Evaluation of effects of pH and ionic strength on colloidal stability of IgG solutions by PEG-induced liquid-liquid phase separation

A tale of dual functions of SERF family proteins in regulating amyloid formation

The abnormal aggregation of proteins is a significant pathological hallmark of diseases, such as the amyloid formation associated with fused in sarcoma protein (FUS) in frontotemporal lobar degeneration and amyotrophic lateral sclerosis diseases. Understanding which cellular components and how these components regulate the process of abnormal protein aggregation in living organisms is crucial for the prevention and treatment of neurodegenerative diseases. MOAG-4/SERF is a conserved family of proteins with rich positive charged residues, which was initially identified as an enhancer for the formation of amyloids in C. elegans. Knocking out SERF impedes the amyloid formation of various proteins, including α-synuclein and β-amyloid, which are linked to Parkinson's and Alzheimer's diseases, respectively. However, recent studies revealed SERF exhibited dual functions, as it could both promote and inhibit the fibril formation of the neurodegenerative disease-related amyloidogenic proteins. The connection between functions and structure basis of SERF in regulating the amyloid formation is still unclear. This review will outline the hallmark proteins in neurodegenerative diseases, summarize the contradictory role of the SERF protein family in promoting and inhibiting the aggregation of neurodegenerative proteins, and finally explore the potential structural basis and functional selectivity of the SERF protein.

Suppression of Liquid‐Liquid Phase Separation and Aggregation of Antibodies by Modest Pressure Application

The high colloidal stability of antibody (immunoglobulin) solutions is important for pharmaceutical applications. Inert cosolutes, excipients, are generally used in therapeutic protein formulations to minimize physical instabilities, such as liquid–liquid phase separation (LLPS), aggregation and precipitation, which are often encountered during manufacturing and storage. Despite their widespread use, a detailed understanding of how excipients modulate the specific protein‐protein interactions responsible for these instabilities is still lacking. In this work, we demonstrate the high sensitivity to pressure of globulin condensates as a suitable means to suppress LLPS and subsequent aggregation of concentrated antibody solutions. The addition of excipients has only a minor effect. The high pressure sensitivity observed is due to the fact that these flexible Y‐shaped molecules create a considerable amount of void volume in the condensed phase, leading to an overall decrease in the volume of the system upon dissociation of the droplet phase by pressure already at a few tens of to hundred bar. Moreover, we show that immunoglobulin molecules themselves are highly resistant to unfolding under pressure, and can even sustain pressures up to about 6 kbar without conformational changes. This implies that immunoglobulins are resistant to the pressure treatment of foods, such as milk, in high‐pressure food‐processing technologies, thereby preserving their immunological activity.

Oriented immobilization of antibodies onto sensing platforms - A critical review

The immunosensor has been proven a versatile tool to detect various analytes, such as food contaminants, pathogenic bacteria, antibiotics and biomarkers related to cancer. To fabricate robust and reproducible immunosensors with high sensitivity, the covalent immobilization of immunoglobulins (IgGs) in a site-specific manner contributes to better performance. Instead of the random IgG orientations result from the direct yet non-selective immobilization techniques, this review for the first time introduces the advances of stepwise yet site-selective conjugation strategies to give better biosensing efficiency. Noncovalently adsorbing IgGs is the first but decisive step to interact specifically with the Fc fragment, then following covalent conjugate can fix this uniform and antigens-favorable orientation irreversibly. In this review, we first categorized this stepwise strategy into two parts based on the different noncovalent interactions, namely adhesive layer-mediated interaction onto homofunctional support and layer-free interaction onto heterofunctional support (which displays several different functionalities on its surface that are capable to interact with IgGs). Further, the influence of ligands characteristics (synthesis strategies, spacer requirements and matrices selection) on the heterofunctional support has also been discussed. Finally, conclusions and future perspectives for the real-world application of stepwise covalent conjugation are discussed. This review provides more insights into the fabrication of high-efficiency immunosensor, and special attention has been devoted to the well-orientation of full-length IgGs onto the sensing platform.

