Effect of Buffer on Protein Stability in Aqueous Solutions: A Simple Protein Aggregation Model

Unveiling the mechanism of activation of the Te(IV) prodrug AS101. New chemical insights towards a better understanding of its medicinal properties

AS101 (Ammonium trichloro (dioxoethylene-O,O') tellurate) is an important hypervalent Te-based prodrug. Recently, we started a systematic investigation on AS101 with the aim to correlate its promising biological effects as a potent immunomodulator drug with multiple medicinal applications and its specific chemical properties. To date, a substantial agreement on the rapid conversion of the initial AS101 species into the corresponding TeOCl3- anion does exist, and this latter species is reputed as the pharmacologically active one. However, we realized that TeOCl3- could quickly undergo further steps of conversion in an aqueous medium, eventually producing the TeO2 species. Using a mixed experimental and theoretical investigation approach, we characterized the conversion process leading to TeO2 occurring both in pure water and in reference buffers at physiological-like pH. Our findings may offer a valuable "chemical tool" for a better description, interpretation -and optimization- of the mechanism of action of AS101 and Te-based compounds. This might be a starting point for improved AS101-based medicinal application.

Understanding the Phase Behavior of a Multistimuli-Responsive Elastin-like Polymer: Insights from Dynamic Light Scattering Analysis

Elastin-like polymers are a class of stimuli-responsive protein polymers that hold immense promise in applications such as drug delivery, hydrogels, and biosensors. Yet, understanding the intricate interplay of factors influencing their stimuli-responsive behavior remains a challenging frontier. Using temperature-controlled dynamic light scattering and zeta potential measurements, we investigate the interactions between buffer, pH, salt, water, and protein using an elastin-like polymer containing ionizable lysine residues. We observed the elevation of transition temperature in the presence of the common buffering agent HEPES at low concentrations, suggesting a "salting-in" effect of HEPES as a cosolute through weak association with the protein. Our findings motivate a more comprehensive investigation of the influence of buffer and other cosolute molecules on elastin-like polymer behavior.

Characterization of a unique pH-dependent amylosucrase from Deinococcus cellulosilyticus

The amylosucrase (ASase, EC 2.4.1.4) utilizes sucrose as the sole substrate to catalyze multifunctional reactions. It can naturally synthesize α-1,4-linked glucans such as amylose as well as sucrose isomers with more favorable properties than sucrose with a lower intestinal digestibility and non-cariogenic properties. The amino acid sequence of the asase gene from Deinococcus cellulosilyticus (DceAS) exhibits low homology with those of other ASases from other Deinococcus species. In this study, we cloned and expressed DceAS and demonstrated its high activity at pH 6 and pH 8 and maintained stability. It showed higher polymerization activity at pH 6 than at pH 8, but similar isomerization activity and produced more turanose and trehalulose at pH 6 than at pH 8 and produced more isomaltulose at pH 8. Furthermore, the molecular weight of DceAS was 226.6 kDa at pH 6 and 145.5 kDa at pH 8, indicating that it existed as a trimer and dimer, respectively under those conditions. Additionally, circular dichroism spectra showed that the DceAS secondary structure was different at pH 6 and pH 8. These differences in reaction products at different pHs can be harnessed to naturally produce sucrose alternatives that are more beneficial to human health.

Investigating the influence of solvent type and pH on protein adsorption onto silica surface by evanescent-wave cavity ring-down spectroscopy

Several studies have explored the adsorption of various proteins onto solid-liquid interfaces, revealing the crucial role of buffer solutions in biological processes. However, a comprehensive evaluation of the buffer's influence on protein absorption onto fused silica is still lacking. This study employs evanescent-wave cavity ring-down spectroscopy (EW-CRDS) to assess the influence of buffer solutions and pH on the adsorption kinetics of three globular proteins: hemoglobin (Hb), myoglobin (Mb), and cytochrome c (Cyt-C) onto fused silica. The EW-CRDS tool, with a ring-down time of 1.4 μ s and a minimum detectable absorbance of 1 × 10 - 6 , enabled precise optical measurements at solid-liquid interfaces. The three heme proteins' adsorption behavior was investigated at pH 7 in three different solvents: deionized (DI) water, tris(hydroxymethyl)-aminomethane hydrochloride (Tris-HCl), and phosphate buffered saline (PBS). For each protein, the surface coverage, the adsorption and desorption constants, and the surface equilibrium constant were optically measured by our EW-CRDS tool. Depending on the nature of each solvent, the proteins showed a completely different adsorption trend on the silica surface. The adsorption of Mb on the silica surface was depressed in the presence of both Tris-HCl and PBS buffers compared with unbuffered (DI water) solutions. In contrast, Cyt-C adsorption appears to be relatively unaffected by the choice of buffer, as it involves strong electrostatic interactions with the surface. Notably, Hb exhibits an opposite trend, with enhanced protein adsorption in the presence of Tris-HCl and PBS buffer. The pH investigations demonstrated that the electrostatic interactions between the proteins and the surface had a major influence on protein adsorption on the silica surface, with adsorption being greatest when the pH values were around the protein's isoelectric point. This study demonstrated the ability of the highly sensitive EW-CRDS tool to study the adsorption events of the evanescent-field-confined protein species in real-time at low surface coverages with fast resolution, making it a valuable tool for studying biomolecule kinetics at solid-liquid interfaces.

