Protein structural perturbation and aggregation on homogeneous surfaces

The detection methods currently available for protein aggregation in neurological diseases

Protein aggregation is a pathological feature in various neurodegenerative diseases and is thought to play a crucial role in the onset and progression of neurological disorders. This pathological phenomenon has attracted increasing attention from researchers, but the underlying mechanism has not been fully elucidated yet. Researchers are increasingly interested in identifying chemicals or methods that can effectively detect protein aggregation or maintain protein stability to prevent aggregation formation. To date, several methods are available for detecting protein aggregates, including fluorescence correlation spectroscopy, electron microscopy, and molecular detection methods. Unfortunately, there is still a lack of methods to observe protein aggregation in situ under a microscope. This article reviews the two main aspects of protein aggregation: the mechanisms and detection methods of protein aggregation. The aim is to provide clues for the development of new methods to study this pathological phenomenon.

Colloidal surface-enhanced Raman spectroscopic study of grouper epidermal mucus using acidified sodium sulphate as the aggregating agent

Fish epidermal mucus is an important reservoir of antipathogenic compounds which serves as the first line of the immune defence. Despite its significant role in the physiology and health of fish, detailed profiling of fish epidermal mucus has yet to be explored. Therefore, this study investigates a label-free colloidal surface-enhanced Raman spectroscopic (SERS) method for profiling grouper mucus. Gold nanoparticles were first synthesised using the standard citrate reduction and characterised using ultraviolet-visible spectroscopy, transmission electron microscopy and dynamic light scattering. The influence of acidified sodium sulphate (Na2SO4) at pH 3 as the aggregating agent on the enhancement of the SERS spectrum of different analyte samples including rhodamine 6G (R6G) dye, lysozyme solution and hybrid grouper (Epinephelus fuscoguttatus × Epinephelus lanceolatus) mucus was observed. Based on the results, an optimal Na2SO4 concentration of 1 M was recorded to achieve the highest enhancement of the SERS signal for R6G and grouper mucus, while the optimal concentration for lysozyme was 0.1 M. The results indicated a higher degree of aggregation induced by lysozyme than R6G and grouper mucus. A few overlapping peaks of the SERS spectra of lysozyme and grouper mucus made it possible to confirm the presence of lysozyme as potential biomarkers.

Amyloid oligomers and their membrane toxicity - A perspective study

Amyloidosis is a condition involving a disparate group of pathologies characterized by the extracellular deposition of insoluble fibrils composed of broken-down proteins. These proteins can accumulate locally, causing peculiar symptoms, or in a widespread way, involving many organs and. causing severe systemic failure. The damage that is created is related not only to the accumulation of. amyloid fibrils but above all to the precursor oligomers of the fibrils that manage to enter the cell in a very particular way. This article analyzes the current state of research related to the entry of these oligomers into the cell membrane and the theories related to their toxicity. The paper proposed here not only aims to review the contents in the literature but also proposes a new vision of amyloid toxicity. that could occur in a multiphase process catalyzed by the cell membrane itself. In this process, the denaturation of the lipid bilayer is followed by the stabilization of a pore through energetically favorable self-assembly processes which are achieved through particular oligomeric structures.

Production of freeze-dried beef powder for complementary food: Effect of temperature control in retaining protein digestibility

This study investigated the effect of temperature control during freeze-drying of beef on the in vitro protein digestibility. Frozen (at - 50 °C for 2 days)-then-aged (at 4 °C for 26 days) beef was freeze-dried at 25 °C (FD1) and 2 °C (FD2) to obtain freeze-dried beef powder. Tryptophan fluorescence intensity and total free sulfhydryl groups of beef myofibrillar proteins decreased (P < 0.05) and increased (P < 0.05) after freeze-drying, respectively. In the myosin fraction of FD2, α-helix increased and β-sheet decreased (P < 0.05) compared to raw beef. In contrast, the actin fraction of FD1 showed a decrease in α-helix and increase in β-sheet (P < 0.05) compared to raw beef. The contents of α-amino group and proteins digested to<3 kDa in the in vitro digesta of beef were retained in FD2 while the α-amino group of FD1 decreased (P < 0.05). Therefore, freeze-drying at 2 °C can efficiently retain in vitro protein digestibility of beef.

Modulation of protein-saccharide interactions by deep-sea osmolytes under high pressure stress

Deep-sea organisms must cope with high hydrostatic pressures (HHP) up to the kbar regime to control their biomolecular processes. To alleviate the adverse effects of HHP on protein stability most organisms use high amounts of osmolytes. Little is known about the effects of these high concentrations on ligand binding. We studied the effect of the deep-sea osmolytes trimethylamine-N-oxide, glycine, and glycine betaine on the binding between lysozyme and the tri-saccharide NAG3, employing experimental and theoretical tools to reveal the combined effect of osmolytes and HHP on the conformational dynamics, hydration changes, and thermodynamics of the binding process. Due to their different chemical makeup, these cosolutes modulate the protein-sugar interaction in different ways, leading to significant changes in the binding constant and its pressure dependence. These findings suggest that deep-sea organisms may down- and up-regulate reactions in response to HHP stress by altering the concentration and type of the intracellular osmolyte.

Wheat gluten amyloid fibrils: Conditions, mechanism, characterization, application, and future perspectives

Amyloid fibrils have excellent structural characteristics, such as a high aspect ratio, excellent stiffness, and a wide availability of functional groups on the surface. More studies are now focusing on the formation of amyloid fibrils using food proteins. Protein fibrillation is now becoming recognized as a promising strategy for enhancing the function of food proteins and expanding their range of applications. Wheat gluten is rich in glutamine (Q), hydrophobic amino acids, and the α-helix structure with high β-sheet tendency. These characteristics make it very easy for wheat gluten to form amyloid fibrils. The conditions, formation mechanism, characterization methods, and application of amyloid fibrils formed by wheat gluten are summarized in this review. Further exploration of amyloid fibrils formed by wheat gluten will reveal how they can play a significant role in food, biology, and other fields, especially in medicine.

