Protein Aggregation and Performance Optimization Based on Microconformational Changes of Aromatic Hydrophobic Regions

Whey protein-structured oleogels: Effect of α-lactalbumin addition and ultrasonication treatment on oleogelation

Research on oleogels has a health and sustainability imperative for reducing saturated-fat intake. Herein, the physicochemical properties of whey protein aggregates (WPA) with α-lactalbumin (α-La) addition (5-10 %), ultrasonication (1-2 min), and heating process (85-95 °C), and consequently, the functional characteristics of WPA-based oleogels (WPO) and their potential for replacing commercial butter were investigated. More α-La incorporation and longer ultrasonication increased the hydrogen bonding and β-sheet (34 %-50 %), while reduced random coil of WPA (27 %-11 %), which promoted WPA formation, increased WPA structural density, and led to a decline in particle size of WPA driven by surface hydrophobicity decrease. Therefore, the WPO exhibited excellent oil-holding capacity, thermal stability, viscoelasticity and spreadability. WPO consisted of 95 °C-heated WPA with 5 % α-La addition or 1 min-ultrasonication showed textural and rheological behavior similar to butter. These results contribute to the formulation of whey protein oleogels with controlled physicochemical and functional properties, showing potential being applied as fat substitutes.

Nonbonded Molecular Interaction Controls Aggregation Kinetics of Hydrophobic Molecules in Water

Molecular aggregation frequently occurs during material synthesis, cellular processes, and drug delivery systems, often resulting in decreased performance and efficiency. One major reason for such aggregation in an aqueous solution is hydrophobicity. While the basic understanding of the aggregation process of hydrophobic molecules from a thermodynamic standpoint is known, the present literature lacks a connection between the aggregation kinetics and the molecular basis of hydrophobicity. This study explores how various fluorescent probes (rhodamine dyes) aggregate in an aqueous solution due to their hydrophobicity. The method employs a combination of modeling and characterization to comprehend the aggregation process by examining the nonbonded intermolecular interactions. The aggregation kinetics was analyzed by measuring the average diffusivity of the molecules using fluorescent correlation spectroscopy and NMR diffusion measurements. Through all-atom molecular dynamics (MD) simulations, it has been observed that the level of hydrophobicity is strongly correlated to the total number of hydrogen bonds between water molecules and dyes. In addition, the aggregation frequency of colliding species, which depends on the concentration, is inversely related to hydrogen bonding and the diffusivity of the molecules. This study of small molecules was applied to predict protein aggregation rates, demonstrating strong alignment with the existing literature. The study has also helped to identify and understand the concentration at which a hydrophobic molecule does not aggregate in an aqueous solution. The method developed here could help investigate the aggregation process and its root causes at the molecular level in aqueous systems to develop strategies to control it.

Protein aggregation monitoring in cells under oxidative stress: a novel fluorescent probe based on a 7-azaindole-BODIPY derivative

The development of new fluorescent probes as molecular sensors is a critical step for the understanding of molecular mechanisms. BODIPY-based probes offer versatility due to their high fluorescence quantum yields, photostability, and tunable absorption/emission wavelengths. Here, we report the synthesis and evaluation of a novel 7-azaindole-BODIPY derivative to probe hydrophobic proteins as well as protein misfolding and aggregation. In organic solvents, this compound shows two efficiently interconverting emissive excited states. In aqueous environments, it forms molecular aggregates with unique photophysical properties. The complex photophysics of the 7-azaindole-BODIPY derivative was explored for sensing applications. In the presence of albumin, the compound is stabilized in hydrophobic protein regions, significantly increasing its fluorescence emission intensity and lifetime. Similar effects occur in the presence of protein aggregates but not with other macromolecules like pepsin, DNA, Ficoll 40, and coconut oil. Fluorescence lifetime imaging microscopy (FLIM) and two-photon fluorescence microscopy on breast (MCF-7) and lung (A549) cancer cells incubated with this compound display longer fluorescence lifetimes and higher emission intensity under oxidative stress. Synchrotron FTIR micro spectroscopy confirmed that the photophysical changes observed were due to protein misfolding and aggregation caused by the oxidative stress. These findings demonstrate that this compound can serve as a fluorescent probe to monitor protein misfolding and aggregation triggered by oxidative stress.