Generation of Rapid and High-Quality Serum by Recombinant Prothrombin Activator Ecarin (RAPClot™)

We recently reported the potential application of recombinant prothrombin activator ecarin (RAPClot™) in blood diagnostics. In a new study, we describe RAPClot™ as an additive to develop a novel blood collection prototype tube that produces the highest quality serum for accurate biochemical analyte determination. The drying process of the RAPClot™ tube generated minimal effect on the enzymatic activity of the prothrombin activator. According to the bioassays of thrombin activity and plasma clotting, γ-radiation (>25 kGy) resulted in a 30-40% loss of the enzymatic activity of the RAPClot™ tubes. However, a visual blood clotting assay revealed that the γ-radiation-sterilized RAPClot™ tubes showed a high capacity for clotting high-dose heparinized blood (8 U/mL) within 5 min. This was confirmed using Thrombelastography (TEG), indicating full clotting efficiency under anticoagulant conditions. The storage of the RAPClot™ tubes at room temperature (RT) for greater than 12 months resulted in the retention of efficient and effective clotting activity for heparinized blood in 342 s. Furthermore, the enzymatic activity of the RAPClot™ tubes sterilized with an electron-beam (EB) was significantly greater than that with γ-radiation. The EB-sterilized RAPClot™ tubes stored at RT for 251 days retained over 70% enzyme activity and clotted the heparinized blood in 340 s after 682 days. Preliminary clinical studies revealed in the two trials that 5 common analytes (K, Glu, lactate dehydrogenase (LD), Fe, and Phos) or 33 analytes determined in the second study in the γ-sterilized RAPClot™ tubes were similar to those in commercial tubes. In conclusion, the findings indicate that the novel RAPClot™ blood collection prototype tube has a significant advantage over current serum or lithium heparin plasma tubes for routine use in measuring biochemical analytes, confirming a promising application of RAPClot™ in clinical medicine.

Structural effects of charge destabilization and amino acid substitutions in amyloid fragments of CsgA

The most studied functional amyloid is the CsgA, major curli subunit protein, which is produced by numerous strains of Enterobacteriaceae. Although CsgA sequences are highly conserved, they exhibit species diversity, which reflects the specific evolutionary and functional adaptability of the major curli subunit. Herein, we performed bioinformatics analyses to uncover the differences in the amyloidogenic properties of the R4 fragments in Escherichia coli and Salmonella enterica and proposed four mutants for more detailed studies: M1, M2, M3, and M4. The mutated sequences were characterized by various experimental techniques, such as circular dichroism, ATR-FTIR, FT-Raman, thioflavin T, transmission electron microscopy and confocal microscopy. Additionally, molecular dynamics simulations were performed to determine the role of buffer ions in the aggregation process. Our results demonstrated that the aggregation kinetics, fibril morphology, and overall structure of the peptide were significantly affected by the positions of charged amino acids within the repeat sequences of CsgA. Notably, substituting glycine with lysine resulted in the formation of distinctive spherically packed globular aggregates. The differences in morphology observed are attributed to the influence of phosphate ions, which disrupt the local electrostatic interaction network of the polypeptide chains. This study provides knowledge on the preferential formation of amyloid fibrils based on charge states within the polypeptide chain.

Protein Thermodynamic Properties, Crystallisation, and the Hofmeister Series

The Hofmeister series is a series of ions ordered according to their ability to precipitate proteins. It has also been linked to a host of (bio)chemical phenomena. Several attempts over the years to correlate the series to the varying success of different salts in crystallising proteins have been largely inconclusive. A correlation, based on published data and crystallisation conditions for several proteins, is proposed here between some thermodynamic properties of proteins and the position in the Hofmeister series of the salts from which they preferentially crystallise. Namely, a high ratio between the entropic or enthalpic protein-solvent interactions contribution to thermodynamic stability and the total thermodynamic stability of a given protein, indicate the protein's high propensity to crystallise in solutions of highly kosmotropic salts. Low such ratios on the other hand, indicate that chaotropic salts can be equally successful, i. e. that the protein in question is rather indifferent to the Hofmeister character of the salt. Testing various model proteins for crystallisation against screens containing salts found at different points on the Hofmeister series, as well as further bibliographic analysis, have yielded results that appear to largely corroborate this hypothesis. These conclusions may conceivably be used as a crystallisation predictive tool.

Buffer choice and pH strongly influence phase separation of SARS-CoV-2 nucleocapsid with RNA

The SARS-CoV-2 nucleocapsid (N) protein is crucial for virus replication and genome packaging. N protein forms biomolecular condensates both in vitro and in vivo in a process known as liquid-liquid phase separation (LLPS), but the exact factors regulating LLPS of N protein are not fully understood. Here, we show that pH and buffer choice have a profound impact on LLPS of N protein. The degree of phase separation is highly dependent on the pH of the solution, which is correlated with histidine protonation in N protein. Specifically, we demonstrate that protonation of H356 is essential for LLPS in phosphate buffer. Moreover, electrostatic interactions of buffer molecules with specific amino acid residues are able to alter the net charge of N protein, thus influencing its ability to undergo phase separation in the presence of RNA. Overall, these findings reveal that even subtle changes in amino acid protonation or surface charge caused by the pH and buffer system can strongly influence the LLPS behavior, and point to electrostatic interactions as the main driving forces of N protein phase separation. Further, our findings emphasize the importance of these experimental parameters when studying phase separation of biomolecules, especially in the context of viral infections where the intracellular milieu undergoes drastic changes and intracellular pH normally decreases.

Design of a Reciprocal Injection Device for Stability Studies of Parenteral Biological Drug Products

Formulation screening, essential for assessing the impact of physical, chemical, and mechanical stresses on protein stability, plays a critical role in biologics drug product development. This research introduces a Reciprocal Injection Device (RID) designed to accelerate formulation screening by probing protein stability under intensified stress conditions within prefilled syringes. This versatile device is designed to accommodate a broad spectrum of injection parameters and diverse syringe dimensions. A commercial drug product was employed as a model monoclonal antibody formulation. Our findings effectively highlight the efficacy of the RID in assessing concentration-dependent protein stability. This device exhibits significant potential to amplify the influences of interfacial interactions, such as those with buffer salts, excipients, air, metals, and silicone oils, commonly found in combination drug products, and to evaluate the protein stability under varied stresses.