Interaction of Lysozyme with Poly(L-lysine)/Hyaluronic Acid Multilayers: An ATR-FTIR Study

Polyelectrolyte multilayers (PEM) loaded with bioactive molecules such as proteins serve as excellent mimics of an extracellular matrix and may find applications in fields such as biomedicine and cell biology. A question which is crucial to the successful employment of PEMs is whether conformation and bioactivity of the loaded proteins is preserved. In this work, the polarized attenuated total reflection Fourier transform infrared (ATR-FTIR) technique is applied to investigate the conformation of the protein lysozyme (Lys) loaded into the poly(L-lysine)/hyaluronic acid (PLL/HA) multilayers. Spectra are taken from the protein in the PEMs coated onto an ATR crystal during protein adsorption and desorption. For comparison, a similar investigation is performed for the case of Lys in contact with the uncoated crystal. The study highlights the presence of both "tightly" and "poorly bound" Lys fractions in the PEM. These fractions differ in their conformation and release behavior from the PEM upon washing. Comparison of spectra recorded with different polarizations suggests preferential orientation of alpha helical structures, beta sheets and turns in the "tightly bound" Lys. In contrast, the "poorly bound" fraction shows isotropic orientation and its conformation is well preserved.

A guide to studying protein aggregation

Disrupted protein folding or decreased protein stability can lead to the accumulation of (partially) un- or misfolded proteins, which ultimately cause the formation of protein aggregates. Much of the interest in protein aggregation is associated with its involvement in a wide range of human diseases and the challenges it poses for large-scale biopharmaceutical manufacturing and formulation of therapeutic proteins and peptides. On the other hand, protein aggregates can also be functional, as observed in nature, which triggered its use in the development of biomaterials or therapeutics as well as for the improvement of food characteristics. Thus, unmasking the various steps involved in protein aggregation is critical to obtain a better understanding of the underlying mechanism of amyloid formation. This knowledge will allow a more tailored development of diagnostic methods and treatments for amyloid-associated diseases, as well as applications in the fields of new (bio)materials, food technology and therapeutics. However, the complex and dynamic nature of the aggregation process makes the study of protein aggregation challenging. To provide guidance on how to analyse protein aggregation, in this review we summarize the most commonly investigated aspects of protein aggregation with some popular corresponding methods.

Effect of Secondary Structures on the Adsorption of Peptides onto Hydrophobic Solid Surfaces Revealed by SALDI-TOF and MD Simulations

The adsorption of peptides and proteins on hydrophobic solid surfaces has received considerable research attention owing to their wide applications to biocompatible nanomaterials and nanodevices, such as biosensors and cell adhesion materials with reduced nanomaterial toxicity. However, fundamental understandings about physicochemical hydrophobic interactions between peptides and hydrophobic solid surfaces are still unknown. In this study, we investigate the effect of secondary structures on adsorption energies between peptides and hydrophobic solid surfaces via experimental and theoretical analyses using surface-assisted laser desorption/ionization-time-of-flight (SALDI-TOF) and molecular dynamics (MD) simulations. The hydrophobic interactions between peptides and hydrophobic solid surfaces measured via SALDI-TOF and MD simulations indicate that the hydrophobic interaction of peptides with random coil structures increased more than that of peptides with an α-helix structure when polar amino acids are replaced with hydrophobic amino acids. Additionally, our study sheds new light on the fundamental understanding of the hydrophobic interaction between hydrophobic solid surfaces and peptides that have diverse secondary structures.

Influence of Centrifugation and Shaking on the Self-Assembly of Lysozyme Fibrils

Protein self-assembly into fibrils and oligomers plays a key role in the etiology of degenerative diseases. Several pathways for this self-assembly process have been described and shown to result in different types and ratios of final assemblies, therewith defining the effective physiological response. Known factors that influence assembly pathways are chemical conditions and the presence or lack of agitation. However, in natural and industrial systems, proteins are exposed to a sequence of different and often complex mass transfers. In this paper, we compare the effect of two fundamentally different mass transfer processes on the fibrilization process. Aggregation-prone solutions of hen egg white lysozyme were subjected to predominantly non-advective mass transfer by employing centrifugation and to advective mass transport represented by orbital shaking. In both cases, fibrilization was triggered, while in quiescent only oligomers were formed. The fibrils obtained by shaking compared to fibrils obtained through centrifugation were shorter, thicker, and more rigid. They had rod-like protofibrils as building blocks and a significantly higher β-sheet content was observed. In contrast, fibrils from centrifugation were more flexible and braided. They consisted of intertwined filaments and had low β-sheet content at the expense of random coil. To the best of our knowledge, this is the first evidence of a fibrilization pathway selectivity, with the fibrilization route determined by the mass transfer and mixing configuration (shaking versus centrifugation). This selectivity can be potentially employed for directed protein fibrilization.

Amyloidogenesis: What Do We Know So Far?

The study of protein aggregation, and amyloidosis in particular, has gained considerable interest in recent times. Several neurodegenerative diseases, such as Alzheimer's (AD) and Parkinson's (PD) show a characteristic buildup of proteinaceous aggregates in several organs, especially the brain. Despite the enormous upsurge in research articles in this arena, it would not be incorrect to say that we still lack a crystal-clear idea surrounding these notorious aggregates. In this review, we attempt to present a holistic picture on protein aggregation and amyloids in particular. Using a chronological order of discoveries, we present the case of amyloids right from the onset of their discovery, various biophysical techniques, including analysis of the structure, the mechanisms and kinetics of the formation of amyloids. We have discussed important questions on whether aggregation and amyloidosis are restricted to a subset of specific proteins or more broadly influenced by the biophysiochemical and cellular environment. The therapeutic strategies and the significant failure rate of drugs in clinical trials pertaining to these neurodegenerative diseases have been also discussed at length. At a time when the COVID-19 pandemic has hit the globe hard, the review also discusses the plausibility of the far-reaching consequences posed by the virus, such as triggering early onset of amyloidosis. Finally, the application(s) of amyloids as useful biomaterials has also been discussed briefly in this review.

The effect of ion environment changes on retention protein behavior during whey ultrafiltration process

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The ions environment changes were investigated during whey ultrafiltration process.

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Whey protein surface structure changes were contributed to the changing ions’ concentration.

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The relationship between ions around whey protein and membrane fouling was analyzed.

