Bovine serum albumin (BSA) exhibits lot-to-lot variability, partly due to differences in fatty acid content. In this study, the structural properties of two BSA lots-fatty acid-bound and -free-were compared using electrophoretic, chromatographic, and spectroscopic techniques. No apparent differences in overall structure were detected by conventional methods, including UV absorbance spectroscopy, reducing and non-reducing SDS-PAGE, gel filtration chromatography, or agarose native gel electrophoresis. However, circular dichroism (CD) analysis of native BSA revealed small but significant differences in folded structure between the two lots, particularly in the microenvironment surrounding one of two tryptophan residues, a known fatty acid-binding region. These differences were further supported by the intrinsic fluorescence measurements. Under heat stress (73-76 °C), the two lots exhibited distinct behaviors. Native gel electrophoresis and CD spectroscopy conformational states with different patterns, including variations in aggregation propensity. These results demonstrate that, for the first time, combining CD and fluorescence spectroscopy with native electrophoresis under heat-stress conditions provides a sensitive and practical approach for detecting subtle conformational differences among BSA lots, offering a valuable tool for assessing protein quality and consistency.

Salts can increase the solubility of proteins, a phenomenon known as the salting-in effect. Although divalent salts exhibit the salting-in effect on proteins, the underlying mechanism, particularly at the functional group level, remains unclear. The present study investigated the effect of divalent cations (Mg2+ and Ca2+) on the solubility of proteins and amino acid derivatives to understand their interactions with specific protein moieties such as carboxyl groups, amino groups, and peptide bonds. Two proteins—β-lactoglobulin and lysozyme—were tested as models at the pH range of approximately 2–5. The results revealed that divalent cations increase protein solubility with increasing pH, particularly above pH 3–4. Monovalent sodium ion did not show the same solubility-enhancing effect as divalent cations. Because the pH region (pH 3–4) is close to the pKa of the carboxyl group, the observed increase in solubility above this pH range is attributable to their attractive interactions with the protein carboxyl groups. This suggestion was supported by the results that divalent cations increase the solubility of N-acetylglycine, which contains a carboxyl group, at pH values higher than 3. Notably, the divalent cations also increased the solubility of N-acetyl oligoglycine amides, indicating their interaction with peptide bond moieties. These findings suggest that the salting-in effect of divalent cations on proteins is primarily due to their interaction with protein carboxyl groups and peptide bonds.

Sodium dodecyl sulfate (SDS) is widely used in protein research. Micellar binding of SDS is accepted as a major mechanism of SDS binding to proteins. Here, we investigated SDS-protein interactions using near-UV circular dichroism (CD), fluorescence spectroscopy, and SDS-gel electrophoresis. Bovine serum albumin (BSA), IgG, and lysozyme showed unfolding by SDS without heating or disulfide reduction as determined by SDS-gel electrophoresis. Near-UV CD and fluorescence spectroscopy showed changes in local structures surrounding tryptophan residues upon addition of 0.05–1

Proteins are extensively used for research, food processing and pharmaceuticals [...]

Arginine is widely used in protein formulations to suppress protein aggregation and prolong the lifetime of the native, functional state which undergoes different stresses during storage, shipping and handling. However, arginine’s differential effects on protein aggregation pathways remain unclear. Here, we investigated the effects of arginine on heat- and acid-induced aggregation of immunoglobulin G and heat-induced aggregation of several model proteins. Arginine suppressed the formation of insoluble aggregates but had limited impact on monomer recovery, particularly on immunoglobulin G. Instead, arginine promoted the formation of soluble aggregates, suggesting a possibility that unfolded proteins possess heterogeneous surface properties, leading to formation of soluble and insoluble aggregates that are modulated by arginine. To explain these kinetic behaviors, we propose a hierarchical aggregation model, in which arginine preferentially modulates weaker intermolecular interactions to inhibit the growth of the soluble aggregates into large insoluble aggregates. Moreover, soluble aggregates were observed in a range of proteins with varying isoelectric points and molecular weights. These results highlight a previously unrecognized aspect of soluble protein aggregation. Understanding the pathway and mechanism of soluble aggregate formation may shed light into physiologically-relevant soluble assemblies, e.g., Alzheimer’s disease-associated oligomers and microtubule-derived double rings in contrast to the soluble amorphous aggregates under current study.