Pharmaceutical proteins at the interfaces and the role of albumin

A critical measure of the quality of pharmaceutical proteins is the preservation of native conformations of the active pharmaceutical ingredients. Denaturation of the active proteins in any step before administration into patients could lead to loss of potency and/or aggregation, which is associated with an increased risk of immunogenicity of the products. Interfacial stress enhances protein instability as their adsorption to the air-liquid and liquid-solid interfaces are implicated in the formation of denatured proteins and aggregates. While excipients in protein formulations have been employed to reduce the risk of aggregation, the roles of albumin as a stabilizer have not been reviewed from practical and theoretical standpoints. The amphiphilic nature of albumin makes it accumulate at the interfaces. In this review, we aim to bridge the knowledge gap between interfacial instability and the influence of albumin as a surface-active excipient in the context of reducing the immunogenicity risk of protein formulations.

Do Ionic Liquids Exhibit the Required Characteristics to Dissolve, Extract, Stabilize, and Purify Proteins? Past-Present-Future Assessment

Proteins are highly labile molecules, thus requiring the presence of appropriate solvents and excipients in their liquid milieu to keep their stability and biological activity. In this field, ionic liquids (ILs) have gained momentum in the past years, with a relevant number of works reporting their successful use to dissolve, stabilize, extract, and purify proteins. Different approaches in protein-IL systems have been reported, namely, proteins dissolved in (i) neat ILs, (ii) ILs as co-solvents, (iii) ILs as adjuvants, (iv) ILs as surfactants, (v) ILs as phase-forming components of aqueous biphasic systems, and (vi) IL-polymer-protein/peptide conjugates. Herein, we critically analyze the works published to date and provide a comprehensive understanding of the IL-protein interactions affecting the stability, conformational alteration, unfolding, misfolding, and refolding of proteins while providing directions for future studies in view of imminent applications. Overall, it has been found that the stability or purification of proteins by ILs is bispecific and depends on the structure of both the IL and the protein. The most promising IL-protein systems are identified, which is valuable when foreseeing market applications of ILs, e.g., in "protein packaging" and "detergent applications". Future directions and other possibilities of IL-protein systems in light-harvesting and biotechnology/biomedical applications are discussed.

Cooperative Membrane Binding of HIV-1 Matrix Proteins

The HIV-1 assembly process begins with a newly synthesized Gag polyprotein being targeted to the inner leaflet of the plasma membrane of the infected cells to form immature viral particles. Gag-membrane interactions are mediated through the myristoylated (Myr) N-terminal matrix (MA) domain of Gag, which eventually multimerize on the membrane to form trimers and higher order oligomers. The study of the structure and dynamics of peripheral membrane proteins like MA has been challenging for both experimental and computational studies due to the complex transient dynamics of protein-membrane interactions. Although the roles of anionic phospholipids (PIP2, PS) and the Myr group in the membrane targeting and stable membrane binding of MA are now well-established, the cooperative interactions between the MA monomers and MA-membrane remain elusive in the context of viral assembly and release. Our present study focuses on the membrane binding dynamics of a higher order oligomeric structure of MA protein (a dimer of trimers), which has not been explored before. Employing time-lagged independent component analysis (tICA) to our microsecond-long trajectories, we investigate conformational changes of the matrix protein induced by membrane binding. Interestingly, the Myr switch of an MA monomer correlates with the conformational switch of adjacent monomers in the same trimer. Together, our findings suggest complex protein dynamics during the formation of the immature HIV-1 lattice; while MA trimerization facilitates Myr insertion, MA trimer-trimer interactions in the immature lattice can hinder the same.

Using Passive Microrheology to Measure the Evolution of the Rheological Properties of NIST mAb Formulations during Adsorption to the Air-Water Interface

The development of novel protein-based therapeutics, such as monoclonal antibodies (mAbs), is often limited due to challenges associated with maintaining the stability of these formulations during manufacturing, storage, and clinical administration. An undesirable consequence of the instability of protein therapeutics is the formation of protein particles. MAbs can adsorb to interfaces and have the potential to undergo partial unfolding as well as to form viscoelastic gels. Further, the viscoelastic properties may be correlated with their aggregation potential. In this work, a passive microrheology technique was used to correlate the evolution of surface adsorption with the evolution of surface rheology of the National Institute of Standards and Technology (NIST) mAb reference material (NIST mAb) and interface-induced subvisible protein particle formation. The evolution of the surface adsorption and interfacial shear rheological properties of the NIST mAb was recorded in four formulation conditions: two different buffers (histidine vs phosphate-buffered saline) and two different pHs (6.0 and 7.6). Our results together demonstrate the existence of multiple stages for both surface adsorption and surface rheology, characterized by an induction period that appears to be purely viscous, followed by a sharp increase in protein molecules at the interface when the film rheology is viscoelastic and ultimately a slowdown in the surface adsorption that corresponds to the formation of solid-like or glassy films at the interface. When the transitions between the different stages occurred, they were dependent on the buffer/pH of the formulations. The onset of these transitions can also be correlated to the number of protein particles formed at the interface. Finally, the addition of polysorbate 80, an FDA-approved surfactant used to mitigate protein particle formation, led to the interface being surfactant-dominated, and the resulting interface remained purely viscous.

Unraveling the Microscopic Mechanism of Molecular Ion Interaction with Monoclonal Antibodies: Impact on Protein Aggregation

Understanding and predicting protein aggregation represents one of the major challenges in accelerating the pharmaceutical development of protein therapeutics. In addition to maintaining the solution pH, buffers influence both monoclonal antibody (mAb) aggregation in solution and the aggregation mechanisms since the latter depend on the protein charge. Molecular-level insight is necessary to understand the relationship between the buffer-mAb interaction and mAb aggregation. Here, we use all-atom molecular dynamics simulations to investigate the interaction of phosphate (Phos) and citrate (Cit) buffer ions with the Fab and Fc domains of mAb COE3. We demonstrate that Phos and Cit ions feature binding mechanisms, with the protein that are very different from those reported previously for histidine (His). These differences are reflected in distinctive ion-protein binding modes and adsorption/desorption kinetics of the buffer molecules from the mAb surface and result in dissimilar effects of these buffer species on mAb aggregation. While His shows significant affinity toward hydrophobic amino acids on the protein surface, Phos and Cit ions preferentially bind to charged amino acids. We also show that Phos and Cit anions provide bridging contacts between basic amino acids in neighboring proteins. The implications of such contacts and their connection to mAb aggregation in therapeutic formulations are discussed.

