Diseases of protein aggregation and the hunt for potential pharmacological agents

Using silver nanoparticle-decorated whey protein isolate amyloid fibrils to modify the electrode surface used for electrochemical detection of para-nitrophenol

Due to their organized structures, remarkable stiffness, and nice biocompatibility and biodegradability, amyloid fibrils serve as building blocks for versatile sustainable materials. Silver nanoparticles (AgNPs) are commonly used as the nano-catalysts for various electrochemical reactions. Given their large specific surface area and high surface energy, AgNPs exhibit high aggregation propensity, which hampers their electrocatalytic performance. Food protein wastes have been identified to be associated with climate change and environmental impacts, and a surplus of whey proteins in dairy industries causes high biological and chemical demands, and greenhouse gas emissions. This study is aimed at constructing sustainable electrode surface modifiers using AgNP-deposited whey protein amyloid fibrils (AgNP/WPI-AFs). AgNP/WPI-AFs were synthesized and characterized via spectroscopic techniques, electron microscopy, and X-ray diffraction. Next, the electrocatalytic performance of AgNP/WPI-AF modified electrode was assessed via para-nitrophenol (p-NP) reduction combined with various electrochemical analyses. Moreover, the reaction mechanism of p-NP electrocatalysis on the surface of AgNP/WPI-AF modified electrode was investigated. The detection range, limit of detection, sensitivity, and selectivity of the AgNP/WPI-AF modified electrode were evaluated accordingly. This work not only demonstrates an alternative for whey valorization but also highlights the feasibility of using amyloid-based hybrid materials as the electrode surface modifier for electrochemical sensing purposes.

Formation of hen egg white lysozyme derived amyloid-based hydrogels using different gelation agents: A potential tool for drug delivery

Amyloids are highly stable protein fibrillar aggregates that get deposited in various parts of our body and cause detrimental diseases. But in nature, the presence of functional amyloids is also noted in bacteria that help them by forming hyphae, biofilm, protein reservoirs, signalling messengers, etc. Keeping this perspective in mind, the idea behind this research was to develop functional amyloids in the form of hydrogel and analyse its potential in the biomedical sector as a drug-delivery tool. The synthesis and characterisation of three types of amyloid-based hydrogels have been reported in this work. Hen Egg-White Lysozyme (HEWL) protein was chosen as the principal ingredient as it is extensively used as a standard protein for studying amyloidogenesis and has inherent antibacterial properties. Comparative studies of different hydrogel properties exhibited variations in the hydrogels based on compositional differences in them. Finally, a drug release assay was done on the synthesized hydrogels to explore their potential as drug delivery tools.

yGPS-P: A Yeast-Based Peptidome Screen for Studying Quality Control-Associated Proteolysis

Quality control-associated proteolysis (QCAP) is a fundamental mechanism that maintains cellular homeostasis by eliminating improperly folded proteins. In QCAP, the exposure of normally hidden cis-acting protein sequences, termed degrons, triggers misfolded protein ubiquitination, resulting in their elimination by the proteasome. To identify the landscape of QCAP degrons and learn about their unique features we have developed an unbiased screening method in yeast, termed yGPS-P, which facilitates the determination of thousands of proteome-derived sequences that enhance proteolysis. Here we describe the fundamental features of the yGPS-P method and provide a detailed protocol for its use as a tool for degron search. This includes the cloning of a synthetic peptidome library in a fluorescence-based reporter system, and data acquisition, which entails the combination of Fluorescence-Activated Cell Sorting (FACS) and Next-Generation Sequencing (NGS). We also provide guidelines for data extraction and analysis and for the application of a machine-learning algorithm that established the evolutionarily conserved amino acid preferences and secondary structure propensities of QCAP degrons.