The cellular modifier MOAG-4/SERF drives amyloid formation through charge complementation

While aggregation-prone proteins are known to accelerate aging and cause age-related diseases, the cellular mechanisms that drive their cytotoxicity remain unresolved. The orthologous proteins MOAG-4, SERF1A, and SERF2 have recently been identified as cellular modifiers of such proteotoxicity. Using a peptide array screening approach on human amyloidogenic proteins, we found that SERF2 interacted with protein segments enriched in negatively charged and hydrophobic, aromatic amino acids. The absence of such segments, or the neutralization of the positive charge in SERF2, prevented these interactions and abolished the amyloid-promoting activity of SERF2. In protein aggregation models in the nematode worm Caenorhabditis elegans, protein aggregation and toxicity were suppressed by mutating the endogenous locus of MOAG-4 to neutralize charge. Our data indicate that MOAG-4 and SERF2 drive protein aggregation and toxicity by interactions with negatively charged segments in aggregation-prone proteins. Such charge interactions might accelerate primary nucleation of amyloid by initiating structural changes and by decreasing colloidal stability. Our study points at charge interactions between cellular modifiers and amyloidogenic proteins as potential targets for interventions to reduce age-related protein toxicity.

Characteristics of colloids and their affinity for heavy metals in road runoff with different traffic in Beijing, China

The characteristics of colloids in urban road runoff with different traffic in Beijing, China, such as concentration, particle size, chemical property, and affinity for heavy metals were determined. The concentration of colloids was high, and an evident first flush effect was found in the runoff of road with heavy traffic. A large portion of colloids were distributed in the range of 1-10 μm. Traffic activity, rainfall intensity, and time of sample collection would not change the size distribution of colloids in the road runoff. The chemical property of colloids in the road runoff would be influenced by the soil erosion nearby green space, causing the content of organic colloids was high. The correlation coefficient between the concentration of colloids in colloidal fractions and the concentration of heavy metals (Cu, Zn, Cd, Pb, Fe, and Mn) in the road runoff with different traffic decreased with the same sequence from 0.02-0.2 μm, 0.2-0.45 μm, 0.45-1 μm, to 1-10 μm, suggesting that the heavy metals had stronger affinity for the colloids with small size. The concentration of Cu, Pb, and Zn exhibited significant correlations with the concentration of organic colloids in the road runoff. More aggregated spherical particles were found in the TEM image of the road runoff with heavy traffic. Zeta potentials and RMV data showed that the colloids with smaller size and the colloids in the road runoff with lighter traffic were much more stable.

Does liquid-liquid phase separation drive peptide folding?

Proline–arginine (PR) dipeptide repeats have been shown to undergo liquid–liquid phase separation and are an example of a growing number of intrinsically disordered proteins that can assemble into membraneless organelles. These structures have been posited as nucleation sites for pathogenic protein aggregation. As such, a better understanding of the effects that the increased local concentration and volumetric crowding within droplets have on peptide secondary structure is necessary. Herein we use Fourier transform infrared (FTIR) and two-dimensional infrared (2DIR) spectroscopy to show that formation of droplets by PR₂₀ accompanies changes in the amide-I spectra consistent with folding into poly-proline helical structures.

Two-dimensional infrared spectroscopy reveals folding of an intrinsically disordered peptide when sequestered into a model “membrane-less” organelle.

Expanding and optimizing 3D bioprinting capabilities using complementary network bioinks

A major challenge in three-dimensional (3D) bioprinting is the limited number of bioinks that fulfill the physicochemical requirements of printing while also providing a desirable environment for encapsulated cells. Here, we address this limitation by temporarily stabilizing bioinks with a complementary thermo-reversible gelatin network. This strategy enables the effective printing of biomaterials that would typically not meet printing requirements, with instrument parameters and structural output largely independent of the base biomaterial. This approach is demonstrated across a library of photocrosslinkable bioinks derived from natural and synthetic polymers, including gelatin, hyaluronic acid, chondroitin sulfate, dextran, alginate, chitosan, heparin, and poly(ethylene glycol). A range of complex and heterogeneous structures are printed, including soft hydrogel constructs supporting the 3D culture of astrocytes. This highly generalizable methodology expands the palette of available bioinks, allowing the biofabrication of constructs optimized to meet the biological requirements of cell culture and tissue engineering.