Correlating Surface Activity with Interface-Induced Aggregation in a High-Concentration mAb Solution

Interface-induced aggregation resulting in protein particle formation is an issue during the manufacturing and storage of protein-based therapeutics. High-concentration formulations of therapeutic proteins are even more prone to protein particle formation due to increased protein-protein interactions. However, the dependence of interface-induced protein particle formation on bulk protein concentration is not understood. Furthermore, the formation of protein particles is often mitigated by the addition of polysorbate-based surfactants. However, the details of surfactant-protein interactions that prevent protein particle formation at high concentrations remain unclear. In this work, a tensiometer technique was used to evaluate the surface pressure of an industrially relevant mAb at different bulk concentrations, and in the absence and presence of a polysorbate-based surfactant, polysorbate 20 (PS20). The adsorption kinetics was correlated with subvisible protein particle formation at the air-water interface and in the bulk protein solution using a microflow imaging technique. Our results showed that, in the absence of any surfactant, the number of subvisible particles in the bulk protein solutions increased linearly with mAb concentration, while the number of protein particles measured at the interface showed a logarithmic dependence on bulk protein concentration. In the presence of surfactants above the critical micelle concentration (CMC), our results for low-concentration mAb solutions (10 mg/mL) showed an interface that is surfactant-dominated, and particle characterization results showed that the addition of the surfactant led to reduced particle formation. In contrast, for the highest concentration (170 mg/mL), coadsorption of proteins and surfactants was observed at the air-water interface, even for surfactant formulations above CMC and the surfactant did not mitigate subvisible particle formation. Our results taken together provide evidence that the ratio between the surfactant and mAb molecules is an important consideration when formulating high-concentration mAb therapeutics to prevent unwanted aggregation.

Programming interchangeable and reversible heterooligomeric protein self-assembly using a bifunctional ligand

Protein design for self-assembly allows us to explore the emergence of protein-protein interfaces through various chemical interactions. Heterooligomers, unlike homooligomers, inherently offer a comprehensive range of structural and functional variations. Besides, the macromolecular repertoire and their applications would significantly expand if protein components could be easily interchangeable. This study demonstrates that a rationally designed bifunctional linker containing an enzyme inhibitor and maleimide can guide the formation of diverse protein heterooligomers in an easily applicable and exchangeable manner without extensive sequence optimizations. As proof of concept, we selected four structurally and functionally unrelated proteins, carbonic anhydrase, aldolase, acetyltransferase, and encapsulin, as building block proteins. The combinations of two proteins with the bifunctional linker yielded four two-component heterooligomers with discrete sizes, shapes, and enzyme activities. Besides, the overall size and formation kinetics of the heterooligomers alter upon adding metal chelators, acidic buffer components, and reducing agents, showing the reversibility and tunability in the protein self-assembly. Given that the functional groups of both the linker and protein components are readily interchangeable, our work broadens the scope of protein-assembled architectures and their potential applications as functional biomaterials.

Factors affecting therapeutic protein purity and yield during chromatographic purification

Therapeutic proteins are recombinant proteins generated through recombinant DNA technology and have attracted a great deal of interest in numerous applications, including pharmaceutical, cosmetic, human and animal health, agriculture, food, and bioremediation. Producing therapeutic proteins on a large scale, mainly in the pharmaceutical industry, necessitates a cost-effective, straightforward, and adequate manufacturing process. In industry, a protein separation technique based mainly on protein characteristics and modes of chromatography will be applied to optimize the purification process. Typically, the downstream process of biopharmaceutical operations may involve multiple chromatography phases that require the use of large columns pre-packed with resins that must be inspected before use. Approximately 20% of the proteins are assumed to be lost at each purification stage during the production of biotherapeutic products. Hence, to produce a high quality product, particularly in the pharmaceutical industry, the correct approach and understanding of the factors influencing purity and yield during purification are necessary.

Investigating the Impact of Network Functionalization on Protein Adsorption to Polymer Nanogels

This study explores the impact of network functionalization and chemical composition on the pH-responsive behavior of polymer nanogels and their adsorption of proteins. Using a thermodynamic theory informed by a molecular model, this work evaluates the interactions of three proteins with varying isoelectric points (insulin, myoglobin, and cytochrome c) and pH-responsive nanogels based on methacrylic acid or allylamine motifs. Three different functionalization strategies are considered, with pH-responsive segments distributed randomly, at the center, or on the surface of the polymer network. Our results show that the spatial distribution of functional units affects both the nanogels' mechanical response to pH changes and the level and localization of adsorbed proteins. The dependence of protein adsorption on the salt concentration is also investigated, with the conclusion that it is best to encapsulate proteins at low salt concentrations and aim for release at high salt concentrations. These results provide valuable information for the design of pH-responsive nanogels as vehicles for protein encapsulation, transport, and administration.

Antibody association in solution: cluster distributions and mechanisms

Understanding factors that affect the clustering and association of antibodies molecules in solution is critical to their development as therapeutics. For 19 different monoclonal antibody (mAb) solutions, we measured the viscosities, the second virial coefficients, the Kirkwood-Buff integrals, and the cluster distributions of the antibody molecules as functions of protein concentration. Solutions were modeled using the statistical-physics Wertheim liquid-solution theory, representing antibodies as Y-shaped molecular structures of seven beads each. We found that high-viscosity solutions result from more antibody molecules per cluster. Multi-body properties such as viscosity are well predicted experimentally by the 2-body Kirkwood-Buff quantity, G22, but not by the second virial coefficient, B22, and well-predicted theoretically from the Wertheim protein-protein sticking energy. Weakly interacting antibodies are rate-limited by nucleation; strongly interacting ones by propagation. This approach gives a way to relate micro to macro properties of solutions of associating proteins.