Silver nanoparticle-deposited whey protein isolate amyloid fibrils as catalysts for the reduction of methylene blue

The unique structural characteristics and superior biocompatibility make the protein nanofibers promising immobilization platforms/substrates for catalysts/enzymes. Metal nanoparticles have been employed as the catalysts in industries due to their excellent catalytic activity and stability, whereas their high surface energy leads to nanoparticle aggregation, thereby hampering their catalytic performance. Here, amyloid fibril (AF) derived from whey protein isolate (WPI) was chosen as the support of silver nanoparticles (AgNP) and utilized for the catalytic reduction of methylene blue (MB). The one-dimensional amyloid-based hybrid materials (AgNP/WPI-AF) were first synthesized via chemical or photochemical route. The characterization of AgNP/WPI-AF by UV-vis spectrophotometry and electron microscopy revealed that the sizes of AgNP on WPI-AF's surface ranged from 2 to 30 nm. Next, the catalytic performances of AgNP/WPI-AF prepared by various routes for MB degradation were investigated. Additionally, the kinetic data were analyzed using two different models and the apparent rate constants and thermodynamic parameters were further determined accordingly. Moreover, the reusability of AgNP/WPI-AF was assessed by monitoring the percentage removal of MB over consecutive filtering cycles. Our results indicated that Langmuir-Hinshelwood-type mechanism better described the catalytic MB reduction using AgNP/WPI-AF. This work provides a nice example of application of nanoparticle-amyloid fibril composite materials for catalysis.

Protection of human γD-crystallin protein from ultraviolet C-induced aggregation by ortho-vanillin

Cataract is known as one of the leading causes of vision impairment worldwide. While the detailed mechanism of cataratogenesis remains unclear, cataract is believed to be correlated with the aggregation and/or misfolding of human ocular lens proteins called crystallins. A 173-residue structural protein human γD-crystallin is a major γ-crystallin protein in the human eye lens and associated with the development of juvenile and mature-onset cataracts. This work is aimed at investigating the effect of a small molecule, e.g., ortho-vanillin, on human γD-crystallin aggregation upon exposure to ultraviolet-C irradiation. According to the findings of right-angle light scattering, transmission electron microscopy, and gel electrophoresis, ortho-vanillin was demonstrated to dose-dependently suppress ultraviolet-C-triggered aggregation of human γD-crystallin. Results from the synchronous fluorescence spectroscopy, tryptophan fluorescence quenching, and molecular docking studies revealed the structural change of γD-crystallin induced by the interaction/binding between ortho-vanillin and protein. We believe the outcome from this work may contribute to the development of potential therapeutics for cataract.

Curcumin Has Protective Effect on the Eye Lens Against Arsenic Toxicity

Arsenic is a highly carcinogenic environmental contaminant. Curcumin, the bioactive component of turmeric, exhibits therapeutic efficacy against several chronic inflammatory and infectious diseases. The present study was carried out to investigate the impact of arsenic on eye lens and evaluate the ameliorative potential of curcumin against arsenic toxicity. Gene expression analysis of α, β, and γ-crystallins and fatty acid profile of lens tissues of arsenic-exposed Labeo rohita was examined and the protective effect of curcumin as diet supplement was evaluated. Curcumin-supplemented diet was prepared at 1.5% and 3% and fed to four groups of fish for 7 days prior to arsenic exposure (at 5 ppm and 15 ppm) for 15 days. Gene expression analysis showed downregulation of α and β-crystallins in the eye lens of arsenic-exposed groups (fed basal diet), whereas the groups fed a curcumin-supplemented diet showed insignificant alterations. Similarly, fatty acid fingerprint of lens lipids arsenic-exposed group exhibited reduction in saturated fatty acid and docosahexaenoic acid (DHA) content. However, in 3% curcumin-supplemented diet-fed and arsenic exposed group group, fatty acid profile remained unchanged. Interestingly, concentration of one non-fatty acid, an antioxidant compound (phenol 2,4-bis 1,1 dimethyl; PD) that was identified in the GC-MS fingerprinting through NIST library (version 2.2, 2014), decreased in response to arsenic exposure which was restored to normal level in curcumin-supplemented groups proving the therapeutic potential of curcumin. The findings of the study suggest that curcumin has a protective effect on eye lens against arsenic toxicity.