The factors affecting membrane fouling are very complex. In this study, the membrane fouling process was revealed from the perspective of ion environment changes, which affected the whey protein structure during ultrafiltration. It was found that the concentrations of Ca²⁺ and Na⁺ were overall increased and the concentrations of K⁺, Mg²⁺ and Zn²⁺ were decreased at an ultrafiltration time of 11 min, which made more hydrophilic groups buried inside and increased the content of α-helix, leading to more protein aggregation. The relatively higher K⁺ ratio in retention could lead to an antiparallel β-sheet configuration, aspartic acid, glutamic acid and tryptophan increased, which resulted in more protein aggregation and deposition on the membrane surface at 17 min. When the ion concentration and ratio restored the balance and were close to the initial state in retention, the protein surface tension decreased, and the hydrophilic ability increased at 21–24 min.

Complex Protein Retention Shifts with a Pressure Increase: An Indication of a Standard Partial Molar Volume Increase during Adsorption?

Studies of protein adsorption on reversed-phase and ion exchange stationary phases demonstrated an increase in retention with increasing pressure, which is interpreted as a standard partial molar volume decrease during the transition of the protein from a mobile to a stationary phase. Investigation of the pressure effect on the retention of lysozyme and IgG on a cation exchange column surprisingly revealed a negative retention trend with the increase of pressure. Further investigation of this phenomenon was performed with β-lactoglobulin, which enabled adsorption to be studied on both cation and anion exchange columns using the same mobile phase with a pH of 5.2. The same surface charge and standard partial molar volume in the mobile phase allowed us to examine only the effect of adsorption. Interestingly, a negative retention trend with a pressure increase occurred on an anion exchange column while a positive trend was present on a cation exchange column. This indicates that the interaction type governs the change in the standard partial molar volume during adsorption, which is independent of the applied pressure. Increasing the protein charge by decreasing the pH of the mobile phase to 4 reversed the retention trend (into a negative) with a pressure increase on the cation exchange column. A further decrease of the pH value resulted in an even more pronounced negative trend. This counterintuitive behavior indicates an increase in the standard partial molar volume during adsorption with the protein charge, possibly due to intermolecular repulsion of adsorbed protein molecules. While a detailed mechanism remains to be elucidated, presented results demonstrate the complexity of ion exchange interactions that can be investigated simply by changing the column pressure.

Anti-amyloidogenic property of gold nanoparticle decorated quercetin polymer nanorods in pH and temperature induced aggregation of lysozyme

Quercetin is an abundant plant polyphenol effective against several diseases due to its antioxidant and anti-inflammatory activity. Herein, we report novel polymeric quercetin nanorods and the former decorated with gold nanoparticles for the first time. The prepared conjugates quercetin-polyvinylpyrrolidone (Q-PVP) and quercetin-polyvinylpyrrolidone-gold nanoparticles (Q-PVP-Au) were characterized by UV-visible spectroscopy, Fourier transform infrared, dynamic light scattering, and zeta potential measurements. The surface morphology of conjugates was analyzed by field emission scanning electron microscopy. These conjugates exhibit harmonized rod-like morphology with a narrow size distribution. Furthermore, the quercetin conjugates with nanorod morphology exhibited enhanced and prolonged drug release over a long period. The synthesized conjugates were investigated for lysozyme aggregation kinetics. ThT binding assay, fibril size measurement, and electron microscopy results revealed that conjugates could suppress fibrillogenesis in lysozyme. The highest amyloid aggregation inhibition activity (IC50) was obtained against Q-PVP and Q-PVP-Au at 32 μg mL-1 and 30 μg mL-1 respectively. The amyloid aggregate disintegration activity (DC50) obtained against Q-PVP and Q-PVP-Au was 27 μg mL-1 and 29 μg mL-1 respectively. The present quercetin conjugates exhibit enhanced bioavailability and stability. They were potent inhibitors of lysozyme aggregation that may find applications as a therapeutic agent in neurological diseases like Alzheimer's and Parkinson's.

Estimating the Neutralizing Effect and Titer Correlation of Semi-Quantitative Anti-SARS-CoV-2 Antibody Immunoassays

For the clinical application of semi-quantitative anti-SARS-CoV-2 antibody tests, the analytical performance and titer correlation of the plaque reduction neutralization test (PRNT) need to be investigated. We evaluated the analytical performance and PRNT titer-correlation of one surrogate virus neutralization test (sVNT) kit and three chemiluminescent assays. We measured the total antibodies for the receptor-binding domain (RBD) of the spike protein, total antibodies for the nucleocapsid protein (NP), and IgG antibodies for the RBD. All three chemiluminescent assays showed high analytical performance for the detection of SARS-CoV-2 infection, with a sensitivity ≥ 98% and specificity ≥ 99%; those of the sVNT were slightly lower. The representativeness of the neutralizing activity of PRNT ND₅₀ ≥ 20 was comparable among the four immunoassays (Cohen’s kappa ≈ 0.80). Quantitative titer correlation for high PRNT titers of ND₅₀ ≥ 50, 200, and 1,000 was investigated with new cut-off values; the anti-RBD IgG antibody kit showed the best performance. It also showed the best linear correlation with PRNT titer in both the acute and convalescent phases (Pearson’s R 0.81 and 0.72, respectively). Due to the slowly waning titer of anti-NP antibodies, the correlation with PRNT titer at the convalescent phase was poor. In conclusion, semi-quantitative immunoassay kits targeting the RBD showed neutralizing activity that was correlated by titer; measurement of anti-NP antibodies would be useful for determining past infections.

A cell-based ELISA as surrogate of virus neutralization assay for RBD SARS-CoV-2 specific antibodies

SARS-CoV-2, the cause of the COVID-19 pandemic, has provoked a global crisis and death of millions of people. Several serological assays to determine the quality of the immune response against SARS-CoV-2 and the efficacy of vaccines have been developed, among them the gold standard conventional virus neutralization assays. However, these tests are time consuming, require biosafety level 3 (BSL3), and are low throughput and expensive. This has motivated the development of alternative methods, including molecular inhibition assays. Herein, we present a safe cell-based ELISA-virus neutralization test (cbE-VNT) as a surrogate for the conventional viral neutralization assays that detects the inhibition of SARS-CoV-2 RBD binding to ACE2-bearing cells independently of species. Our test shows a very good correlation with the conventional and molecular neutralization assays and achieves 100% specificity and 95% sensitivity. cbE-VNT is cost-effective, fast and enables a large-scale serological evaluation that can be performed in a BSL2 laboratory, allowing its use in pre-clinical and clinical investigations.