Experimental procedures to investigate fibrillation of proteins

The unwanted phenomenon of protein fibrillation is observed in vivo and during therapeutic protein development in the industry. Protein aggregation is associated with various degenerative disorders and might induce immune-related challenges post-administration of biopharmaceutics. A pipeline for early detection, identification, and removal of pre-formed fibrils is needed to improve the quality, efficacy, and effectiveness of the formulation. Protein fibril formation is accompanied by unfolding, secondary structural changes and the formation of larger aggregates. However, most detection processes come with extensive sample preparation steps and inefficient repeatability, incurring a financial burden on research. The current article summarizes and critically discusses six simple yet powerful methods to detect aggregation phenomena in the line of detecting fibrillar aggregates in heat-induced bovine serum albumin protein. Comparing the native and heat-induced protein samples would provide insights about aggregates. Easy, inexpensive and optimized protocols for detecting the fibrillation of proteins are explained. The procedures mentioned here detected the appearance of β-sheet-rich fibrils in the heat-induced protein sample. The aggregation is characterized by enhanced thioflavin-T fluorescence, alteration in the intrinsic fluorescence, decrease in helicity and subsequent increase in β-sheet and appearance of particles with larger hydrodynamic diameters. •This article summarizes various analytical techniques to easily characterize the fibrillation of proteins.•Various techniques to detect the formation of β-sheet rich structures, changes in the secondary structures and size of aggregates have been discussed.•The stated methodologies are validated on a model protein, albumin.

Protein Association in Solution: Statistical Mechanical Modeling

Protein molecules associate in solution, often in clusters beyond pairwise, leading to liquid phase separations and high viscosities. It is often impractical to study these multi-protein systems by atomistic computer simulations, particularly in multi-component solvents. Instead, their forces and states can be studied by liquid state statistical mechanics. However, past such approaches, such as the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory, were limited to modeling proteins as spheres, and contained no microscopic structure-property relations. Recently, this limitation has been partly overcome by bringing the powerful Wertheim theory of associating molecules to bear on protein association equilibria. Here, we review these developments.

Sulfated Polysaccharides as a Fighter with Protein Non-Physiological Aggregation: The Role of Polysaccharide Flexibility and Charge Density

Proteins can lose native functionality due to non-physiological aggregation. In this work, we have shown the power of sulfated polysaccharides as a natural assistant to restore damaged protein structures. Protein aggregates enriched by cross-β structures are a characteristic of amyloid fibrils related to different health disorders. Our recent studies demonstrated that model fibrils of hen egg white lysozyme (HEWL) can be disaggregated and renatured by some negatively charged polysaccharides. In the current work, using the same model protein system and FTIR spectroscopy, we studied the role of conformation and charge distribution along the polysaccharide chain in the protein secondary structure conversion. The effects of three carrageenans (κ, ι, and λ) possessing from one to three sulfate groups per disaccharide unit were shown to be different. κ-Carrageenan was able to fully eliminate cross-β structures and complete the renaturation process. ι-Carrageenan only initiated the formation of native-like β-structures in HEWL, retaining most of the cross-β structures. In contrast, λ-carrageenan even increased the content of amyloid cross-β structures. Furthermore, κ-carrageenan in rigid helical conformation loses its capability to restore protein native structures, largely increasing the amount of amyloid cross-β structures. Our findings create a platform for the design of novel natural chaperons to counteract protein unfolding.

Cooperative Membrane Binding of HIV-1 Matrix Proteins

The HIV-1 assembly process begins with a newly synthesized Gag polyprotein being targeted to the inner leaflet of the plasma membrane of the infected cells to form immature viral particles. Gag-membrane interactions are mediated through the myristoylated(Myr) N-terminal matrix (MA) domain of Gag which eventually multimerize on the membrane to form trimers and higher-order oligomers. The study of the structure and dynamics of peripheral membrane proteins like MA has been challenging for both experimental and computational studies due to the complex dynamics of protein-membrane interactions. Although the roles of anionic phospholipids (PIP2, PS) and the Myr group in the membrane targeting and stable membrane binding of MA are now well-established, the cooperative interactions between MA monomers and MA-membrane still remain elusive. Our present study focuses on the membrane binding dynamics of a higher-order oligomeric structure of MA protein (a dimer of trimers), which has not been explored before. Employing time-lagged independent component analysis (tICA) to our microsecond-long trajectories, we investigate conformational changes of the matrix protein induced by membrane binding. Interestingly, the Myr switch of a MA monomer correlates with the conformational switch of adjacent monomers in the same trimer. Together, our findings suggest that MA trimerization facilitates Myr insertion, but MA trimer-trimer interactions in the lattice of immature HIV-1 particles can hinder the same. Additionally, local lipid density patterns of different lipid species provide a signature of the initial stage of lipid-domain formation upon membrane binding of the protein complex.

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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.

