Conformational Variability of Amyloid-β and the Morphological Diversity of Its Aggregates

Protein folding is the most fundamental and universal example of biomolecular self-organization and is characterized as an intramolecular process. In contrast, amyloidogenic proteins can interact with one another, leading to protein aggregation. The energy landscape of amyloid fibril formation is characterized by many minima for different competing low-energy structures and, therefore, is much more enigmatic than that of multiple folding pathways. Thus, to understand the entire energy landscape of protein aggregation, it is important to elucidate the full picture of conformational changes and polymorphisms of amyloidogenic proteins. This review provides an overview of the conformational diversity of amyloid-β (Aβ) characterized from experimental and theoretical approaches. Aβ exhibits a high degree of conformational variability upon transiently interacting with various binding molecules in an unstructured conformation in a solution, forming an α-helical intermediate conformation on the membrane and undergoing a structural transition to the β-conformation of amyloid fibrils. This review also outlines the structural polymorphism of Aβ amyloid fibrils depending on environmental factors. A comprehensive understanding of the energy landscape of amyloid formation considering various environmental factors will promote drug discovery and therapeutic strategies by controlling the fibril formation pathway and targeting the consequent morphology of aggregated structures.     

Surface film pressure of β-lactoglobulin, α-lactalbumin and bovine serum albumin at the air/water interface studied by wilhelmy plate and drop volume

The surface film pressure (II) of β-lactoglobulin, α-lactalbumin, and bovine serum albumin was studied in simulated milk ultrafiltrate (SMUF) and in water at concentrations from 10⁻⁶ up to 1% (w/v) at times from 30 s to 14 h and the results were analyzed with regard to adsorption transport and kinetics. In SMUF at low concentrations, β-lactoglobulin was the most “surface active” protein. There was little difference in the surface film pressure between β-lactoglobulin and α-lactalbumin at high concentrations. Bovine serum albumin showed the lowest surface activity, but did not reach a constant II, even after 14 h. As the pH approached the isoelectric point, the surface film pressure increased, and in the case of bovine serum albumin II increased faster. In water, however, the surface film pressures were lower than in SMUF, and for bovine serum albumin II developed more slowly. The transport to the interface was found to be controlled by diffusion only for a small concentration range of approximately 10⁻⁴%. It was controlled by initial flow disturbances at higher concentrations and free convection at lower concentrations. The rate of increase of the surface film pressure was not a simple function of surface film pressure and bulk concentration under any of the conditions studied.     

The Effects of Charged Amino Acid Side-Chain Length on Diagonal Cross-Strand Interactions between Carboxylate- and Ammonium-Containing Residues in a β-Hairpin

The β-sheet is one of the common protein secondary structures, and the aberrant aggregation of β-sheets is implicated in various neurodegenerative diseases. Cross-strand interactions are an important determinant of β-sheet stability. Accordingly, both diagonal and lateral cross-strand interactions have been studied. Surprisingly, diagonal cross-strand ion-pairing interactions have yet to be investigated. Herein, we present a systematic study on the effects of charged amino acid side-chain length on a diagonal ion-pairing interaction between carboxylate- and ammonium-containing residues in a β-hairpin. To this end, 2D-NMR was used to investigate the conformation of the peptides. The fraction folded population and the folding free energy were derived from the chemical shift data. The fraction folded population for these peptides with potential diagonal ion pairs was mostly lower compared to the corresponding peptide with a potential lateral ion pair. The diagonal ion-pairing interaction energy was derived using double mutant cycle analysis. The Asp2-Dab9 (Asp: one methylene; Dab: two methylenes) interaction was the most stabilizing (−0.79 ± 0.14 kcal/mol), most likely representing an optimal balance between the entropic penalty to enable the ion-pairing interaction and the number of side-chain conformations that can accommodate the interaction. These results should be useful for designing β-sheet containing molecular entities for various applications.     

Detergent-Induced Removal of β-Lactoglobulin from Stainless Steel Surfaces as Influenced by Surface Pretreatment

The adsorption of β-lactoglobulin to stainless steel and its subsequent removal were followed using in situ null ellipsometry. The influence of the surface pretreatment on the protein removal by the surfactant SDS and by sodium hydroxide was studied. All surfaces were precleaned in strongly alkaline solution. Some surfaces received no further pretreatment, while others were either passivated in nitric acid or plasma-cleaned prior to experiments. Stainless steel surfaces subjected to different surface pretreatments showed considerable differences in cleaning behavior. Cleaning, using NaOH, of surfaces which had been precleaned with alkali only or with plasma resulted in practically complete β-lactoglobulin removal. In contrast, appreciable amounts of protein remained on passivated stainless steel. Protein removal by SDS was limited and comparable for all three surface pretreatments investigated. Only minor effects on the protein adsorption tendency were observed. The amounts of β-lactoglobulin adsorbed tended to be somewhat lower on the passivated surfaces.     