Small conformational changes in IgG1 detected as acidic charge variants by cation exchange chromatography

Fully characterizing the post-translational modifications present in charge variants of therapeutic monoclonal antibodies (mAbs), particularly acidic variants, is challenging and remains an open area of investigation. In this study, to test the possibility that chromatographically separated acidic fractions of therapeutic mAbs contain conformational variants, we undertook a mAb refolding approach using as a case study an IgG1 that contains many unidentified acidic peaks with few post-translational modifications, and examined whether different acidic peak fractions could be generated corresponding to these variants. The IgG1 drug substance was denatured by guanidine hydrochloride, without a reducing agent present, and gradually refolded by stepwise dialysis against arginine hydrochloride used as an aggregation suppressor. Each acidic chromatographic peak originally contained in the IgG1 drug substance was markedly increased by this stepwise refolding process, indicating that these acidic variants are conformational variants. However, no conformational changes were detected by small-angle X-ray scattering experiments for the whole IgG1, indicating that the conformational changes are minor. Chromatographic, thermal and fluorescence analyses suggested that the conformational changes are a localized denaturation effect centred around the aromatic amino acid regions. This study provides new insights into the characterization of acidic variants that are currently not fully understood.

Accelerating therapeutic protein design with computational approaches toward the clinical stage

Therapeutic protein, represented by antibodies, is of increasing interest in human medicine. However, clinical translation of therapeutic protein is still largely hindered by different aspects of developability, including affinity and selectivity, stability and aggregation prevention, solubility and viscosity reduction, and deimmunization. Conventional optimization of the developability with widely used methods, like display technologies and library screening approaches, is a time and cost-intensive endeavor, and the efficiency in finding suitable solutions is still not enough to meet clinical needs. In recent years, the accelerated advancement of computational methodologies has ushered in a transformative era in the field of therapeutic protein design. Owing to their remarkable capabilities in feature extraction and modeling, the integration of cutting-edge computational strategies with conventional techniques presents a promising avenue to accelerate the progression of therapeutic protein design and optimization toward clinical implementation. Here, we compared the differences between therapeutic protein and small molecules in developability and provided an overview of the computational approaches applicable to the design or optimization of therapeutic protein in several developability issues.

Effect of Structural Targeted Modifications on the Potential Allergenicity of Peanut Allergen Ara h 2

Protein structure affects allergenicity, and critical structural elements, especially conformational epitopes that determine allergenicity, have attracted a great deal of interest. In this study, we aimed to identify the localized structure that affects the potential allergenicity of protein by making targeted modifications of Ara h 2 and comparing the structure and allergenicity of mutants with those of the wide-type allergen. The structures of the allergen and its mutants were characterized by circular dichroism and ultraviolet absorption spectroscopy and simulated by molecular dynamics. The allergenicity was assessed by Western blotting, an indirect competitive enzyme-linked immunosorbent assay, a cell model, and a mouse model. Then, the structures that affect allergenicity were analyzed and screened. Our results showed that mutations in amino acids changed the nearby localized structure and the overall structures. The structural changes affected the IgE binding capacity of the allergen and reduced its potential allergenicity. The solvent accessible surface area (SASA) of aromatic residues was positively correlated with the IgE binding capacity. The integrity of the disulfide bond is also critical for the binding of IgE to allergens. Interestingly, different mutations induced similar electrostatic potential and allergenicity changes, such as localized structure R⁶²DPYSPSQDPYSPS⁷⁵. In conclusion, the disulfide bond and the SASA of aromatic residues are important for the allergenicity of Ara h 2. The localized structure R⁶²DPYSPSQDPYSPS⁷⁵ is also crucial for the allergenicity of Ara h 2.

Hampering the early aggregation of PrP-E200K protein by charge-based inhibitors: a computational study

A multilayered computational workflow was designed to identify a druggable binding site on the surface of the E200K pathogenic mutant of the human prion protein, and to investigate the effect of the binding of small molecules in the inhibition of the early aggregation of this protein. At this purpose, we developed an efficient computational tool to scan the molecular interaction properties of a whole MD trajectory, thus leading to the characterization of plausible binding regions on the surface of PrP-E200K. These structural data were then employed to drive structure-based virtual screening and fragment-based approaches to the seeking of small molecular binders of the PrP-E200K. Six promising compounds were identified, and their binding stabilities were assessed by MD simulations. Therefore, analyses of the molecular electrostatic potential similarity between the bound complexes and unbound protein evidenced their potential activity as charged-based inhibitors of the PrP-E200K early aggregation.