Evidence of Atypical Structural Flexibility of the Active Site Surrounding of an [FeFe] Hydrogenase from Clostridium beijerinkii

[FeFe] hydrogenase from Clostridium beijerinkii (CbHydA1) is an unusual hydrogenase in that it can withstand prolonged exposure to O₂ by reversibly converting into an O₂-protected, inactive state (H_inact). It has been indicated in the past that an atypical conformation of the "SC₃₆₇CP" loop near the [2Fe]_H portion of the six-iron active site (H-cluster) allows the Cys367 residue to adopt an "off-H⁺-pathway" orientation, promoting a facile transition of the cofactor to H_inact. Here, we investigated the electronic structure of the H-cluster in the oxidized state (H_ox) that directly converts to H_inact under oxidizing conditions and the related CO-inhibited state (H_ox-CO). We demonstrate that both states exhibit two distinct forms in electron paramagnetic resonance (EPR) spectroscopy. The ratio between the two forms is pH-dependent but also sensitive to the buffer choice. Our IR and EPR analyses illustrate that the spectral heterogeneity is due to a perturbation of the coordination environment of the H-cluster's [4Fe4S]_H subcluster without affecting the [2Fe]_H subcluster. Overall, we conclude that the observation of two spectral components per state is evidence of heterogeneity of the environment of the H-cluster likely associated with conformational mobility of the SCCP loop. Such flexibility may allow Cys367 to switch rapidly between off- and on-H⁺-pathway rotamers. Consequently, we believe such structural mobility may be the key to maintaining high enzymatic activity while allowing a facile transition to the O₂-protected state.

Stability of ACE2 Peptide Mimetics and Their Implications on the Application for SARS-CoV2 Detection

The SARS-CoV-2 worldwide outbreak prompted the development of several tools to detect and treat the disease. Among the new detection proposals, the use of peptides mimetics has surged as an alternative to avoid the use of antibodies, of which there has been a shortage during the COVID-19 pandemic. However, the use of peptides in detection systems still presents some questions to be answered, mainly referring to their stability under different environmental conditions. In this work, we synthesized an ACE2 peptide mimic and evaluated its stability in different pH, salinity, polarity, and temperature conditions. Further, the same conditions were assessed when using the ability of the peptide mimic to detect the recombinant SARS-CoV-2 spike protein in a biotin-streptavidin-enzyme-linked assay. Finally, we also tested the capacity of the peptide to detect SARS-CoV-2 from patients' samples. The results indicate that the peptide is structurally sensitive to the medium conditions, with relevance to the pH, where basic pH favored its performance when used as a SARS-CoV-2 detector. Further, the proposed peptide mimic was able to detect SARS-CoV-2 comparably to RT-qPCR results. Therefore, the present study promotes knowledge advancement, particularly in terms of stability considerations, in the application of peptide mimics as a replacement for antibodies in detection systems.

Cation and buffer specific effects on the DNA-lipid interaction

Knowledge of DNA - lipid layer interactions is key for the development of biosensors, synthetic nanopores, scaffolds, and gene-delivery systems. These interactions are strongly affected by the ionic composition of the solvent. We have combined quartz crystal microbalance (QCM) and ellipsometry measurements to reveal how pH, buffers and alkali metal chloride salts affect the interaction of DNA with lipid bilayers (DOTAP/DOPC 30:70 in moles). We found that the thickness of the DNA layer adsorbed onto the lipid bilayer decreased in the order citrate > phosphate > Tris > HEPES. The effect of cations on the thickness of the DNA layer decreased in the order (K⁺ > Na⁺ > Cs⁺ ∼ Li⁺). Rationalization of the experimental results requires that adsorption, due to cation specific charge screening, is driven by the simultaneous action of two mechanisms namely, the law of matching water affinities for kosmotropes (Li⁺) and ion dispersion forces for chaotropes (Cs⁺). The outcome of these two opposing mechanisms is a ^"bell-shaped" specific cations sequence. Moreover, a superimposed buffer specificity, which goes beyond the simple effect of pH regulation, further modulated cation specificity. In summary, DNA-lipid bilayer interactions are maximized if citrate buffer (50 mM, pH 7.4) and KCl (100 mM) are used.

Engineering of an ene-reductase for producing the key intermediate of antiepileptic drug Brivaracetam

(R)-4-Propyldihydrofuran-2(3H)-one (R-PDFO) is the key chiral intermediate for the antiepileptic drug Brivaracetam. Lacking a simple and economical method to approaching R-PDFO, the production of R-PDFO also remains environmentally unfriendly. Here, we developed a straightforward bioreduction way from easily synthesized 4-propylfuran-2(5H)-one (PFO) using ene-reductases. After screened with 27 ene-reductases, E116 stood out with 25.7% yield and 97% ee (R) as the starting enzyme. To improve the catalytic efficiency of E116, several rounds of directed evolution were first carried out. Through rational design, alanine scanning and random mutagenesis, engineered ene-reductase E116-M3 was obtained, with a 2.63-fold improvement in yields over WT, a 12.6-fold improvement in k_cat/K_m over WT, and stereoselectivity increased to 99% (R). To further improve the yield of R-PDFO, the reaction conditions were then optimized. The catalytic activity of the optimized reaction system was increased again by 2.3 times and the turnover number (TON) of E116-M3 reached 705. Subsequently, whole cells harboring E116-M3 were also shown to have similar capabilities of synthesizing R-PDFO. Finally, E116-M3 was employed in the 50-mL-scale synthesis of R-PDFO under 20 mM of PFO loading to achieve 81% isolated yield and 99% ee. In conclusion, this new approach of engineered ene-reductase catalyzing the asymmetric reduction of PFO could be a green alternative for the efficient synthesis of R-PDFO. KEY POINTS: • An ene-reductase library was first used to screen the bioreduction of PFO. • Rational design contributed to the enhanced R-stereoselectivity of PFO reduction. • E116-M3 was obtained with high activity and stereoselectivity for R-PDFO.