Understanding the role of hydrophobic patches in protein disaggregation

Protein folding is a very complex process and, so far, the mechanism of folding still intrigues the research community. Despite a large conformational space available (O(10⁴⁷) for a 100 amino acid residue), most proteins fold into their native state within a very short time. While small proteins fold relatively fast (a few microseconds) large globular proteins may take as long as several milliseconds to fold. During the folding process, the protein synthesized in the ribosome is exposed to the crowded environment of the cell and is easily prone to misfolding and aggregation due to interactions with other proteins or biomacromolecules present within the cell. These large proteins, therefore, rely on chaperones for their folding and repair. Chaperones are known to have hydrophobic patchy domains that play a crucial role in shielding the protein against misfolding and disaggregation of aggregated proteins. In the current article, Monte Carlo simulations carried out in the framework of the hydrophobic-polar (H-P) lattice model indicate that hydrophobic patchy domains drastically reduce the inter-protein interactions and are efficient in disaggregating proteins. The effectiveness of the disaggregation depends on the size and distribution of these patches on the surface and also on the strength of the interaction between the protein and the surface. Further, our results indicate that when the patch is complementary to the exposed hydrophobic patch of the protein, protein disaggregation is accompanied by stabilization of the protein even relative to its bulk behavior due to favorable protein-surface interactions. We believe that these findings shed light on the role of the class of chaperones known as heat shock proteins (Hsps) on protein disaggregation and refolding.

Elevated temperatures accelerate the formation of toxic amyloid fibrils of hen egg-white lysozyme

The formation of amyloid fibrils is critical for neurodegenerative diseases. Some physiochemical conditions can promote the conversion of proteins from soluble globular shapes into insoluble well‐organized amyloid fibrils. The aim of this study was to investigate the effect of temperatures on amyloid fibrils formation in vitro using the protein model of hen egg‐white lysozyme (HEWL). The HEWL fibrils were prepared at temperatures of 37, 45, 50 and 57°C in glycine solution of pH 2.2. Under transmission electron microscopy, we found the well‐organized HEWL amyloid fibrils at temperatures of 45, 50 and 57°C after 10 days of incubation. Thioflavin T and Congo red florescence assays confirmed that the formation and growth of HEWL fibrils displayed a temperature‐dependent increase, and 57°C produced the most amounts. Meanwhile, the surface hydrophobicity of aggregates was greatly increased by ANS binding assay, and β‐sheet contents by circular dichroism analysis were increased by 17.8%, 22.0% and 34.9%, respectively. Furthermore, the HEWL fibrils formed at 57°C caused significant cytotoxicity in SH‐SY5Y cells after 48 hr exposure, and the cell viability determined by MTT assay was decreased, with 81.35 ± 0.29% for 1 μM, 61.45 ± 2.62% for 2 μM, and 11.58 ± 0.39% (p < .01) for 3 μM. Nuclear staining results also confirmed the apoptosis features. These results suggest that the elevated temperatures could accelerate protein unfolding of the native structure and formation of toxic amyloid fibrils, which can improve understanding the mechanisms of the unfolding and misfolding process of prion protein.

A New SARS-CoV-2 Dual-Purpose Serology Test: Highly Accurate Infection Tracing and Neutralizing Antibody Response Detection

Many severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) serology tests have proven to be less accurate than expected and do not assess antibody function as neutralizing, correlating with protection from reinfection. A new assay technology measuring the interaction of the purified SARS-CoV-2 spike protein receptor binding domain (RBD) with the extracellular domain of the human angiotensin-converting enzyme 2 (hACE2) receptor detects these important antibodies.

Many severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) serology tests have proven to be less accurate than expected and do not assess antibody function as neutralizing, correlating with protection from reinfection. A new assay technology measuring the interaction of the purified SARS-CoV-2 spike protein receptor binding domain (RBD) with the extracellular domain of the human angiotensin-converting enzyme 2 (hACE2) receptor detects these important antibodies. The cPass surrogate virus neutralization test (sVNT), compared directly with eight SARS-CoV-2 IgG serology and two live-cell neutralization tests, gives similar or improved accuracy for qualitative delineation between positive and negative individuals in a fast, scalable, and high-throughput assay. The combined data support the cPass sVNT as a tool for highly accurate SARS-CoV-2 immunity surveillance of infected/recovered and/or vaccinated individuals as well as drug and convalescent-phase donor screening. The data also preview a novel application for the cPass sVNT in calibrating the stringency of live-cell neutralization tests and its use in longitudinal testing of recovered and/or vaccinated patients.

Deltamethrin modulates the native structure of Hen Egg White Lysozyme and induces its aggregation at physiological pH

Deltamethrin, a type II pyrethroid pesticide was initially considered as safe for human use. Recent studies have reported several pathophysiological effects of deltamethrin on human and non-human species. However, its effect on structure and function of protein leading to progressive neurodegeneration is poorly understood. In present study, we investigated the interaction of deltamethrin with Hen Egg White Lysozyme (HEWL) at physiological pH and tried to understand the effect of pesticide on structure and function of protein. Employing different biophysical techniques, we shown that deltamethrin induces in vitro aggregation of HEWL in concentration dependent manner. Interaction of pesticide with different amino acids, followed by exposure of hydrophobic regions was driving force of aggregation process. Apart from modulating the hydrophobic domain, deltamethrin is observed to reduce α-helical and promote β-sheet content of lysozyme, eventually converting the globular protein into ThT sensitive amyloid fibrils and amorphous aggregates. Our study also indicate that deltamethrin induced aggregation reduces the catalytic activity of lysozyme.