Examining the effect of bovine serum albumin on the properties and drug release behavior of β-lactoglobulin-derived amyloid fibril-based hydrogels

Herein, we report the use of β-lactoglobulin (β-LG) combined with bovine serum albumin (BSA) for the preparation of amyloid-based hydrogels with aim of delivering riboflavin. The incorporation of BSA enhanced β-LG fibrillogenesis and protected β-LG fibrils from losing fibrillar structure due to the pH shift. The mechanical properties of hydrogels were observed to be positively correlated with the number of amyloid fibrils. While the addition of BSA induced amyloid fibril formation, its presence between the fibril chains interfered with the entanglement of fibril chains, thus adversely affecting the hydrogels' mechanical properties. Hydrogels' surface microstructure became more compact as the number of amyloid fibrils rose and the presence of BSA could improve hydrogels' surface homogeneity. In vitro riboflavin (RF) release rate was found to be correlated with the number of fibrils and BSA-RF binding affinity. However, when the digestive enzymes were present, the influence of BSA-RF affinity was alleviated due to enzymes' destructive and/or degradative effects on BSA and/or hydrogels, thus the release rate relied on the number of fibrils, which could be adjusted by the amount of BSA. Results indicate that the additional component, BSA, plays an important role in modulating the properties and functions of β-LG fibril-based hydrogels.

Investigating the effect of sugar-terminated nanoparticles on amyloid fibrillogenesis of β-lactoglobulin

In vivo tissue deposition of fibrillar protein aggregates is the cause of several degenerative diseases. Evidence suggests that interfering with the pathology-associated amyloid fibrillogenesis by inhibitory molecules is envisaged as the primary therapeutic strategy. Amyloid fibril formation of proteins has been demonstrated to be influenced by nanoparticles/nanomaterials. As compared with their molecular form counterpart, this work examined the effect of sucrose-terminated nanoparticles on the in vitro amyloid fibrillogenesis and structural properties of β-lactoglobulin at pH 2.0 and 80 °C. ThT binding and electron microscopy results demonstrated that sucrose-terminated nanoparticles were able to suppress β-lactoglobulin fibrillogenesis in a concentration-dependent fashion. Importantly, sucrose-terminated nanoparticles showed better β-lactoglobulin fibril-inhibiting ability than sucrose molecules. ANS fluorescence and right-angle light scattering results showed reduced solvent exposure and decreased aggregation, respectively, in the β-lactoglobulin samples upon treatment with sucrose-terminated nanoparticles. Moreover, fluorescence quenching analyses revealed that the static quenching mechanism and formation of a non-fluorescent fluorophore-nanoparticle complex are involved in the nanoparticle-β-lactoglobulin interaction. We believe that the results from this study may suggest that the nanoparticle form of biocompatible sugar-related osmolytes may serve as effective inhibiting/suppressing agents toward protein fibrillogenesis.

Precipitation-free high-affinity multivalent binding by inline lectin ligands

Multivalent ligand-protein interactions are a key concept in biology mediating, for example, signalling and adhesion. Multivalent ligands often have tremendously increased binding affinities. However, they also can cause crosslinking of receptor molecules leading to precipitation of ligand-receptor complexes. Plaque formation due to precipitation is a known characteristic of numerous fatal diseases limiting a potential medical application of multivalent ligands with a precipitating binding mode. Here, we present a new design of high-potency multivalent ligands featuring an inline arrangement of ligand epitopes with exceptionally high binding affinities in the low nanomolar range. At the same time, we show with a multi-methodological approach that precipitation of the receptor is prevented. We distinguish distinct binding modes of the ligands, in particular we elucidate a unique chelating binding mode, where four receptor binding sites are simultaneously bridged by one multivalent ligand molecule. The new design concept of inline multivalent ligands, which we established for the well-investigated model lectin wheat germ agglutinin, has great potential for the development of high-potency multivalent inhibitors as future therapeutics.