Protein association on multimodal chromatography media

The phenomenon of protein-protein association on multimodal chromatography resins was described for two different case study examples. The adsorption pattern of single-component solutions of calcium-rich alpha-lactalbumin (aLaCa) and calcium-depleted alpha-lactalbumin (aLa) and their mixtures with bovine serum albumin was determined on a multimodal anion-exchange chromatography medium. In single-component solutions, both aLaCa and aLa exhibited identical adsorption behavior at low resin loadings, whereas at high loadings the adsorption strength of aLa markedly exceeded that of alaCa. In binary mixtures, the adsorption of BSA enhanced at high concentrations of aLa or aLaCa in the adsorbed phase. The unusual adsorption patterns observed were attributed to the tendency of the proteins for molecular association in the adsorbed phase in single and binary solutions. The phenomena was examined for different pH of the solution: pH 6, 7, 8, and different solvent environments: phosphate buffer (PB), bis tris buffer (BT), 100 mM NaCl in BT and bis tris propane buffer (BTP). The strongest effect was observed for PB and for 100 mM NaCl in BT. Its occurrence was also evidenced for other case study example, i.e., adsorption of single-component solutions and binary mixtures of a monoclonal antibody (mAb) and lysozyme (LYZ) on a multimodal cation-exchange chromatography medium. The enhancement of adsorption of mAb was observed at high concentrations of LYZ in the adsorbed phase. To quantify the underlying effects, a mechanistic model was used, which accounted for both protein association and exclusion resulting from attractive and repulsive protein-protein iterations in the adsorbed phase.

The Effect of Arginine on the Phase Stability of Aqueous Hen Egg-White Lysozyme Solutions

The effect of arginine on the phase stability of the hen egg-white lysozyme (HEWL) has been studied via molecular dynamics computer simulations, as well as experimentally via cloud-point temperature determination. The experiments show that the addition of arginine increases the stability of the HEWL solutions. The computer simulation results indicate that arginine molecules tend to self-associate. If arginine residues are located on the protein surface, the free arginine molecules stay in their vicinity and prevent the way protein molecules "connect" through them to form clusters. The results are not sensitive to a particular force field and suggest a possible microscopic mechanism of the stabilizing role of arginine as an excipient.

BioMThermDB 1.0: Thermophysical Database of Proteins in Solutions

We present here a freely available web-based database, called BioMThermDB 1.0, of thermophysical and dynamic properties of various proteins and their aqueous solutions. It contains the hydrodynamic radius, electrophoretic mobility, zeta potential, self-diffusion coefficient, solution viscosity, and cloud-point temperature, as well as the conditions for those determinations and details of the experimental method. It can facilitate the meta-analysis and visualization of data, can enable comparisons, and may be useful for comparing theoretical model predictions with experiments.

A new fibrillization mechanism of β-lactoglobulin in glycine solutions

Even though amyloid aggregates were discovered many years ago the mechanism of their formation is still a mystery. Because of their connection to many of untreatable neurodegenerative diseases the motivation for finding a common aggregation path is high. We report a new high heat induced fibrillization path of a model protein β-lactoglobulin (BLG) when incubated in glycine instead of water at pH 2. By combining atomic force microscopy (AFM), transmission emission microscopy (TEM), dynamic light scattering (DLS) and circular dichroism (CD) we predict that the basic building blocks of fibrils made in glycine are not peptides, but rather spheroid oligomers of different height that form by stacking of ring-like structures. Spheroid oligomers linearly align to form fibrils by opening up and combining. We suspect that glycine acts as an hydrolysation inhibitor which consequently promotes a different fibrillization path. By combining the known data on fibrillization in water with our experimental conclusions we come up with a new fibrillization scheme for BLG. We show that by changing the fibrillization conditions just by small changes in buffer composition can dramatically change the aggregation pathway and the effect of buffer shouldn't be neglected. Fibrils seen in our study are also gaining more and more attention because of their pore-like structure and a possible cytotoxic mechanism by forming pernicious ion-channels. By preparing them in a simple model system as BLG we opened a new way to study their formation.

Unlocking the Treasure Box: The Role of HEPES Buffer in Disassembling an Uncommon Ferritin Nanoparticle

Ferritins are ideal nanoparticles as drug delivery systems due to their hollow-sphere structure and the ability to target specific receptors on the cell surface. Here, we develop and characterize a new ferritin derived from the chimeric humanized A. fulgidus one, already designed to recognize the TfR1 receptor. Starting from the synthetic gene of this chimeric protein, we replaced two positively charged amino acids with two alanine residues to close the large triangular pores on its surface. These mutations make the protein nanoparticle suitable to incorporate even small therapeutics without leakage. Size-exclusion chromatography shows that the assembling/disassembling of this new protein cage can be easily fine-tuned by varying the HEPES buffer and MgCl2 concentration. The protein cage can be opened using 150 mM HEPES buffer without magnesium ions. Adding this divalent cation to the solution promotes the quick assembly of the ferritin as a 24-mer. The development of this new protein cage paves the way for encapsulation and delivery studies of small molecules for therapeutic and diagnostic purposes.

Understanding specific ion effects and the Hofmeister series

Specific ion effects (SIE), encompassing the Hofmeister Series, have been known for more than 130 years since Hofmeister and Lewith's foundational work. SIEs are ubiquitous and are observed across the medical, biological, chemical and industrial sciences. Nevertheless, no general predictive theory has yet been able to explain ion specificity across these fields; it remains impossible to predict when, how, and to what magnitude, a SIE will be observed. In part, this is due to the complexity of real systems in which ions, counterions, solvents and cosolutes all play varying roles, which give rise to anomalies and reversals in anticipated SIEs. Herein we review the historical explanations for SIE in water and the key ion properties that have been attributed to them. Systems where the Hofmeister series is perturbed or reversed are explored, as is the behaviour of ions at the liquid-vapour interface. We discuss SIEs in mixed electrolytes, nonaqueous solvents, and in highly concentrated electrolyte solutions - exciting frontiers in this field with particular relevance to biological and electrochemical applications. We conclude the perspective by summarising the challenges and opportunities facing this SIE research that highlight potential pathways towards a general predictive theory of SIE.