Studies on the Structure and Properties of Membrane Phospholipase A1 Inclusion Bodies Formed at Low Growth Temperatures Using GFP Fusion Strategy

The effect of cultivation temperatures (37, 26, and 18 °C) on the conformational quality of Yersinia pseudotuberculosis phospholipase A₁ (PldA) in inclusion bodies (IBs) was studied using green fluorescent protein (GFP) as a folding reporter. GFP was fused to the C-terminus of PldA to form the PldA-GFP chimeric protein. It was found that the maximum level of fluorescence and expression of the chimeric protein is observed in cells grown at 18 °C, while at 37 °C no formation of fluorescently active forms of PldA-GFP occurs. The size, stability in denaturant solutions, and enzymatic and biological activity of PldA-GFP IBs expressed at 18 °C, as well as the secondary structure and arrangement of protein molecules inside the IBs, were studied. Solubilization of the chimeric protein from IBs in urea and SDS is accompanied by its denaturation. The obtained data show the structural heterogeneity of PldA-GFP IBs. It can be assumed that compactly packed, properly folded, proteolytic resistant, and structurally less organized, susceptible to proteolysis polypeptides can coexist in PldA-GFP IBs. The use of GFP as a fusion partner improves the conformational quality of PldA, but negatively affects its enzymatic activity. The PldA-GFP IBs are not toxic to eukaryotic cells and have the property to penetrate neuroblastoma cells. Data presented in the work show that the GFP-marker can be useful not only as target protein folding indicator, but also as a tool for studying the molecular organization of IBs, their morphology, and localization in E. coli, as well as for visualization of IBs interactions with eukaryotic cells.     

Competitive adsorption of -α-lysophosphatidylcholine/β-lactoglobulin mixtures at the interfaces of foams and foam lamellae

The stability of foams formed with the protein β-lactoglobulin as a function of increasing concentration of the lipid analogue -α-lysophosphatidylcholine were investigated using a microconductivity technique. The drainage, surface diffusion and thickness properties of thin liquid films (foam lamallae) were also studied using optical microscopy including epi-illumination, fluorescence recovery after photobleaching and film interferometry techniques. In addition, the surfactant binding properties of the protein were examined. The addition of small quantities of -α-lysophosphatidylcholine to β-lactoglobulin (molar ratio, R < 7:1) increased the foam stability, whereas a slightly higher concentration of surfactant in the mixture (R = 10) caused foam destabilisation. The explanation of these observations is based on changes in the composition and structure of the adsorbed interfacial layers of the thin films caused by competitive displacement of the protein by the surfactant.     

Effects of Curcumin and Ferulic Acid on the Folding of Amyloid-β Peptide

The polyphenols curcumin (CU) and ferulic acid (FA) are able to inhibit the aggregation of amyloid-β (Aβ) peptide with different strengths. CU is a strong inhibitor while FA is a weaker one. In the present study, we examine the effects of CU and FA on the folding process of an Aβ monomer by 1 µs molecular dynamics (MD) simulations. We found that both inhibitors increase the helical propensity and decrease the non-helical propensity of Aβ peptide. They prevent the formation of a dense bulk core and shorten the average lifetime of intramolecular hydrogen bonds in Aβ. CU makes more and longer-lived hydrogen bonds, hydrophobic, π–π, and cation–π interactions with Aβ peptide than FA does, which is in a good agreement with the observed stronger inhibitory activity of CU on Aβ aggregation.     

Zinc and Copper Ions Induce Aggregation of Human β-Crystallins

Cataracts are defined as the clouding of the lens due to the formation of insoluble protein aggregates. Metal ions exposure has been recognized as a risk factor in the cataract formation process. The γ and β crystallins are members of a larger family and share several structural features. Several studies have shown that copper and zinc ions induce the formation of γ-crystallins aggregates. However, the interaction of metal ions with β-crystallins, some of the most abundant crystallins in the lens, has not been explored until now. Here, we evaluate the effect of Cu(II) and Zn(II) ions on the aggregation of HβA1, as a representative of the acidic form, and HβB2, as a representative of the basic β-crystallins. We used several biophysical techniques and computational methods to show that Cu(II) and Zn(II) induce aggregation following different pathways. Both metal ions destabilize the proteins and impact protein folding. Copper induced a small conformational change in HβA1, leading to high-molecular-weight light-scattering aggregates, while zinc is more aggressive towards HβB2 and induces a larger conformational change. Our work provides information on the mechanisms of metal-induced aggregation of β-crystallins.     