Magnetic Precipitation: A New Platform for Protein Purification

One of the trends in downstream processing comprises the use of "anything-but-chromatography" methods to overcome the current downfalls of standard packed-bed chromatography. Precipitation and magnetic separation are two techniques already proven to accomplish protein purification from complex media, yet never used in synergy. With the aim to capture antibodies directly from crude extracts, a new approach combining precipitation and magnetic separation is developed and named as affinity magnetic precipitation. A precipitation screening, based on the Hofmeister series, and a commercial precipitation kit are tested with affinity magnetic particles to assess the best condition for antibody capture from human serum plasma and clarified cell supernatant. The best conditions are obtained when using PEG3350 as precipitant at 4 °C for 1 h, reaching 80% purity and 50% recovery of polyclonal antibodies from plasma, and 99% purity with 97% recovery yield of anti-TNFα mAb from cell supernatants. These results show that the synergetic use of precipitation and magnetic separation can represent an alternative for the efficient capture of antibodies.

Relationship of PEG-induced precipitation with protein-protein interactions and aggregation rates of high concentration mAb formulations at 5 °C

Native protein-protein interactions can play an important role in determining the tendency of monoclonal antibodies (mAbs) to aggregate under storage conditions. In this context, phase separation of mAb solutions induced by the addition of neutral polymers such as poly(ethylene glycol) (PEG) represents a simple method to assess the tendency of proteins to self-associate in the native state. Here, we investigated their relationships between PEG-induced phase separation, protein-protein interactions and long-term aggregation rate of several formulations of four mAbs at 100 mg/mL and 5 °C over 12 weeks of storage. We observed that the location of the phase boundary correlated well with the osmotic second virial coefficient B₂₂ determined in absence of the polymer, indicating that for our solutions PEG primarily leads to depletion forces between protein molecules, which are additive to protein-protein interactions. However, limited correlation between aggregation rate at 5 °C and phase behavior was observed across different mAbs, pH values and ionic strengths, indicating that colloidal stability is not the only determinant of aggregation even at such low temperature and high protein concentration. Our results contribute to the growing realization that aggregation propensity in the context of antibody developability is a complex feature, which depends on a variety of biophysical properties rather than one single parameter.

Accelerating Biologics Manufacturing by Modeling: Process Integration of Precipitation in mAb Downstream Processing

The demand on biologics has been constantly rising over the past decades and has become crucial in modern medicine. Promising approaches to cope with widespread diseases like cancer and diabetes are gene therapy, plasmid DNA, virus-like particles, and exosomes. Due to progress that has been made in upstream processing (USP), difficulties arise in downstream processing and demand for innovative solutions. This work focuses on the integration of precipitation using a quality by design (QbD) approach for process development. Selective precipitation is achieved with PEG 4000 resulting in an HCP depletion of ≥80% respectively to IgG. Dissolution was executed with a sodium phosphate buffer (pH = 5/50 mM) reaching an IgG recovery of ≥95%. However, the central challenge in process development is still an optimal process design, which is transferable for a broad molecular variety of new products. This is where rigorous modeling becomes vital in order to generate digital twins to support early-stage process development and reduce the experimental overhead. Therefore, a model development and validation concept for construction of a process model for precipitation is also presented.