Singlet oxygen-induced protein aggregation: Lysozyme crosslink formation and nLC-MS/MS characterization

Singlet molecular oxygen (¹ O₂ ) has been associated with a number of physiological processes. Despite the recognized importance of ¹ O₂ -mediated protein modifications, little is known about the role of this oxidant in crosslink formation and protein aggregation. Thus, using lysozyme as a model, the present study sought to investigate the involvement of ¹ O₂ in crosslink formation. Lysozyme was photochemically oxidized in the presence of rose bengal or chemically oxidized using [¹⁸ O]-labeled ¹ O₂ released from thermolabile endoperoxides. It was concluded that both ¹ O₂ generating systems induce lysozyme crosslinking and aggregation. Using SDS-PAGE and nano-scale liquid chromatography coupled to electrospray ionization mass spectrometry, the results clearly demonstrated that ¹ O₂ is directly involved in the formation of covalent crosslinks involving the amino acids histidine, lysine, and tryptophan.

Interaction and inhibitory influence of the azo dye carmoisine on lysozyme amyloid fibrillogenesis

The azo dye carmoisine has a significant inhibitory effect on fibrillogenesis in lysozyme.

Digging for Buried Amino Acids Unearths New Protein Quality Control Treasure

Proteins rely on three-dimensional structure for function, yet many proteins are marginally stable and prone to misfolding. In this issue of Structure, Brock et al. (2015) present a novel computational modeling method to gain insights into protein stability and misfolding.

Discovery and characterization of a photo-oxidative histidine-histidine cross-link in IgG1 antibody utilizing ¹⁸O-labeling and mass spectrometry

A novel photo-oxidative cross-linking between two histidines (His-His) has been discovered and characterized in an IgG1 antibody via the workflow of XChem-Finder, ¹⁸O labeling and mass spectrometry (Anal. Chem.2013, 85, 5900−590823634697). Its structure was elucidated by peptide mapping with multiple proteases with various specificities (e.g., trypsin, Asp-N, and GluC combined with trypsin or Asp-N) and mass spectrometry with complementary fragmentation modes (e.g., collision-induced dissociation (CID) and electron-transfer dissociation (ETD)). Our data indicated that cross-linking occurred across two identical conserved histidine residues on two separate heavy chains in the hinge region, which is highly flexible and solvent accessible. On the basis of model studies with short peptides, it has been proposed that singlet oxygen reacts with the histidyl imidazole ring to form an endoperoxide and then converted to the 2-oxo-histidine (2-oxo-His) and His+32 intermediates, the latter is subject to a nucleophilic attack by the unmodified histidine; and finally, elimination of a water molecule leads to the final adduct with a net mass increase of 14 Da. Our findings are consistent with this mechanism. Successful discovery of cross-linked His-His again demonstrates the broad applicability and utility of our XChem-Finder approach in the discovery and elucidation of protein cross-linking, particularly without a priori knowledge of the chemical nature and site of cross-linking.

Cellular maintenance of nuclear protein homeostasis

The accumulation and aggregation of misfolded proteins is the primary hallmark for more than 45 human degenerative diseases. These devastating disorders include Alzheimer's, Parkinson's, Huntington's, and amyotrophic lateral sclerosis. Over 15 degenerative diseases are associated with the aggregation of misfolded proteins specifically in the nucleus of cells. However, how the cell safeguards the nucleus from misfolded proteins is not entirely clear. In this review, we discuss what is currently known about the cellular mechanisms that maintain protein homeostasis in the nucleus and protect the nucleus from misfolded protein accumulation and aggregation. In particular, we focus on the chaperones found to localize to the nucleus during stress, the ubiquitin-proteasome components enriched in the nucleus, the signaling systems that might be present in the nucleus to coordinate folding and degradation, and the sites of misfolded protein deposition associated with the nucleus.