Speculation on How RIC-3 and Other Chaperones Facilitate α7 Nicotinic Receptor Folding and Assembly

The process of how multimeric transmembrane proteins fold and assemble in the endoplasmic reticulum is not well understood. The alpha7 nicotinic receptor (α7 nAChR) is a good model for multimeric protein assembly since it has at least two independent and specialized chaperones: Resistance to Inhibitors of Cholinesterase 3 (RIC-3) and Nicotinic Acetylcholine Receptor Regulator (NACHO). Recent cryo-EM and NMR data revealed structural features of α7 nAChRs. A ser-ala-pro (SAP) motif precedes a structurally important but unique “latch” helix in α7 nAChRs. A sampling of α7 sequences suggests the SAP motif is conserved from C. elegans to humans, but the latch sequence is only conserved in vertebrates. How RIC-3 and NACHO facilitate receptor subunits folding into their final pentameric configuration is not known. The artificial intelligence program AlphaFold2 recently predicted structures for NACHO and RIC-3. NACHO is highly conserved in sequence and structure across species, but RIC-3 is not. This review ponders how different intrinsically disordered RIC-3 isoforms from C. elegans to humans interact with α7 nAChR subunits despite having little sequence homology across RIC-3 species. Two models from the literature about how RIC-3 assists α7 nAChR assembly are evaluated considering recent structural information about the receptor and its chaperones.     

In Silico Approach of Glycinin and Conglycinin Chains of Soybean By-Product (Okara) Using Papain and Bromelain

This study explores utilization of a sustainable soybean by-product (okara) based on in silico approach. In silico approaches, as well as the BIOPEP database, PeptideRanker database, Peptide Calculator database (Pepcalc), ToxinPred database, and AllerTop database, were employed to evaluate the potential of glycinin and conglycinin derived peptides as a potential source of bioactive peptides. These major protein precursors have been found as protein in okara as a soybean by-product. Furthermore, primary structure, biological potential, and physicochemical, sensory, and allergenic characteristics of the theoretically released antioxidant peptides were predicted in this research. Glycinin and α subunits of β-conglycinin were selected as potential precursors of bioactive peptides based on in silico analysis. The most notable among these are antioxidant peptides. First, the potential of protein precursors for releasing bioactive peptides was evaluated by determining the frequency of occurrence of fragments with a given activity. Through the BIOPEP database analysis, there are several antioxidant bioactive peptides in glycinin and β and α subunits of β-conglycinin sequences. Then, an in silico proteolysis using selected enzymes (papain, bromelain) to obtain antioxidant peptides was investigated and then analyzed using PeptideRanker and Pepcalc. Allergenic analysis using the AllerTop revealed that all in silico proteolysis-derived antioxidant peptides are probably nonallergenic peptides. We also performed molecular docking against MPO (myeloperoxidases) for this peptide. Overall, the present study highlights that glycinin and β and α subunits of β-conglycinin could be promising precursors of bioactive peptides that have an antioxidant peptide for developing several applications.     

Changes in Intestinal Permeability Ex Vivo and Immune Cell Activation by Three Commonly Used Emulsifiers

Food additives such as emulsifiers are used in increasing quantities in the food industry. The aim of this study was to compare three different emulsifiers (polysorbate 80 (P80), carboxymethyl cellulose (CMC), and β-lactoglobulin (β-lac) with regards to their effect on the stimulation of immune cells and intestinal permeability. The immune stimulatory effects were studied in the myeloid cell line MUTZ-3-cells, while the change in intestinal permeability was studied in the Caco-2 cell line and ex vivo in the Ussing chamber system using small intestinal fragments from rats. The tested concentrations of the emulsifiers ranged from 0.02% up to 1%, which are concentrations commonly used in the food industry. The results showed that P80 affected both the myeloid cells and the intestinal permeability more than CMC (p < 0.05) and β-lac (p < 0.05) at the highest concentration. CMC was found to neither affect the permeability in the intestine nor the MUTZ-3 cells, while β-lac changed the permeability in the total part of the small intestine in rats. These findings indicate that P80 might be more cytotoxic compared to the other two emulsifiers.     

