Correlation Between Thermal Aggregation and Stability of Lysozyme with Salts Described by Molar Surface Tension Increment: An Exceptional Propensity of Ammonium Salts as Aggregation Suppressor

Exploring the structure and stability of pentameric amyloid β peptide aggregates in aqueous ammonium-based ionic liquid solutions

The self-assembly of amyloid beta (Aβ) proteins into fibrils is linked to Alzheimer's disease (AD). Soluble pentamers, particularly those formed in the early stages of Aβ aggregation, are considered highly neurotoxic. This study uses molecular dynamics simulations to explore how trimethylammonium chloride (TMAC), cholinium chloride (ChoC), and tetrabutylammonium chloride (TBAC) ionic liquids (ILs) affect the conformational stability and the association mechanism of Aβ pentameters. These ILs, characterized by varying hydrophilicity/hydrophobicity, exert differential effects on the conformatioanl flexibility of Aβ pentameters. Computational analyses reveal that TBAC induces greater conformational flexibility and multiple energetically favorable states for the Aβ pentamer, potentially driving the pentamerization process along various pathways to form different polymorphic Aβ fibrillar structures. Moreover, analysis of solvent distributions demonstrates that exchange of water by IL ion pairs at the pentamer's exterior surface primarily occurs beyond the first layer of surface-bound water molecules. Particularly, hydrophobic TBA cations show an enhanced propensity to replace weakly interacting water molecules on the surface. Mechanistic insights derived from umbrella sampling simulations further elucidate how ILs modulate the association/dissociation of Aβ monomers within pentameric aggregates. Our findings indicate that the binding of the Aβ peptide becomes less favorable and the binding free energy decreases when transitioning from TMAC to TBAC solutions, as compared to a pure aqueous solution. Finally, energy landscape analysis of Aβ peptide docking to Aβ pentameters reveals multiple low-energy conformations, which are more dispersed in the presence of ChoC and TBAC solutions, potentially hindering Aβ prefibril growth.

Molecular mechanism of the interactions between coffee polyphenols and milk proteins

The interaction between coffee polyphenols and milk proteins enhances the chemical stability of coffee polyphenols; however, the mechanism underlying this interaction remains elusive, especially at the amino acid level of the proteins. This study investigated the non-covalent interactions of coffee polyphenols (chlorogenic and caffeic acids) with various milk proteins (α-casein, β-casein, κ-casein, α-lactalbumin, and β-lactoglobulin). Fluorescence spectroscopy was used to examine the affinity of the coffee polyphenols for the milk proteins. The fluorescence intensity was found to be dependent on the proline residue content in the milk proteins. Coffee polyphenols were approximately twice as soluble in proline solution as in water, indicating thermodynamically favorable interactions with proline. Molecular dynamics simulations indicated that caffeic acid interacts with the proline side chains of peptides, which is attributable to hydrophobic interaction. The present findings provide mechanistic insights into the interactions between coffee polyphenols and milk proteins at the amino acid level, thereby contributing to a deeper understanding of the enhanced chemical stability of coffee polyphenols in the presence of milk proteins. This work also presents general cautions regarding the spectroscopy of polyphenols.

Elucidating the mechanisms of additive effects at high concentrations on hydrophobic interaction chromatography

Hydrophobic interaction chromatography (HIC) is a commonly used chromatography technique for purifying proteins. It utilizes salting-out salts to facilitate the binding of native proteins to weakly hydrophobic ligands. There have been three proposed mechanisms for the promoting effects of salting-out salts, which include the dehydration of proteins by salts, cavity theory, and salt exclusion. To evaluate the above three mechanisms, an HIC study was conducted on Phenyl Sepharose using four different additives. These additives included a salting-out salt (NH₄)₂SO₄, sodium phosphate that increases the surface tension of water, a salting-in salt MgCl₂, and an amphiphilic protein-precipitant polyethylene glycol (PEG). Results indicated that the first two salts resulted in protein binding, while MgCl₂ and PEG led to flow-through. These findings were then used to interpret the three proposed mechanisms, which showed that MgCl₂ and PEG deviated from the dehydration mechanism, and MgCl₂ also deviated from the cavity theory. The observed effects of these additives on HIC were reasonably well explained for the first time by their interactions with proteins.

