each disease, all of them share similar features including beta-sheet-rich secondary structure and fibril-like protein aggregates. A number of proteins can form amyloid-like fibrils in vitro, resembling structural features of disease-related amyloids. Given these generic structural properties of amyloid and amyloid-like fibrils, generic inhibitors of fibril formation would be of interest for treatment of amyloid diseases. Recently, we identified five outstanding inhibitors of insulin amyloid-like fibril formation among the pool of 265 commercially available flavone derivatives. Here we report testing of these five compounds and of epi-gallocatechine-3-gallate (EGCG) on aggregation of alpha-synuclein and beta-amyloid. We used a Thioflavin T (ThT) fluorescence assay, relying on halftimes of aggregation as the measure of inhibition. This method avoids large numbers of false positive results. Our data indicate that four of the five flavones and EGCG inhibit alpha-synuclein aggregation in a concentration-dependent manner. However none of these derivatives were able to increase halftimes of aggregation of beta-amyloid.

Studies of Polymorphism of Amyloid-β 42 Peptide from Different Suppliers

The aim of this study was to investigate the process of amyloidogenesis of amyloid-β (Aβ)42 peptide, by means of fluorescence spectroscopy, electron microscopy, X-ray diffraction, and mass spectrometry. It has been repeatedly reported in the literature that the process of fibril formation by Aβ42 peptide depends considerably not only upon the specific conditions (ionic conditions, pH, temperature, mixing, etc.), as well as the manufacturing route (synthetic or recombinant), but also on the methods of synthesis and purification. We have, for the first time, systematically analyzed samples of Aβ42 peptide supplied by five different companies (Anaspec, Invitrogen, Enzo, Sigma-Aldrich, and SynthAssist) and obtained evidence of significant variability, including lot to lot variations. All studied samples formed amyloid-like fibrils at pH3-6, and the fibrils contained cross-β structures. Samples from Anaspec, Invitrogen, and Enzo formed one particular type of amyloid-like fibrils, while the samples from Sigma-Aldrich and SynthAssist formed another distinct type of fibrils. The observed polymorphism emphasizes the capacity of the Aβ42 peptide to act as a prion agent with varying structural characteristics. The presented data have allowed us to propose a possible mechanism of formation of amyloid-like fibrils.

Flavone derivatives as inhibitors of insulin amyloid-like fibril formation.

Several natural and synthetic flavone derivatives have been reported to inhibit formation of amyloid fibrils or to remodel existing fibrils. These studies suggest that the numbers and positions of hydroxyl groups on the flavone rings determine their effectiveness as amyloid inhibitors. In many studies the primary method for determining the effectiveness of inhibition is measuring Thioflavin T (ThT) fluorescence. This method demonstrably results in a number of false positives for inhibition. We studied the effects of 265 commercially available flavone derivatives on insulin fibril formation. We enhanced the effectiveness of ThT fluorescence measurements by fitting kinetic curves to obtain halftime of aggregation (t 50). Maximal values of ThT fluorescence varied two fold or more in one third of all cases, but this did not correlate with changes in t 50. Changes in t 50 values were more accurate measures of inhibition of amyloid formation. We showed that without a change in an assay, but just by observing complete kinetic curves it is possible to eliminate numbers of false positive and sometimes even false negative results. Examining the data from all 265 flavones we confirmed previous observations that identified the importance of hydroxyl groups for inhibition. Our evidence suggests the importance of hydroxyl groups at locations 5, 6, 7, and 4’, and the absence of a hydroxyl group at location 3, for inhibiting amyloid formation. However, the main conclusion is that the positions are not additive. The structures and their effects must be thought of in the context of the whole molecule.

The unexpected role of polyubiquitin chains in the formation of fibrillar aggregates.

Ubiquitin is known to be one of the most soluble and stably folded intracellular proteins, but it is often found in inclusion bodies associated with various diseases including neurodegenerative disorders and cancer. To gain insight into this contradictory behaviour, we have examined the physicochemical properties of ubiquitin and its polymeric chains that lead to aggregate formation. We find that the folding stability of ubiquitin chains unexpectedly decreases with increasing chain length, resulting in the formation of amyloid-like fibrils. Furthermore, when expressed in cells, polyubiquitin chains covalently linked to EGFP also form aggregates depending on chain length. Notably, these aggregates are selectively degraded by autophagy. We propose a novel model in which the physical and chemical instability of polyubiquitin chains drives the formation of fibrils, which then serve as an initiation signal for autophagy.

Evaluating Polyglutamine Peptide Monomers and Dimers with Enhanced Sampling MD Simulations

Huntington's disease is a neurodegenerative disease characterized by mutations causing polyglutamine (polyQ) repeats in proteins. Mutated proteins misfold, aggregate, and form amyloid-like fibrils in the neuron. Experimental techniques such as resonance Raman, circular dichroism, and ssNMR are used to analyze properties of polyQ systems, but lack the ability to monitor the molecular aggregation mechanism. In this work, polyQ peptide monomers and dimers are studied using molecular dynamics (MD) methods in order to better understand early stages of aggregation. We have characterized the monomeric conformational ensemble of D2Q10K2 peptides in aqueous and protein-globule environments. We also investigate dimerization properties of these peptides. Adaptive biasing force paired with MD is used to evaluate the dimerization free energies and conformations of D2Q10K2 peptides. Classical MD is used to simulate the favorable dimeric conformations in equilibrium, as to better understand the interactions and dynamics of these structures. These results will be presented and discussed.

Light and heat control over secondary structure and amyloid-like fiber formation in an overcrowded-alkene-modified Trp zipper.

The external photocontrol over peptide folding, by the incorporation of molecular photoswitches into their structure, provides a powerful tool to study biological processes. However, it is limited so far to switches that exhibit only a rather limited geometrical change upon photoisomerization and that show thermal instability of the photoisomer. Here we describe the use of an overcrowded alkene photoswitch to control a model β-hairpin peptide. This photoresponsive unit undergoes a large conformational change and has two thermally stable isomers which has major influence on the secondary structure and the aggregation of the peptide, permitting the phototriggered formation of amyloid-like fibrils.