Methods for producing microstructured hydrogels for targeted applications in biology

Hydrogels have been broadly studied for applications in clinically motivated fields such as tissue regeneration, drug delivery, and wound healing, as well as in a wide variety of consumer and industry uses. While the control of mechanical properties and network structures are important in all of these applications, for regenerative medicine applications in particular, matching the chemical, topographical and mechanical properties for the target use/tissue is critical. There have been multiple alternatives developed for fabricating materials with microstructures with goals of controlling the spatial location, phenotypic evolution, and signaling of cells. The commonly employed polymers such as poly(ethylene glycol) (PEG), polypeptides, and polysaccharides (as well as others) can be processed by various methods in order to control material heterogeneity and microscale structures. We review here the more commonly used polymers, chemistries, and methods for generating microstructures in biomaterials, highlighting the range of possible morphologies that can be produced, and the limitations of each method. With a focus in liquid-liquid phase separation, methods and chemistries well suited for stabilizing the interface and arresting the phase separation are covered. As the microstructures can affect cell behavior, examples of such effects are reviewed as well. STATEMENT OF SIGNIFICANCE: Heterogeneous hydrogels with enhanced matrix complexity have been studied for a variety of biomimetic materials. A range of materials based on poly(ethylene glycol), polypeptides, proteins, and/or polysaccharides, have been employed in the studies of materials that by virtue of their microstructure, can control the behaviors of cells. Methods including microfluidics, photolithography, gelation in the presence of porogens, and liquid-liquid phase separation, are presented as possible strategies for producing materials, and their relative advantages and disadvantages are discussed. We also describe in more detail the various processes involved in LLPS, and how they can be manipulated to alter the kinetics of phase separation and to yield different microstructured materials.

Quantitative Evaluation of Protein Solubility in Aqueous Solutions by PEG-Induced Liquid-Liquid Phase Separation

This chapter describes an experimental method to quantitatively evaluate the solubility of proteins in aqueous solutions. Measurement of protein solubility can be challenging because low solubility can be manifested through various pathways (e.g., crystallization, aggregation, gelation, and liquid-liquid phase separation), some of which may occur over long periods of time. In the method described here, a nonionic polymer, polyethylene glycol (PEG), is added to a protein solution of interest to induce instantaneous formation of protein-rich liquid droplets. After incubation at a given temperature, the samples are centrifuged. The protein concentration in the supernatant is measured at various PEG concentrations to calculate an equilibrium binding free energy, which provides a measure of protein solubility. Based on the first principles of thermodynamics, this method is highly reproducible and applicable to various proteins and buffer conditions.

Evaluating the Effects of Hinge Flexibility on the Solution Structure of Antibodies at Concentrated Conditions

Employing 2 different coarse-grained models, we evaluated the effect of intramolecular domain-domain distances and hinge flexibility on the general solution structure of monoclonal antibodies (mAbs), within the context of protein-protein steric repulsion. These models explicitly account for the hinge region, and represent antibodies at either domain or subdomain levels (i.e., 4-bead and 7-bead representations, respectively). Additionally, different levels of mAb flexibility are also considered. When evaluating mAbs as rigid structures, analysis of small-angle scattering profiles showed that changes in the relative internal distances between Fc and Fab domains significantly alter the local arrangement of neighboring molecules, as well as the molecular packing of the concentrated mAb solutions. Likewise, enabling hinge flexibility in either of the mAb models led to qualitatively similar results, where flexibility increases the spatial molecular arrangement at elevated concentrations. This occurs because fluctuations in mAb quaternary structure are modulated by the close proximity between molecules at elevated concentrations (>50 mg mL^-1), yielding an increased molecular packing and osmotic compressibility. However, our results also showed that the mechanism behind this synergy between flexibility and packing strongly depends on both the level of structural detail and the number of degrees-of-freedom considered in the coarse-grained model.