Protein-protein interactions at high concentrations: Effects of ArgHCl and NaCl on the stability, viscosity and aggregation mechanisms of protein solution

The aim of this work was to use the diffusion coefficient ration (D_m/D_line) as a parameter to characterize the stability of protein at high concentration, to compare the effects of ArgHCl and NaCl on the interaction of highly concentrated proteins under different pH conditions, and to explore the correlation with protein stability. For this purpose, a high-concentration bovine serum albumin solution (BSA) was selected as the model system, and the diffusion coefficient, aggregation degree, conformational stability, and solution viscosity of the protein were studied by dynamic light scattering (DLS) and spectral detection techniques. The result showed that there was a significant correlation between the D_m/D_line and the protein aggregation. The D_m/D_line of the protein was minimum at pH 7.4, which corresponded to the maximum degree of aggregation and the highest solution viscosity. At pH 7.4, the hydrophobic interactions and the increased conformational stability of ArgHCl maximized the stability of the protein and reduced the viscosity of the solution by 69.3%. At pH 3.0, the strong charge shielding effect of ArgHCl and NaCl and the decreased conformational stability induced protein aggregation and the gel formation. These findings provided valuable insights into the mechanism of protein aggregation and the diffusion coefficient ration (D_m/D_line) could be a potential tool for the pre-formulation studies.

Potential involvement of environmental triggers in protein aggregation with mercuric chloride as a model

Heavy metal based toxicity has a direct relation with the perturbation of protein structure. We have investigated the progressive unfolding of ovalbumin, in the presence of increasing concentration mercury (0-6.25 μM) using different spectroscopic techniques. Formation of amorphous aggregate has been observed at the physiological pH. Initial addition of HgCl₂ resulted in the association of monomers to oligomers that proceeded to non-fibrillar aggregates on further addition. The sigmoidal curve obtained from the Stern-Volmer plot clearly divided into three stage transition. A strong lag phase is observed indicating the time dependence for the association of competent monomers. The second stage was resolved into non-cooperative binding. These results match very well with the data from atomic force microscopy and the free energy change observed in the regions. Raman spectroscopic studies indicated toxic antiparallel β-sheets structure. Time dependent atomic force microscopy study revealed the off-pathway nature of amorphous aggregates. At molten globular state, similar quenching behaviour is observed. The atomic force microscopy images clearly indicate at pH 2.2 the initiation of fibril formation occurs at lower concentration of HgCl₂ itself. Our results revealed the conformation switch of ovalbumin upon the contact of an environmental toxin and its possible way of toxicity.

The distinct binding modes of pesticides affect the phase transitions of lysozyme

Studying the aggregation and nucleation of proteins in the presence of organic molecules is helpful for disclosing the mechanisms of protein crystallization.

Effect of the heating process on the physicochemical characteristics and nutritional properties of whole cotyledon soymilk and tofu

This study focused on the effect of the heating process on the whole cotyledon soymilk and tofu. Whole cotyledon soymilk was made from soybean cotyledon and processed by enzymatic hydrolysis using cellulase and high-pressure homogeneity. In this study, a one-step heating method was selected for the cooking process of whole cotyledon soybean milk, and the whole cotyledon soybean milk was heated to 90 °C and held for 4 min. Results showed that the protein, total saccharides and dietary fiber content of the whole cotyledon soymilk were higher than those of the tradition soymilk due to the existence of bean dregs (okara). Both protein aggregation and protein-polysaccharide interaction were observed during the heating process. We also found a change in soymilk physicochemical characteristics such as particle size distribution, viscosity, surface hydrophobicity and soluble protein during the heating process. The results in this study showed that compared with traditional tofu, the phytic acid and trypsin inhibitor content in whole cotyledon tofu was lower, so its protein had higher digestibility in vitro. In conclusion, whole cotyledon tofu had better health properties and application prospects.

Damage of proteins at the air/water interface: Surface tension characterizes globulin interface stability

In the present study, we aimed to see what circumstances may cause protein damage at air/water interface and reveal the correlation between the surface properties of protein solution and the interface stability. The surface hydrophobicity and β-sheet of protein were determined by exogenous fluorescent probes, and the changes in the spatial structure of proteins were characterized by steady-state fluorescence spectroscopy. The surface tension was determined by the plate method, and such value was used to establish the correlation with the hydrophobicity and structure of the protein. Moreover, degree of aggregation in the presence or absence of Hofmeister salt in protein solution was investigated. There was a significant correlation between the surface tension and hydrophobicity of the protein solution (P < 0.05). The surface tension and structure of the protein also showed a significant correlation under the induction of pH (P < 0.05). Furthermore, when the protein was induced by the air/water interface, the surface tension, hydrophobicity, and structure of proteins were correlated, and protein aggregation was increased. When the additive induced a decrease in the surface tension of the protein solution, the protein aggregation was promoted. These findings provided valuable insights into the relationship between surface tension of the protein solution and interfacial stability and paved the way for future pre-formulation studies of therapeutic proteins.