Efficient extraction and preservation of thermotolerant phycocyanins from red alga Cyanidioschyzon merolae

C-Phycocyanin (PC) is a protein used commercially as a natural blue pigment produced by cyanobacteria, cryptophytes, and rhodophytes. Although it is industrially synthesized from the cyanobacterium Arthrospira platensis, PC requires high levels of energy for its extraction, which involves freezing of cells. However, as a protein, PC is easily denatured at extreme temperatures. In this study, we extracted PC from the red alga Cyanidioschyzon merolae, denoted as CmPC, and found that this protein was tolerant to high temperatures and acidic pH. CmPC was extracted by suspending cells in water mixed with various salts and organic acids without freeze-drying or freeze-thaw. The stability of CmPC varied with salt concentration and was destabilized by organic acids. Our results indicate that C. merolae is a potential candidate for PC production with thermotolerant properties.

Cation Specific Effects on the Domain-Domain Interaction of Heterogeneous Dimeric Protein Revealed by FRET Analysis

Specific monovalent cation effects on the domain-domain interaction of heterogeneous dimeric protein were investigated using green fluorescent protein (GFP)-glutathione-s-transferase (GST) fusion protein as a model protein. Conjugating N-terminal of GST domain with a fluorescence probe Cyanine3, complementary increase and decrease of fluorescence intensities of Cyanine3 and GFP were recognized on the exclusive excitation of GFP and further the fluorescence decay of GFP was remarkably accelerated to show that an excellent Förster type of resonance excitation energy transfer (FRET) pair was constructed between GFP- and GST-domain. The spectral overlap integral and critical distance of the FRET pair were estimated to be 5.96×10¹³ M^-1cm³ and 62.5 Å, respectively. The FRET rate and efficiency evaluated by fluorescence lifetime of the energy donor, GFP, were influenced by the monovalent cations included in the buffer solution to suggest that the domain-domain interactions of GFP-GST fusion protein would be susceptible to cation species and their concentrations. The order affecting the domain-domain interaction was estimated to be Li⁺>NH₄⁺ >Na⁺>K⁺>Cs⁺, almost corresponding to the reverse Hofmeister series.

Effect of additives on liquid droplets and aggregates of proteins

This review briefly summarizes the effect of additives on the formation of liquid droplets and aggregates of proteins. Proteins have the property of forming liquid droplets and aggregates both in vivo and in vitro. The liquid droplets of proteins are mainly stabilized by electrostatic and cation-π interactions, whereas the amorphous aggregates are mainly stabilized by hydrophobic interactions. Crowders usually stabilize liquid droplets, whereas ions and hexandiols destabilize the droplets. Additives such as kosmotropes, sugars, osmolytes, and crowders promote the formation of amorphous aggregates, whereas additives such as arginine and chaotropes can prevent the formation of amorphous aggregates. Further, amyloid has a different mechanism for its formation from amorphous aggregates because it is primarily stabilized by a cross-β structure. These systematic analyses of additives will provide clues to controlling protein aggregations and will aid the true understanding of the transition of proteins from liquid droplets and aggregates.

Apparent protein cloud point temperature determination using a low volume high-throughput cryogenic device in combination with automated imaging

Short-term parameters correlating to long-term protein stability, such as the protein cloud point temperature (T_cloud), are of interest to improve efficiency during protein product development. Such efficiency is reached if short-term parameters are obtained in a low volume and high-throughput (HT) manner. This study presents a low volume HT detection method for (sub-zero) T_cloud determination of lysozyme, as such an experimental method is not available yet. The setup consists of a cryogenic device with an automated imaging system. Measurement reproducibility (median absolute deviation of 0.2 °C) and literature-based parameter validation (Pearson correlation coefficient of 0.996) were shown by a robustness and validation study. The subsequent case study demonstrated a partial correlation between the obtained apparent T_cloud parameter and long-term protein stability as a function of lysozyme concentration, ion type, ionic strength, and freeze/thaw stress. The presented experimental setup demonstrates its ability to advance short-term strategies for efficient protein formulation development.

Correlating multidimensional short-term empirical protein properties to long-term protein physical stability data via empirical phase diagrams

Identification of long-term stable biopharmaceutical formulations is essential for biopharmaceutical product development. Reduction of the number of long-term storage experiments and a well-defined formulation search space requires knowledge-based formulation screenings and a detailed protein phase behavior understanding. To achieve this, short-term analytical techniques can serve as predictors for long-term protein phase behavior. Protein phase behavior studies that investigate this concept commonly display shortcomings such as limited and small datasets, sample adjustments, or simplistic data analysis. To overcome these shortcomings, 150 unique lysozyme solutions were analyzed using six different short-term analytical techniques. Lysozyme's structural properties, conformational stability, colloidal stability, surface charge, and surface hydrophobicity were obtained directly after formulation preparation. Employing the empirical phase diagram method, this short-term data was correlated to long-term physical stability data obtained during 40 days of storage. Short-term protein properties showed partial correlation to long-term phase behavior. Structural differences, changing surface properties, colloidal stability, and conformation stability as a function of formulation conditions were observed. This study contributes to long-term protein phase behavior research by presenting a systematic, data-dependent, and multidimensional data evaluation workflow to create a comprehensive overview of short-term protein analytics in relation to long-term protein phase behavior.