The role of surfaces on amyloid formation

Interfaces can strongly accelerate or inhibit protein aggregation, destabilizing proteins that are stable in solution or, conversely, stabilizing proteins that are aggregation-prone. Although this behaviour is well-known, our understanding of the molecular mechanisms underlying surface-induced protein aggregation is still largely incomplete. A major challenge is represented by the high number of physico-chemical parameters involved, which are highly specific to the considered combination of protein, surface properties, and solution conditions. The key aspect determining the role of interfaces is the relative propensity of the protein to aggregate at the surface with respect to bulk. In this review, we discuss the multiple molecular determinants that regulate this balance. We summarize current experimental techniques aimed at characterizing protein aggregation at interfaces, and highlight the need to complement experimental analysis with theoretical modelling. In particular, we illustrate how chemical kinetic analysis can be combined with experimental methods to provide insights into the molecular mechanisms underlying surface-induced protein aggregation, under both stagnant and agitation conditions. We summarize recent progress in the study of important amyloids systems, focusing on selected relevant interfaces.

Adsorption and Conformation Behavior of Lysozyme on a Gold Surface Determined by QCM-D, MP-SPR, and FTIR

The physicochemical properties of protein layers at the solid–liquid interface are essential in many biological processes. This study aimed to link the structural analysis of adsorbed lysozyme at the water/gold surface at pH 7.5 in a wide range of concentrations. Particular attention was paid to the protein’s structural stability and the hydration of the protein layers formed at the interface. Complementary methods such as multi-parameter surface plasmon resonance (MP-SPR), quartz crystal microbalance with energy dissipation (QCM-D), and infrared spectroscopy (FTIR) were used for this purpose. The MP-SPR and QCM-D studies showed that, during the formation of a monolayer on the gold surface, the molecules’ orientation changes from side-on to end-on. In addition, bilayer formation is observed when adsorbing in the high-volume concentration range >500 ppm. The degree of hydration of the monolayer and bilayer varies depending on the degree of surface coverage. The hydration of the system decreases with filling the layer in both the monolayer and the bilayer. Hydration for the monolayer varies in the range of 50–70%, because the bilayer is much higher than 80%. The degree of hydration of the adsorption layer has a crucial influence on the protein layers’ viscoelastic properties. In general, an increase in the filling of a layer is characterized by a rise in its rigidity. The use of infrared spectroscopy allowed us to determine the changes taking place in the secondary structure of lysozyme due to its interaction with the gold surface. Upon adsorption, the content of II-structures corresponding to β-turn and random lysozyme structures increases, with a simultaneous decrease in the content of the β-sheet. The increase in the range of β-turn in the structure determines the lysozyme structure’s stability and prevents its aggregation.

Pathological ATX3 Expression Induces Cell Perturbations in E. coli as Revealed by Biochemical and Biophysical Investigations

Amyloid aggregation of human ataxin-3 (ATX3) is responsible for spinocerebellar ataxia type 3, which belongs to the class of polyglutamine neurodegenerative disorders. It is widely accepted that the formation of toxic oligomeric species is primarily involved in the onset of the disease. For this reason, to understand the mechanisms underlying toxicity, we expressed both a physiological (ATX3-Q24) and a pathological ATX3 variant (ATX3-Q55) in a simplified cellular model, Escherichia coli. It has been observed that ATX3-Q55 expression induces a higher reduction of the cell growth compared to ATX3-Q24, due to the bacteriostatic effect of the toxic oligomeric species. Furthermore, the Fourier transform infrared microspectroscopy investigation, supported by multivariate analysis, made it possible to monitor protein aggregation and the induced cell perturbations in intact cells. In particular, it has been found that the toxic oligomeric species associated with the expression of ATX3-Q55 are responsible for the main spectral changes, ascribable mainly to the cell envelope modifications. A structural alteration of the membrane detected through electron microscopy analysis in the strain expressing the pathological form supports the spectroscopic results.

Purification, characterization and biological functions of metalloprotein isolated from haemolymph of mud crab Scylla serrata (Forskal, 1775)

In recent years, an enormous number of naturally occurring biological macromolecules has been reported worldwide due to its antibacterial and anticancerous potential. Among them, in this study, the copper containing respiratory protein namely haemocyanin (HC) was isolated from the haemolymph of mud crab Scylla serrata. The isolated metalloprotein HC was purified using Sepharose column by gel filtration chromatography. The purified HC was separated by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and molecular weight of the protein was identified as 95 kDa. Fourier transform infrared spectrophotometer (FT-IR) and nuclear magnetic resonance (¹H NMR) spectral data revealed the presence of amino acid constituents. Liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis based mass ion search exposed that the purified protein was HC. HC exhibited an in vitro bacteriostatic effects against the bacterial pathogens and also elevated ROS levels in the treated samples. The half maximal (50%) inhibitory concentration (IC₅₀) of HC was found to be 80 μg/mL against lung cancer cells (A549). Our study collectively addressed the potential antibacterial and anti-cancerous activity of HC. The results obtained from this study suggest that HC can be used for therapeutical application in the near future.

Mechanism of lysozyme adsorption onto gold surface determined by quartz crystal microbalance and surface plasmon resonance

In this study, the physicochemical characterization of lysozyme adsorbed on gold was investigated. Through the use of MP-SPR it was possible to establish that the orientation of molecules changes from side-on to between or end-on with increasing surface coverage. The data confirms that the process of adsorption is driven primarily by electrostatic interactions but also by hydrophobic forces. MP-SPR data was compared with the Random Sequential Adsorption model for a molecule with an ellipsoidal shape. Contact angle measurements showed that higher surface coverage also translates in more hydrophilic properties of obtained lysozyme layer. Comparison of CD and PM-IRRAS spectra in solution and adsorbed state respectively showed changes in the secondary structures of lysozyme. These changes are dependent on pH, but fundamentally they go in the direction of the increase of β-turn/random content with a simultaneous decrease in β-sheet fraction, which suggests that aggregation is not occurring. The combination of MP-SPR and QCM-D measurements allowed the estimation of the number of water molecules associated with the lysozymes films. It has been observed that hydration decreases from 70% in pH = 4 to 30% in pH = 11. This data indicates that hydration is driven mainly by the degree of protonation of lysozyme molecules.