Activation of apoptosis by rationally constructing NIR amphiphilic AIEgens: surmounting the shackle of mitochondrial membrane potential for amplified tumor ablation

In recent years, the use of aggregation-induced emission luminogens (AIEgens) for biological imaging and phototherapy has become an area of intense research. However, most traditional AIEgens suffer from undesired aggregation in aqueous media with “always on” fluorescence, or their targeting effects cannot be maintained accurately in live cells with the microenvironment changes. These drawbacks seriously impede their application in the fields of bio-imaging and antitumor therapy, which require a high signal-to-noise ratio. Herein, we propose a molecular design strategy to tune the dispersity of AIEgens in both lipophilic and hydrophilic systems to obtain the novel near-infrared (NIR, ∼737 nm) amphiphilic AIE photosensitizer (named TPA-S-TPP) with two positive charges as well as a triplet lifetime of 11.43 μs. The synergistic effects of lipophilicity, electrostatic interaction, and structure-anchoring enable the wider dynamic range of AIEgen TPA-S-TPP for mitochondrial targeting with tolerance to the changes of mitochondrial membrane potential (ΔΨ_m). Intriguingly, TPA-S-TPP was difficult for normal cells to be taken up, indicative of low inherent toxicity for normal cells and tissues. Deeper insight into the changes of mitochondrial membrane potential and cleaved caspase 3 levels further revealed the mechanism of tumor cell apoptosis activated by AIEgen TPA-S-TPP under light irradiation. With its advantages of low dark toxicity and good biocompatibility, acting as an efficient theranostic agent, TPA-S-TPP was successfully applied to kill cancer cells and to efficiently inhibit tumor growth in mice. This study will provide a new avenue for researchers to design more ideal amphiphilic AIE photosensitizers with NIR fluorescence.

In this contribution, based on a “step-by-step” molecular design strategy, a novel NIR amphiphilic AIEgen TPA-S-TPP with a triplet lifetime of 11.43 μs and surmounting the shackle of MMP was successfully fabricated for amplified tumor ablation.     

The structure and dynamic properties of mixed adsorption and penetration layers of α-dipalmitoylphosphatidylcholine/β-lactoglobulin at water/fluid interfaces

The interfacial tensions of mixed α-dipalmitoylphosphatidylcholine (DPPC)/β-lactoglobulin layers at the chloroform/water interface have been measured by the pendent drop and drop volume techniques. In certain intervals, the adsorption kinetics of these mixed layers was strongly influenced by the concentrations of both protein and DPPC. However, at low protein concentration, C_{β-lactoglobulin}=0.1 mg l⁻¹, the adsorption rate of mixed interfacial layers was mainly controlled by the variation of the DPPC concentration. As C_{β-lactoglobulin} was increased to 0.8 mg l⁻¹, the interfacial activity was abruptly increased, and within the concentration range of C_DPPC=10⁻⁴–10⁻⁵ mol l⁻¹, the DPPC has very little effect on the whole adsorption process. In this case, the adsorption rate of mixed layers was mainly dominated by the protein adsorption. This phenomenon also happened as the protein concentration was further increased to 3.6 mg l⁻¹. When C_DPPC>3 · 10^–5 mol l⁻¹, the adsorption behaviour was very similar to that of the pure DPPC although the protein concentration was changed. The equilibrium interfacial tensions of the mixed layers are dramatically effected by the lipid as compared to the pure protein adsorption at the same concentration. It reveals the estimation of which composition of lipid and protein decreases the interfacial tension. The combination of Brewster angle microscopy (BAM) with a conventional LB trough was applied to investigate the morphology of the mixed DPPC/β-lactoglobulin layers at the air/water interface. The mixed insoluble monolayers were produced by spreading the lipid at the water surface and the protein adsorbed from the aqueous buffer subphase. The BAM images allow to visualise the protein penetration and distribution into the DPPC monolayer on compression of the complex film. It is shown that a homogeneous distribution of β-lactoglobulin in lipid layers preferentially happens in the liquid fluid state of the monolayer while the protein can be squeezed out at higher surface pressures.     

Experimental Determination and Computational Prediction of Dehydroabietic Acid Solubility in (−)-α-Pinene + (−)-β-Caryophyllene + P-Cymene System