Specific Ion Effects on Protein Thermal Aggregation from Dilute Solutions to Crowded Environments

We have investigated specific ion effects on protein thermal aggregation from dilute solutions to crowded environments. Ovalbumin and poly(ethylene glycol) have been employed as the model protein and crowding agent, respectively. Our studies demonstrate that the rate-limiting step of ovalbumin thermal aggregation is changed from the aggregation of unfolded protein molecules to the unfolding of the protein molecules, when the solution conditions are varied from a dilute solution to a crowded environment. The specific ion effects acting on the thermal aggregation of ovalbumin generated by kosmotropic and chaotropic ions are different. The thermal aggregation of ovalbumin molecules is promoted by kosmotropic anions in dilute solutions via an increase in protein hydrophobic interactions. In contrast, ovalbumin thermal aggregation is facilitated by chaotropic ions in crowded environments through accelerated unfolding of protein molecules. Therefore, there are distinct mechanisms causing the ion specificities of protein thermal aggregation between dilute solutions and crowded environments. The ion specificities are dominated by ion-specific hydrophobic interactions between protein molecules and ion-specific unfolding of protein molecules in dilute solutions and crowded environments, respectively.

Allantoin and hydantoin as new protein aggregation suppressors

Allantoin is widely used in pharmaceutical and cosmetic products, and is composed of a hydantoin ring and a ureido group. Recent reports showed that allantoin suppresses thermal aggregation of hen egg white lysozyme (LYZ). However, structural insight into the properties of allantoin on protein aggregation and whether allantoin controls the aggregation of other proteins under different stress conditions remain unclear. Here we studied the structural properties of allantoin in terms of its effects on protein aggregation by comparing allantoin with urea and hydantoin. Furthermore, we analyzed the effects of allantoin and its derivatives on the aggregation of LYZ, carbonic anhydrase from bovine erythrocytes (BCA), albumin from chicken egg white (OVA), and immunoglobulin G (IgG) by various stresses in comparison with arginine. These four proteins are widely different in charged state and molecular size. Allantoin suppressed the aggregation and inactivation of LYZ comparing to arginine without affecting the melting temperature of proteins, and was responsible for the slightly improved formation of soluble oligomers and insoluble aggregates of IgG with thermal and acidic stresses. In contrast, hydantoin increased the solubility of aromatic amino acids more effectively than arginine and allantoin. The structural properties underlying the observed effects of allantoin as an aggregation suppressor include hydrophobic interactions between hydantoin moiety and aromatic ring on the surface of proteins, which is reflected on the difference between allantoin and arginine. These results show that the backbone of hydantoin ring may be a new category of additives for development of small aggregation suppressors.

Thermal aggregation of hen egg white proteins in the presence of salts

Hen egg white contains more than 40 kinds of proteins with concentrations reaching 100 mg/mL. Highly concentrated protein mixtures are common in the food industry, but the effects of a crowded environment containing salts on protein stability and aggregation have only been investigated using pure protein solutions. Here, we investigated the thermal aggregation of hen egg white protein (EWP) at various concentrations in the presence of inorganic salts by solubility measurements and SDS-PAGE. EWP at 1 mg/mL formed aggregates with increasing temperature above 55 °C; the aggregation temperatures increased in the presence of inorganic salt with the Hofmeister series. Namely, the chaotrope 0.5 M NaSCN completely suppressed the thermal aggregation of 1 mg/mL EWP. As the protein concentration increased, NaSCN unexpectedly enhanced the protein aggregation; the aggregation temperature of 10 and 100 mg/mL EWP solutions were dramatically decreased at 62 and 47 °C, respectively. This decrease in aggregation temperatures due to the chaotrope was described by the excluded volume effect, based on a comparative experiment using Ficoll 70 as a neutral crowder. By contrast, the kosmotrope Na2SO4 did not affect the aggregation temperature at concentrations from 1 to 100 mg/mL EWPs. The unexpected fact that a chaotrope rather enhanced the protein aggregation at high concentration provides new insight into the aggregation phenomena with the Hofmeister effect as well as the crude state of highly concentrated proteins.