Hydrophobic pore space constituted in macroporous ZIF-8 for lipase immobilization greatly improving lipase catalytic performance in biodiesel preparation

BACKGROUND

During lipase-mediated biodiesel production, by-product glycerol adsorbing on immobilized lipase is a common trouble that hinders enzymatic catalytic activity in biodiesel production process. In this work, we built a hydrophobic pore space in macroporous ZIF-8 (named as M-ZIF-8) to accommodate lipase so that the generated glycerol would be hard to be adsorbed in such hydrophobic environment. The performance of the immobilized lipase in biodiesel production as well as its characteristics for glycerol adsorption were systematically studied. The PDMS (polydimethylsiloxane) CVD (chemical vapor deposition) method was utilized to get hydrophobic M-ZIF-8-PDMS with hydrophobic macropore space and then ANL (Aspergillus niger lipase) was immobilized on M-ZIF-8 and M-ZIF-8-PDMS by diffusion into the macropores.

RESULTS

ANL@M-ZIF-8-PDMS presented higher enzymatic activity recovery and better biodiesel production catalytic performance compared to ANL@M-ZIF-8. Further study revealed that less glycerol adsorption was observed through the hydrophobic modification, which may attribute to the improved immobilized lipase performance during biodiesel production and ANL@M-ZIF-8-PDMS remained more than 96% activity after five cycles' reuse. Through secondary structure and kinetic parameters' analysis, we found that ANL@M-ZIF-8-PDMS had lower extent of protein aggregation and twice catalytic efficiency (V _max/K _m) than ANL@M-ZIF-8.

CONCLUSIONS

Hydrophobic pore space constituted in macroporous ZIF-8 for lipase immobilization greatly improved lipase catalytic performance in biodiesel preparation. The hydrophobic modification time showed negligible influence on the reusability of the immobilized lipase. This work broadened the prospect of immobilization of enzyme on MOFs with some inspiration.

Synergistic effect of hen egg white lysozyme and lysosomotropic surfactants on cell viability and membrane permeability

The interactions between two types of quaternary ammonium surfactants (N,N,N-trimethyl-2-(dodecanoyloxy)ethaneammonium bromide (DMM-11) and N,N,N-trimethyl-2-(dodecanoyloxy)propaneammonium bromide (DMPM-11)) and hen egg white lysozyme were studied through several techniques, including isothermal titration calorimetry (ITC), circular dichroism (CD) and fluorescence spectroscopy, and surface tension measurement. The average number of surfactants interacting with each molecule of lysozyme was calculated from the biophysical results. Moreover, the CD results showed that the conformation of lysozyme changed in the presence of DMM-11 and DMPM-11. The studies drew a detailed picture on the physicochemical nature of interactions between both surfactants and lysozyme. Both DMM-11 and DMPM-11, with and without lysozyme were studied against three target microorganisms, including Gram-negative (Escherichia coli) and Gram-positive (Enterococcus hirae and Enterococcus faecalis) bacteria. The results revealed a broad spectrum of antibacterial nature of surfactant/lysozyme complexes, as well as their effect on the membrane damage, hence providing the basis to further explore DMM-11 and DMPM-11 combined with lysozyme as possible antibacterial tools.

Mechanochemically Induced Controlled Glycation of Lysozyme and Its Effect on Enzymatic Activity and Conformational Changes

Protein glycation through heating of a mixture of protein and reducing sugars is one of the most commonly used methods of protein modification; however, in most cases, this approach can lead to uncontrolled glycation. The hypothesis that mechanical energy supplied through ball milling can induce glycation of proteins was tested using a well-characterized enzyme lysozyme. The Q-TOF/MS analysis of the milled samples has indicated that the milling of sugar-protein mixtures in stainless steel jars for 30 min and at a frequency of 30 Hz generated mainly monoglycated proteins even with the highly reactive ribose. Increasing the sugar concentration or the milling time did not influence the overall yield or generate more glycoforms. Enzymatic activity measurements, FTIR, and fluorescence spectroscopic studies have indicated that milling of lysozyme alone leads to a significant loss in enzymatic activity and structural integrity in contrast to milling in the presence of sugars.

Peptide Self-Assembly and Its Modulation: Imaging on the Nanoscale

This chapter intends to review the progress in obtaining site-specific structural information for peptide assemblies using scanning tunneling microscopy. The effects on assembly propensity due to mutations and modifications in peptide sequences, small organic molecules and conformational transitions of peptides are identified. The obtained structural insights into the sequence-dependent assembly propensity could inspire rational design of peptide architectures at the molecular level.

Go with the Flow-Microfluidics Approaches for Amyloid Research

The rapid development of cost-efficient microfluidic devices has received tremendous attention from scientists of diverse fields. The growing potential of utilizing microfluidic platforms has further advanced the ability to integrate existing technology into microfluidic devices. Thus, allowing scientists to approach questions in fundamental fields, such as amyloid research, using new and otherwise unachievable conditions. Amyloids are associated with neurodegeneration and are in the forefront of many research efforts worldwide. The newly emerged microfluidic technology can serve as a novel research tool providing a platform for developing new methods in this field. In this review, we summarize the recent progress in amyloid research using microfluidic approaches. These approaches are driven from various fields, including physical chemistry, electrochemistry, biochemistry, and cell biology. Moreover, the new insights into novel microfluidic approaches for amyloid research reviewed here can be easily modified for other research interests.

Study on the oxidation of fibrinogen using Fe3O4 magnetic nanoparticles and its influence to the formation of fibrin

Oxidative stress accompanies various diseases associated with chronic inflammation. In this work, H₂O₂ and H₂O₂-Fe₃O₄ magnetic nanoparticles were used as two reactive oxygen species to study the oxidative stress for the structure and polymerization behaviour of fibrinogen molecules. The alterations of secondary structure and component of fibrinogen molecule were characterized by circular dichroism spectra, ultraviolet-visible spectra and fluorescence spectra, the viscoelasticity of fibrinogen solution was studied by dynamic light scattering microrheology. Based on the molecular dynamics simulations and fluorescence properties, the possible oxidative stress sites were analyzed and confirmed by Tb³⁺ probe. The hydrophobicity/philicity and electrostatic net charges present on the exterior part of the fibrinogen molecules were measured with zeta potential. The height and image analysis obtained from atomic force microscope indicated that oxidative stress of fibrinogen molecules could influence the equilateral junctions of protofibrils and the different cross-linking patterns between the α- and γ-chains, result in the decrease of the fibre size, form a higher proportion of branching and a denser aggregation state. This study will provide insights into the misfolding and fibril formation of disease-associated fibrinogen, facilitate an increased understanding of how oxidative stress in vivo affects the formation and polymerization of fibrin, and support efforts for the improved treatment of patients suffering from the thrombotic disease.