Modeling the depletion effect caused by an addition of polymer to monoclonal antibody solutions

We present a theoretical study of colloidal stability of the model mixtures of monoclonal antibody molecules and non-adsorbing (no polymer-protein attraction) polymers. The antibodies are pictured as an assembly of seven hard spheres assuming a Y-like shape. Polymers present in the mixture are modeled as chain-like molecules having from 32 up to 128 monomers represented as hard spheres. We use Wertheim's thermodynamic perturbation theory to construct the two molecular species and to calculate measurable properties. The calculations are performed in the osmotic ensemble. In view that no direct attractive interaction is present in the model Hamiltonian, we only account for the entropic contribution to the phase equilibrium. We calculate chemical potentials and the equation of state for the model mixture to determine the liquid-liquid part of the phase diagram. We investigate how the critical antibody number density depends on the degree of polymerization and the bead size ratio of the polymer and protein components. The model mixture qualitatively correctly predicts some basic features of real systems. The effects of the model 'protein' geometry, that is the difference in results for the flexible Y-shaped protein versus the rigid spherical one, are also examined.

Impact of macromolecular crowding on RNA/spermine complex coacervation and oligonucleotide compartmentalization

We report the effect of neutral macromolecular crowders poly(ethylene glycol) (PEG) (8 kDa) and Ficoll (70 kDa) on liquid-liquid phase separation in a polyuridylic acid (polyU)/spermine complex coacervate system. The addition of PEG decreased both the amount of spermine required for phase separation and the coacervation temperature (T_C). We interpret these effects on phase behavior as arising due to excluded volume and preferential interactions on both the secondary structure/condensation of spermine-associated polyU molecules and on the association of soluble polyU/spermine polyelectrolyte complexes to form coacervate droplets. Examination of coacervates formed in the presence of fluorescently-labeled PEG or Ficoll crowders indicated that Ficoll is accumulated while PEG is excluded from the coacervate phase, which provides further insight into the differences in phase behavior. Crowding agents impact distribution of a biomolecular solute: partitioning of a fluorescently-labeled U15 RNA oligomer into the polyU/spermine coacervates was increased approximately two-fold by 20 wt% Ficoll 70 kDa and by more than two orders of magnitude by 20 wt% PEG 8 kDa. The volume of the coacervate phase decreased in the presence of crowder relative to a dilute buffer solution. These findings indicate that potential impacts of macromolecular crowding on phase behavior and solute partitioning should be considered in model systems for intracellular membraneless organelles.

Optimization of high-concentration endostatin formulation: Harmonization of excipients' contributions on colloidal and conformational stabilities

Recently, increasing research efforts have been devoted into developing high-concentration protein drugs for subcutaneous injection, especially for those with short half-lives and high-dose requirement. Proteins at high concentrations normally present increased colloidal and structural instability, such as aggregation, fibrillation and gelation, which significantly challenges the high-concentration formulation development of protein drugs. Here we used endostatin, a 20kD recombinant protein, as a model drug for high-concentration formulation optimization. The colloidal and conformational stability of endostatin at high concentration of 30mg/mL were investigated in formulations containing various excipients, including saccharides (mannitol, sorbitol and sucrose), salts (ArgHCl and NaCl), and surfactants (tween 20 and 80). Protein fibrillation was characterized and semi-quantified by optical polarized light microscopy and transmission electron microscopy, and the amount of fiber formation at elevated temperature of 40°C was determined. The soluble protein aggregates were characterized by dynamic and static light scattering before and after dilution. The conformational stability were characterized by polyacrylamide gel electrophoresis, fluorescence, circular dichroism, and differential scanning calorimetry. We observed that the soluble aggregation, fibrillation and gelation, induced by conformational and colloidal instabilities of the protein solution, could be substantially optimized by using suitable stabilizers such as combinations of saccharides and surfactants; while formation of gel and soluble aggregates at high protein concentration (e.g., 30mg/mL) and elevated temperature (40°C) could be prevented by avoiding the usage of salts. It's worth emphasizing that some stabilizers, such as salts and surfactants, could show opposite contributions in conformational and colloidal stabilities of endostatin. Therefore, cautions are needed when one attempts to correlate the colloidal stability of high-concentration proteins with their conformational stability, and the colloidal and conformational protein stabilities must be harmonized by a balanced selection of various types of excipients.