The Combined Effect of High Hydrostatic Pressure and Calcium Salts on the Stability, Solubility and Gel Formation of β-Lactoglobulin

Stability, aggregation and gelation of β-Lactoglobulin are affected by high pressure and salts of the Hofmeister series. Little is known about their combined effects on structure formation processes of β-Lactoglobulin, mainly because many salts of the series are not suitable for use in food. Here, we investigate the effect of calcium salts on the strength of pressure-induced gels, inspired by the fact that high pressure and salts change the water structure in a similar way. We find that the larger the applied pressures, the higher the strength of the gels. In addition to pressure, there is a significant influence by the type of anions and the amount of added calcium salts. Gel strength increases in the order CaCl₂ < Ca (NO₃)₂ < CaI₂. This trend correlates with the position of the salts in the Hofmeister series. The results are explained by analogy with the thermal aggregate formation by taking reaction rates for unfolding and aggregation, as well as specific/non-specific salts effect into consideration.

Modulation of the stability of amyloidogenic precursors by anion binding strongly influences the rate of amyloid nucleation

A deep understanding of the physicochemical factors modulating amyloid aggregation of proteins is crucial to develop therapeutic and preventive approaches for amyloid-related diseases. The earliest molecular events of the aggregation cascade represent some of the main targets as indicated by the toxic nature of certain early oligomers. Here, we study how different types of salt ions influence the kinetics of amyloid assembly of the N47A mutant α-spectrin SH3 domain using a battery of techniques. The salts influenced aggregation rates to different extents without altering the overall mechanism and the high apparent order of the experimental kinetics. A quantitative analysis of the initial aggregation rates measured by thioflavine-T fluorescence using a simple nucleation model allowed us to estimate the kinetic and thermodynamic magnitudes of crucial aggregation precursors, as well as to evaluate the impact of each type of ion on the earliest amyloid nucleation stages. Whilst cations did not have any noticeable effect under our experimental conditions, anions stabilized an amyloidogenic intermediate state and also increased the rate of the conformational conversion from dynamic oligomers to amyloid nuclei, resulting in a strong acceleration of the nucleation process. Anions appear to act by preferential binding to the amyloidogenic intermediate state, thus enhancing its population and subsequent oligomerization. Overall, our results contribute to the rationalization of the effect of ions on the amyloid nucleation stage and give insight into the properties of the crucial intermediate precursors of amyloid aggregation.

Oligoethylene glycols prevent thermal aggregation of α-chymotrypsin in a temperature-dependent manner: implications for design guidelines

Protein aggregation is problematic in various fields, where aggregation can frequently occur during routine experiments. This study showed that tetraethylene glycol (TEG) and tetraethylene glycol dimethyl ether (TEGDE) act as aggregation suppressors that have different unique properties from typical additives to prevent protein aggregation, such as arginine (Arg) and NaCl. Thermal aggregation of α-chymotrypsin was well suppressed with the addition of both TEG and TEGDE. Interestingly, the suppressive effects of Arg and NaCl on thermal aggregation were almost unchanged when temperature was shifted from 65°C to 85°C, whereas both TEG and TEGDE significantly decreased the aggregation rate with increasing temperature. Note that the effects of TEG and TEGDE were higher than Arg above 75°C. This temperature-dependent behavior of TEG and TEGDE provides a novel design guideline to develop aggregation suppressors for use at high temperature, i.e., the importance of the ethylene oxide group.

Chemical assistance in refolding of bacterial inclusion bodies

Escherichia coli is one of the most widely used hosts for the production of recombinant proteins but insoluble expression of heterologous proteins is a major bottleneck in production of recombinant proteins in E. coli. In vitro refolding of inclusion body into proteins with native conformations is a solution for this problem but there is a need for optimization of condition for each protein specifically. Several approaches have been described for in vitro refolding; most of them involve the use of additives for assisting correct folding. Cosolutes play a major role in refolding process and can be classified according to their function as aggregation suppressors and folding enhancers. This paper presents a review of additives that are used in refolding process of insoluble recombinant proteins in small scale and industrial processes.

Ternary system of solution additives with arginine and salt for refolding of beta-galactosidase

(L)-Arginine hydrochloride (Arg HCl) has been used for protein refolding as a universal aggregation suppressor for monomeric proteins. This paper presents an investigation of the refolding of tetrameric beta-galactosidase (beta-gal) using Arg HCl and other salts. In a binary system using only Arg HCl, the refolding yield of beta-gal increased with increasing concentration up to 0.2 M. However, the refolding yield sharply decreased above this concentration, reaching the level below the control yield of 5% at 0.5 M and near zero above 0.75 M, an observation unexpected from monomeric proteins. In a ternary system using both 0.2 M Arg HCl and another salt, the refolding yield increased up to 1.5-fold higher than that in the binary system. These data indicate that aggregation suppressive effects of protein increase with Arg HCl concentration, but also are deleterious to self-association of the protein. This dual nature of Arg HCl effects may have to be taken into account in its application for refolding of oligomeric proteins.