Bovine serum albumin oligomers in the E- and B-forms at low protein concentration and ionic strength

The manuscript describes the study of the oligomerization process of bovine serum albumin (BSA) in two different structural monomeric forms: the extended-form (E) at pH 2.0 and the basic-form (B) at pH 9.0. The study was conducted at low protein concentration (1mg/ml) and relatively short incubation time (maximum 56 days) in order to investigate early oligomerization events rather than the formation of mature fibrils. The comparison between the two isoforms show that oligomers form much faster (∼6 days) in the E-form than in the B-form where formation of oligomers requires ∼4 weeks. The oligomers appear to be limited to a maximum of tetramers with size <30 nm. Hydrophobic interactions from exposed neutral amino acid residues in the elongated E-form are the likely cause for the quick formation of aggregates at acidic pH. We used an array of biophysical techniques for the study and determined that oligomerization occurs without further large changes in the secondary structure of the monomers. Under the conditions adopted in this study, aggregation does not seem to exceed the formation of tetramers, even though a very small amount of much larger aggregates seem to form.

Substrate recognition in nuclear protein quality control degradation is governed by exposed hydrophobicity that correlates with aggregation and insolubility

Misfolded proteins present an escalating deleterious challenge to cells over the course of their lifetime. One mechanism the cell possesses to prevent misfolded protein accumulation is their destruction by protein quality control (PQC) degradation systems. In eukaryotes, PQC degradation typically proceeds via multiple ubiquitin-protein ligases that act throughout the cell to ubiquitinate misfolded proteins for proteasome degradation. What the exact feature of misfolding that each PQC ubiquitin-protein ligase recognizes in their substrates remains an open question. Our previous studies of the budding yeast nuclear ubiquitin-protein ligase San1 indicated that it recognizes exposed hydrophobicity within its substrates, with the threshold of hydrophobicity equivalent to that of 5 contiguous hydrophobic residues. Here, we uncover an additional parameter: the nature of the exposed hydrophobicity that confers San1-mediated degradation correlates with significant protein insolubility. San1 particularly targets exposed hydrophobicity that leads to insolubility and aggregation above a certain threshold. Our studies presented here provide additional insight into the details of misfolded nuclear protein recognition and demonstrate that there is selectivity for the type of exposed hydrophobicity.

Emerging trends in plasma-free manufacturing of recombinant protein therapeutics expressed in mammalian cells

Mammalian cells are the expression system of choice for therapeutic proteins, especially those requiring complex post‐translational modifications. Traditionally, these cells are grown in medium supplemented with serum and other animal‐ or human‐derived components to support viability and productivity. Such proteins are also typically added as excipients and stabilizers in the final drug formulation. However, the transmission of hepatitis B in the 1970s and of hepatitis C and HIV in the 1980s through plasma‐derived factor VIII concentrates had catastrophic consequences for hemophilia patients. Thus, due to regulatory concerns about the inherent potential for transmission of infectious agents as well as the heterogeneity and lack of reliability of the serum supply, a trend has emerged to eliminate the use of plasma‐derived additives in the production and formulation of recombinant protein therapeutics. This practice began with products used in the treatment of hemophilia and is progressively expanding throughout the entire industry. The plasma‐free method of producing recombinant therapeutics is accomplished by the use of both cell culture media and final product formulations that do not contain animal‐ or human‐derived additives. A number of recombinant therapeutic proteins for the treatment of several different diseases have been produced by plasma‐free processes, with the objective of improving safety by eliminating blood‐borne pathogens or by reducing immunogenicity. This review describes the factors that drove the development of plasma‐free protein therapeutics and provides examples of advances in manufacturing that have made possible the removal of human and animal‐derived products from all steps of recombinant protein production.