The solubility of dehydroabietic acid in (−)-α-pinene, p-cymene, (−)-β-caryophyllene, (−)-α-pinene + p-cymene, (−)-β-caryophyllene + p-cymene and (−)-α-pinene + (−)-β-caryophyllene were determined using the laser monitoring method at atmospheric pressure. The solubility of dehydroabietic acid was positively correlated with temperature from 295.15 to 339.46 K. (−)-α-pinene, p-cymene, and (−)-β-caryophyllene were found to be suitable for the solubilization of dehydroabietic acid. In addition, the non-random two liquid (NRTL), universal quasi-chemical (UNIQUAC), modified Apelblat, modified Wilson, modified Wilson–van’t Hoff, and λh models were applied to correlate the determined solubility data. The modified Apelblat model gave the minor deviation for dehydroabietic acid in monosolvents, while the λh equation showed the best result in the binary solvents. A comparative analysis of compatibility between solutes and solvents was carried out using Hansen solubility parameters. The thermodynamic functions of Δ_solH⁰, Δ_solS⁰, Δ_solG⁰ were calculated according to the van’t Hoff equation, indicating that the dissolution was an entropy-driven heat absorption process. The Conductor-like Screening Model for Real Solvents (COSMO-RS) combined with an experimental value was applied to predict the reasonable solubility data of dehydroabietic acid in the selected solvents systems. The interaction energy of the dehydroabietic acid with the solvent was analyzed by COSMO-RS.     

Identification of a nanomolar affinity α-synuclein fibril imaging probe by ultra-high throughput in silico screening

Small molecules that bind with high affinity and specificity to fibrils of the α-synuclein (αS) protein have the potential to serve as positron emission tomography (PET) imaging probes to aid in the diagnosis of Parkinson''s disease and related synucleinopathies. To identify such molecules, we employed an ultra-high throughput in silico screening strategy using idealized pseudo-ligands termed exemplars to identify compounds for experimental binding studies. For the top hit from this screen, we used photo-crosslinking to confirm its binding site and studied the structure–activity relationship of its analogs to develop multiple molecules with nanomolar affinity for αS fibrils and moderate specificity for αS over Aβ fibrils. Lastly, we demonstrated the potential of the lead analog as an imaging probe by measuring binding to αS-enriched homogenates from mouse brain tissue using a radiolabeled analog of the identified molecule. This study demonstrates the validity of our powerful new approach to the discovery of PET probes for challenging molecular targets.     

Equilibrium and Dynamic Characteristics of Protein Adsorption Layers at Gas-Liquid Interfaces: Theoretical and Experimental Data

Within the framework of a nonideal two-dimensional solution model, equations are derived for the state of a surface layer, adsorption isotherms, and the distribution function of adsorbed protein molecules with respect to their states characterized by different molar surface areas. The derived equations satisfactorily describe the known experimental dependences obtained for equilibrium adsorption layers of some proteins (serum albumin, β-casein, and β-lactoglobulin): the dependences of the surface pressure on concentration and adsorption, the surface layer thickness on adsorption, and the limiting high-frequency elastic modulus of an adsorption layer on the surface pressure. All dependences for a given protein are described by the same set of parameters of the theoretical model. It is shown that the kinetics of protein adsorption studied by dynamic tensiometry, ellipsometry, and the radiotracer technique is consistent with the diffusion model comprising the Ward-Tordai equation and the set of equations describing the equilibrium. The kinetics of protein desorption from the adsorption layer at a liquid-fluid interface is analyzed. The kinetics of β-lactoglobulin desorption is shown to be described by the barrier mechanism.__________Translated from Kolloidnyi Zhurnal, Vol. 67, No. 4, 2005, pp. 437–449.Original Russian Text Copyright © 2005 by Fainerman, Miller.     

Characterizing affinity epitopes between prion protein and β-amyloid using an epitope mapping immunoassay

Cellular prion protein, a membrane protein, is expressed in all mammals. Prion protein is also found in human blood as an anchorless protein, and this protein form is one of the many potential sources of misfolded prion protein replication during transmission. Many studies have suggested that β-amyloid_1–42 oligomer causes neurotoxicity associated with Alzheimer''s disease, which is mediated by the prion protein that acts as a receptor and regulates the hippocampal potentiation. The prevention of the binding of these proteins has been proposed as a possible preventative treatment for Alzheimer''s disease; therefore, a greater understanding of the binding hot-spots between the two molecules is necessary. In this study, the epitope mapping immunoassay was employed to characterize binding epitopes within the prion protein and complementary epitopes in β-amyloid. Residues 23–39 and 93–119 in the prion protein were involved in binding to β-amyloid_1–40 and _1–42, and monomers of this protein interacted with prion protein residues 93–113 and 123–166. Furthermore, β-amyloid antibodies against the C-terminus detected bound β-amyloid_1–42 at residues 23–40, 104–122 and 159–175. β-Amyloid epitopes necessary for the interaction with prion protein were not determined. In conclusion, charged clusters and hydrophobic regions of the prion protein were involved in binding to β-amyloid_1–40 and _1–42. The 3D structure appears to be necessary for β-amyloid to interact with prion protein. In the future, these binding sites may be utilized for 3D structure modeling, as well as for the pharmaceutical intervention of Alzheimer''s disease.