Conformational and Organizational Insights into Serum Proteins during Competitive Adsorption on Self-Assembled Monolayers

Physicochemical interactions of proteins with surfaces mediate the interactions between the implant and the biological system. Surface chemistry of the implant is crucial as it regulates the events at the interface. The objective of this study was to explore the performance of modified surfaces for such interactions relevant to various biomedical applications. Because of a wide range of surface wettability, we aimed to study protein behavior (i.e., conformational changes and their packing) during competitive protein adsorption. Three serum proteins (bovine serum albumin, BSA; fibrinogen, FB; and immunoglobulin G, IgG) were tested for their conformational changes and orientation upon adsorption on hydrophilic (COOH and amine), moderately hydrophobic (mixed and hybrid), and hydrophobic (octyl) surfaces generated via silanization. Modified surfaces were characterized using Fourier-transform infrared spectroscopy, contact angle, and atomic force microscopy (AFM) techniques. Adsorbed masses of proteins from single and binary protein solutions on different surfaces were quantified along with their secondary structure analyses. Maximum adsorbed protein masses were found to be on negatively charged and hydrophobic (octyl) surfaces because of ionic and hydrophobic interactions between protein molecules and surfaces, respectively. Side-on and end-on orientations of adsorbed protein molecules were analyzed using theoretical and AFM analyses. We observed compact and elongated forms of BSA molecules on hydrophilic and hydrophobic surfaces, respectively. We further found a linear increase in the α-helix content of BSA and β-sheet contents of FB and IgG proteins with the increasing side-on (%)-oriented protein molecules on the surfaces. This indicates that side-on orientations of adsorbed FB and IgG lead to the formation of β-sheets. Sodium dodecyl sulfate polyacrylamide gel electrophoresis was employed to quantify the protein types and their ratio in competitively adsorbed proteins on different surfaces. A theoretical analysis was also used to determine the % secondary structures of competitively adsorbed proteins from BSA/FB and BSA/IgG solutions, which very well agreed with experimental results. The competitive protein adsorption from both BSA/FB and BSA/IgG solutions was found to be entropy-driven, as revealed by thermodynamic studies performed using isothermal titration calorimetry.

Molecular dynamics simulations of β2-microglobulin interaction with hydrophobic surfaces

Hydrophobic surfaces are known to adsorb and unfold proteins, a process that has been studied only for a few proteins. Here we address the interaction of β2-microglobulin, a paradigmatic protein for the study of amyloidogenesis, with hydrophobic surfaces. A system with 27 copies of the protein surrounded by a model cubic hydrophobic box is studied by implicit solvent molecular dynamics simulations. Most proteins adsorb on the walls of the box without major distortions in local geometry, whereas free molecules maintain proper structures and fluctuations as observed in explicit solvent molecular dynamics simulations. The major conclusions from the simulations are as follows: (i) the adopted implicit solvent model is adequate to describe protein dynamics and thermodynamics; (ii) adsorption occurs readily and is irreversible on the simulated timescale; (iii) the regions most involved in molecular encounters and stable interactions with the walls are the same as those that are important in protein-protein and protein-nanoparticle interactions; (iv) unfolding following adsorption occurs at regions found to be flexible by both experiments and simulations; (v) thermodynamic analysis suggests a very large contribution from van der Waals interactions, whereas unfavorable electrostatic interactions are not found to contribute much to adsorption energy. Surfaces with different degrees of hydrophobicity may occur in vivo. Our simulations show that adsorption is a fast and irreversible process which is accompanied by partial unfolding. The results and the thermodynamic analysis presented here are consistent with and rationalize previous experimental work.

In Silico Study of Recognition between Aβ40 and Aβ40 Fibril Surfaces: An N-Terminal Helical Recognition Motif and Its Implications for Inhibitor Design

The recent finding that the surface of amyloid-β (Aβ) fibril can recruit Aβ peptides and convert them into toxic oligomers has rendered fibril surfaces attractive as inhibition targets. Through extensive simulations with hybrid-resolution and all-atom models, we have investigated how Aβ_1-40 recognizes its own fibril surfaces. These calculations give a ∼2.6-5.6 μM half-saturation concentration of Aβ on the surface (cf. experimental value ∼6 μM). Aβ was found to preferentially bind to region 16-24 of Aβ₄₀ fibrils through both electrostatic and van der Waals forces. Both terminal regions of Aβ contribute significantly to binding energetics. A helical binding pose of the N-terminal region of Aβ (Aβ_3-14) not seen before is highly preferred on the fibril surface. Aβ_3-14 in a helical form can arrange side chains with similar properties on the same sides of the helix and maximize complementary interactions with side chain arrays characteristic of amyloid fibrils. Helix formation on a fibril surface implies a helix-mediated mechanism for Aβ oligomerization catalyzed by fibrils. We propose an Aβ_3-14 analogue that can exhibit enhanced helical character and interactions with Aβ fibrils and may thus be used as a template with which to pursue potent inhibitors of Aβ-fibril interactions.

Investigation on Secondary Structure Perturbations of Proteins Embedded in Solid Lipid Matrices as a Novel Indicator of their Biological Activity upon In Vitro Release

Protein biologics are prone to conformational changes during formulation development. Limited methods are available for conformational analysis of proteins in solid state and in the presences of formulation excipients. The aim of this study was to investigate the secondary structures of proteins encased in solid lipid matrices as a novel indicator of their stability upon in vitro release. Model proteins namely catalase and lysozyme were incorporated into lipid namely Precirol® AT05 (glycerol palmitostearate, melting point 58°C) at 30% w/w loading using melting and mixing and wet granulation methods. Attenuated total reflectance (ATR-FTIR) spectroscopy, size-exclusion chromatography (SEC) and biological activity analyses were performed. The information about secondary structure was acquired using second derivative analysis of amide-I band (1600-1700 cm^-1). ATR analysis demonstrated interference of lipid spectrum with protein amide-I band which was subsequently subtracted to allow the analysis of the secondary structure. ATR spectra amide-I bands showed shifts peak band positions compared to native protein for matrices prepared using wet granulation. SEC analysis gave evidence of protein aggregation for catalase which was increased using wet granulation. The biological activity of catalase was statistically different from that of control and was affected by the incorporation method and was found to be in alignment with ATR spectral changes and extent of aggregation. In conclusion, ATR spectroscopy could analyze protein secondary structure in lipid matrices provided lipid interference was minimized. The ATR spectral changes and formation of aggregates can indicate the loss in biological activity of protein released from solid lipid matrices.