Computational models for studying physical instabilities in high concentration biotherapeutic formulations

Computational prediction of the behavior of concentrated protein solutions is particularly advantageous in early development stages of biotherapeutics when material availability is limited and a large set of formulation conditions needs to be explored. This review provides an overview of the different computational paradigms that have been successfully used in modeling undesirable physical behaviors of protein solutions with a particular emphasis on high-concentration drug formulations. This includes models ranging from all-atom simulations, coarse-grained representations to macro-scale mathematical descriptions used to study physical instability phenomena of protein solutions such as aggregation, elevated viscosity, and phase separation. These models are compared and summarized in the context of the physical processes and their underlying assumptions and limitations. A detailed analysis is also given for identifying protein interaction processes that are explicitly or implicitly considered in the different modeling approaches and particularly their relations to various formulation parameters. Lastly, many of the shortcomings of existing computational models are discussed, providing perspectives and possible directions toward an efficient computational framework for designing effective protein formulations.

Interaction of Aqueous Bovine Serum Albumin with Silica Aerogel Microparticles: Sorption Induced Aggregation

Mesoporous silica aerogels have a wide range of potential applications in biotechnology, the food industry, pharmacy and medicine. Understanding the nature of the interactions of biomolecules with these porous nanostructured materials is essential for achieving optimum performance in the targeted applications. In this study, the well-characterized bovine serum albumin (BSA) was chosen as a model protein to probe protein–aerogel interactions in the solution phase. Aqueous BSA was mixed with suspended silica aerogel microparticles, and the colloid system was monitored on-line by UV–vis spectrophotometry and turbidimetry. The global mathematical analysis of the time-resolved data reveals that the fast sorption of the protein on the aerogel microparticles follows a multistep binding mechanism. The extensive sorption of the protein eventually induces the aggregation of the covered aerogel due to the alteration of the electrical double layer of the particles. The interaction of BSA and silica aerogel is the strongest between pH = 4 and 5, because their native surface charges are the opposite in this pH range, as indicated by their respective zeta potentials.

Computational methods to predict protein aggregation

In most cases, protein aggregation stems from the establishment of non-native intermolecular contacts. The formation of insoluble protein aggregates is associated with many human diseases and is a major bottleneck for the industrial production of protein-based therapeutics. Strikingly, fibrillar aggregates are naturally exploited for structural scaffolding or to generate molecular switches and can be artificially engineered to build up multi-functional nanomaterials. Thus, there is a high interest in rationalizing and forecasting protein aggregation. Here, we review the available computational toolbox to predict protein aggregation propensities, identify sequential or structural aggregation-prone regions, evaluate the impact of mutations on aggregation or recognize prion-like domains. We discuss the strengths and limitations of these algorithms and how they can evolve in the next future.

Formation and physicochemical properties of glycogen phosphorylase in complex with a cationic polyelectrolyte

The accumulation of rabbit muscle glycogen phosphorylase b (RMGPb) in electrostatic complexes with the cationic polyelectrolyte poly 2-(dimethylamino) ethyl methacrylate in its quenched form (QPDMAEMA) was studied in two buffer solutions. In the N-bis(2-hydroxyethyl)-2-aminoethanesulfonic acid (BES) buffer, large complexes of RMGPb-QPDMAEMA were formed which adopted smaller sizes as QPDMAEMA concentration increased. However, in N-(2-hydroxyethyl)piperazine-N'-(2-ethanesulfonic acid) (HEPES) buffer, the hydrodynamic radius of the formed complexes gradually increased as the polymer concentration increased. Zeta potential measurements (ζ_p) showed that RMGPb significantly changed the ζ_p of the QPDMAEMA aggregates. Fluorescence studies showed that the interaction between RMGPb and QPDMAEAMA was enhanced as polymer concentration increased. Specifically, 8-anilinonaphthalene-1-sulfonic acid (ANS) fluorescence indicated that in the BES buffer the aggregates became denser as more QPDMAEMA was added, while in the HEPES buffer the density of the formed structures decreased. RMGPb's secondary structure was examined by Attenuated Total Reflection - Fourier Transform Infrared (ATR-FTIR) and Circular Dichroism (CD) showing that QPDMAEMA interaction with RMGPb does not induce any changes to the secondary structure of the enzyme. These observations suggest that cationic polyelectrolytes may be utilized for the formulation of RMGPb in multifunctional nanostructures and be further exploited in innovative biotechnology applications and bioinspired materials development.

Influence of Low Molecular Weight Salts on the Viscosity of Aqueous-Buffer Bovine Serum Albumin Solutions

Pharmaceutical design of protein formulations aims at maximum efficiency (protein concentration) and minimum viscosity. Therefore, it is important to know the nature of protein-protein interactions and their influence on viscosity. In this work, we investigated the dependence of the viscosity of BSA in an aqueous 20 mM acetate buffer at pH = 4.3 on protein concentration and on temperature (5-45 °C). The viscosity of the solution increased with protein concentration and was 230% higher than the viscosity of the protein-free formulation at 160 mg/mL. The viscosity decreased by almost 60% in the temperature range from 5 to 45 °C. The agreement of the modified Arrhenius theory with experiment was quantitative, whereas a hard-sphere model provided only a qualitative description of the experimental results. We also investigated the viscosity of a 100 mg/mL BSA solution as a function of the concentration of added low molecular weight salts (LiCl, NaCl, KCl, RbCl, CsCl, NaBr, NaI) in the range of salt concentrations up to 1.75 mol/L. In addition, the particle size and zeta potential of BSA-salt mixtures were determined for solutions containing 0.5 mol/L salt. The trends with respect to the different anions followed a direct Hofmeister series (Cl^- > Br^- > I^-), whereas for cations in the case of viscosity the indirect Hofmeister series was observed (Li⁺ > Na⁺ > K⁺ > Rb⁺ > Cs⁺), but the values of particle sizes and zeta potential did not show cation-specific effects. Since the protein is positively charged at pH = 4.3, anions are more attracted to the protein surface and shield its charge, while the interaction with cations is less pronounced. We hypothesize that salt surface charge shielding reduces protein colloidal stability and promotes protein aggregate formation.