The Role of Surface Properties on Protein Aggregation Behavior in Aqueous Solution of Different pH Values

This study aimed to investigate the effect of pH-mediated surface properties of bovine serum albumin (BSA) on protein aggregation and the changes of protein structure and colloidal stability at different solution pH levels. The hydrophobicity of BSA surface was characterized by endogenous fluorescence spectroscopy, fluorescence quenching of acrylamide, and fluorescence probe. The results showed that the hydrophobicity of BSA surface was similar at pH 5, 6, 7.4, followed by pH 4, 8, 9, 10, and finally by pH 3 and 11 with strong acidity and alkalinity. The positive charge on the BSA surface was increased gradually with the decrease of solution pH, while the negative charge on protein surface was increased gradually with the increase of solution pH. The degree of protein aggregation was examined by turbidimetry, flow cytometry, and SDS-PAGE. The results showed that the oscillating aggregation of BSA did not change with the solution pH, but was partially dependent on the relative contribution of electrostatic and hydrophobic interactions between the protein molecules. In addition, the secondary structure, conformational stability, unfolding degree, and colloidal stability of proteins were investigated by circular dichroism, fluorescence spectroscopy, protein pulse hydrolysis, and dynamic light scattering, respectively. The results suggested that the solution pH could change the structure and stability of the protein at different levels. Solution pH has distinct effects on the structural stability of protein at different levels. The change of protein surface properties mediated by solution pH is related to protein aggregation.

Inhibition effect of thiol-type antioxidants on protein oxidative aggregation caused by free radicals

This study was aimed to investigate the inhibition effect of thiol-type antioxidants on protein oxidative aggregation caused by free radicals and the underlying mechanisms using six different thiol-type antioxidants (N-acetyl-L-cysteine, methionine, taurine, alpha-lipoic acid, glutathione and thioproline), Cu²⁺-H₂O₂ as a free radical generator (mainly a hydroxyl radical generator) and bovine serum albumin as the model protein. The inhibition effect of these antioxidants on protein oxidative aggregation and protective effect against oxidative damage in mouse brain tissues were investigated using SDS-PAGE, intrinsic fluorescence, simultaneous fluorescence, thioflavin T fluorescence, Congo red absorbance and inverted microscope. The results showed that all six antioxidants could inhibit protein oxidative aggregation by scavenging free radicals. In addition, alpha-lipoic acid could also bind to proteins via hydrophobic interactions and thioproline could bind to proteins via hydrogen bonds and van der Waals forces, thereby showing much stronger inhibition effect than others. Moreover, alpha-lipoic acid and thioproline could effectively prevent oxidative damage of mouse brain tissues. These results suggest that alpha-lipoic acid and thioproline can effectively inhibit free radical-induced protein aggregation and brain damage, which are worth testing for further anti-Alzheimer properties.

Non-polyphenolic natural inhibitors of amyloid aggregation

Protein misfolding diseases (PMDs) are chronic and progressive, with no effective therapy so far. Aggregation and misfolding of amyloidogenic proteins are closely associated with the onset and progression of PMDs, such as amyloid-β (Aβ) in Alzheimer's disease, α-Synuclein (α-Syn) in Parkinson's disease and human islet amyloid polypeptide (hIAPP) in type 2 diabetes. Inhibiting toxic aggregation of amyloidogenic proteins is regarded as a promising therapeutic approach in PMDs. The past decade has witnessed the rapid progresses of this field, dozens of inhibitors have been screened and verified in vitro and in vivo, demonstrating inhibitory effects against the aggregation and misfolding of amyloidogenic proteins, together with beneficial effects. Natural products are major sources of small molecule amyloid inhibitors, a number of natural derived compounds have been identified with great bioactivities and translational prospects. Here, we review the non-polyphenolic natural inhibitors that potentially applicable for PMDs treatment, along with their working mechanisms. Future directions are proposed for the development and clinical applications of these inhibitors.