Examining lysozyme structures on polyzwitterionic brush surfaces

Conformational structures of lysozyme at the interfaces of hydrophilic polymer poly[2-(methacryloyloxy)ethyl dimethyl-(3-sulfopropyl)ammonium hydroxide] (PMEDSAH), are examined to understand the role of protein-polymer interactions on the stability of lysozyme. This work underpins the effect of hydration layer on the structures of physically adsorbed lysozyme on PMEDSAH brushes. Hydrophilic nature and strength of hydration layers around brushes are controlled by varying the brush thickness and temperature. We measured that lysozyme is structurally less stable on 15nm thick hydrophilic PMEDSAH brushes at 75°C than at room temperature. To the contrary, 5-8nm thick brushes stretch in hydrated state by heating, hence yield higher structural stability of lysozyme. These results suggest that short polyzwitterionic brushes can facilitate improved biomaterial interactions that are essential for biosensors performing at elevated temperatures.

Structural perturbation by arsenic triggers the aggregation of hen egg white lysozyme by promoting oligomers formation

Arsenic trioxide is one of the most common metallic pollutants entering the food chain both by human activities and nature. Its entry inside the living organism through food, air and water results into the accumulation of heavy metal in several tissues which manifest several metabolic or hormonal disorders. Till now the effect of arsenic trioxide on protein misfolding and aggregation culminating into several neurodegenerative disorders is poorly understood. In the present study, we reveal the aggregation process of Hen Egg White Lysozyme (HEWL) in presence of arsenic trioxide (As₂O₃) at physiological conditions. We show that As₂O₃ promote the in vitro aggregation of HEWL in concentration dependent manner. Early phase of aggregation is observed to be induced by exposure of hydrophobic surfaces which later reorganized to promote further self-association leading to β sheet structure. Presence of lower ordered oligomers after two days and higher ordered oligomers along with amorphous aggregates after week long incubation indicate that As₂O₃ drives the self-assembly of lysozyme towards oligomeric form.

Cadherin Diffusion in Supported Lipid Bilayers Exhibits Calcium-Dependent Dynamic Heterogeneity

Ca²⁺ ions are critical to cadherin ectodomain rigidity, which is required for the activation of adhesive functions. Therefore, changes in Ca²⁺ concentration, both in vivo and in vitro, can affect cadherin conformation and function. We employed single-molecule tracking to measure the diffusion of cadherin ectodomains tethered to supported lipid bilayers at varying Ca²⁺ concentrations. At a relatively high Ca²⁺ concentration of 2 mM, cadherin molecules exhibited a fast diffusion coefficient that was identical to that of individual lipid molecules in the bilayer (D_fast ≈ 3 μm²/s). At lower Ca²⁺ concentrations, where cadherin molecules were less rigid, the ensemble-average cadherin diffusion coefficient was systematically smaller. Individual cadherin trajectories were temporally heterogeneous, exhibiting alternating periods of fast and slow diffusion; the periods of slow diffusion (D_slow ≈ 0.1 μm²/s) were more prevalent at lower Ca²⁺ concentration. These observations suggested that more flexible cadherin ectodomains at lower Ca²⁺ concentration alternated between upright and lying-down conformations, where the latter interacted with more lipid molecules and experienced greater viscous drag.

Catechol-Containing Hydroxylated Biomimetic 4-Thiaflavanes as Inhibitors of Amyloid Aggregation

The study of compounds able to interfere in various ways with amyloid aggregation is of paramount importance in amyloid research. Molecules characterized by a 4-thiaflavane skeleton have received great attention in chemical, medicinal, and pharmaceutical research. Such molecules, especially polyhydroxylated 4-thiaflavanes, can be considered as structural mimickers of several natural polyphenols that have been previously demonstrated to bind and impair amyloid fibril formation. In this work, we tested five different 4-thiaflavanes on the hen egg-white lysozyme (HEWL) amyloid model for their potential anti-amyloid properties. By combining a thioflavin T assay, atomic force microscopy, and a cell toxicity assay, we demonstrated that such compounds can impair the formation of high-order amyloid aggregates and mature fibrils. Despite this, the tested 4-thiaflavanes, although non-toxic per se, are not able to prevent amyloid toxicity on human neuroblastoma cells. Rather, they proved to block early aggregates in a stable, toxic conformation. Accordingly, 4-thiaflavanes can be proposed for further studies aimed at identifying blocking agents for the study of toxicity mechanisms of amyloid aggregation.

Confinement effect on the structure and elasticity of proteins interfacing polymers

The ordered nanostructured surfaces provide confined environments that allow functionalization of proteins. Here, we used the nanopores of poly(methyl methacrylate) films to attach fibrinogen and lysozyme, and discussed the changes in proteins' structures and elasticity upon confinement. Fourier-transform infrared spectroscopic analysis of protein secondary structures reveals that fibrinogen undergoes less structural change and behaves less stiff when the pore size is close to the protein size. Lysozyme, on the other hand, retains its native-like structure, however, it exhibits the highest modulus in 15 nm pores due to the lower macromolecular crowding effect the protein faces compared to lysozyme within larger pores. These findings manifest the effect of confinement and crowding on the conformation and elasticity of different shaped proteins tethered on surfaces.

Comparative effect of cationic gemini surfactant and its monomeric counterpart on the conformational stability and activity of lysozyme

Protein interactions with surfactants are dependent on their physiochemical properties.

Comparative effect of cationic gemini surfactant and its monomeric counterpart on the conformational stability and activity of lysozyme

Protein interactions with surfactants are dependent on their physiochemical properties.