Circular dichroism (CD) is widely used to characterize proteins and assess the quality of biopharmaceuticals including proteins and nucleic acids. Rapid data acquisition is of great importance to broaden the range of CD applications. However, there are no consistent guidelines for selecting operating parameters such as bandwidth, digital integration time (DIT) and scan speed, so that an empirical rule of thumb approach is generally used. Here, we systematically investigated these parameters using rituximab as a model antibody. We found that a bandwidth of 2 nm, a scan speed of 50 nm/min, and a DIT of 4 s (far-UV) or 2 s (near-UV) preserved key spectral features while reducing noise and measurement time. Compared with conventional parameter values, this reduced the acquisition time for a CD spectrum to 1.4 min (far-UV) and 1.8 min (near-UV)-a 20- and ∼10-fold gain in efficiency, respectively. The secondary structure estimated from far-UV CD spectra remained consistent for all the parameter values used in this study, and was in agreement with the results of crystallographic analysis. Also, the acquisition time for single-wavelength thermal denaturation measurements was reduced from 70 to 18 min, and that for temperature-ramping spectra measurements from 270 to 90 min. These experiments allowed rapid evaluation of the stability of rituximab and revealed that aggregation-induced structural changes occurred immediately after denaturation.

The Ferguson plot is a simple method for determining the molecular weight of native proteins and their complexes. In this study, we tested the validity of the Ferguson plot based on agarose native gel electrophoresis using multimeric chaperone protein, ClpB, derived from a moderate halophile that forms a native hexamer. The Ferguson plot showed a single band with a molecular weight of 1,500 kDa, approximately twice the size of the native hexamer. This result is consistent with the structure of other chaperons that form a double ring assembly comprising two hexameric units, i.e., a dodecamer. Supporting this, dynamic light scattering experiment showed two peaks, which likely correspond to the hexamer and dodecamer structures.

Genetic fusion of a tag sequence to a target protein, or protein of interest (POI), is one of the most widely used technologies for recombinant expression. Tag-fusion proteins can enhance soluble expression, prolong half-life, increase binding avidity, and facilitate protein purification or refolding. In addition, tag-fusion proteins can be used to identify POI-binding partners through pull-down or immunoprecipitation assays. Beyond these classical applications, tags have evolved to serve as multifunctional tools, enabling real-time imaging, spatial localization, targeted delivery, and regulation of protein activity in living systems. Some engineered tags also allow conditional control, such as pH or ligand-dependent stabilization, thus expanding their utility in synthetic biology and therapeutic design. Here, we summarize protein-based and peptide-based tags, as well as methods for tag removal. While not fully comprehensive, this review aims to help researchers design suitable tag formats for specific goals.

Recombinant proteins play many important roles in development of biological reagents and biopharmaceuticals. Here, we will mainly review refolding of recombinant proteins when expressed in inclusion bodies, although strategies to enhance soluble expression are described as an alternative to refolding inclusion bodies. These strategies include, but not limited to, adding chemical chaperones in cell culture media, modifying cell lysis buffer and using solubility-enhacing fusion tags. Another solubility enhancement was to generate lipid complex for membrane proteins that form insoluble proteins without lipid. Among various solubilization and refolding technologies, those using denaturant, alkaline pH and pressure are also desribed, while we focus on solubilization and refolding using detergents, which are effective and cost-friendly. Sodium dodecylsulfate, lauroyl-glutamate, sarkosyl and cetyltrimethylammonium have been extensively used, as summarized in this review. Slow or step-wise removal of denaturants or ionic detergents used to solubilize appears to play a critical role in successful refolding by maintaining the solubility of proteins during refolding. In alkaline refolding, slow pH adjustment also helps maintain protein solubility. In pressure refolding, small amount of guanidine hydrochloride assisted refolding.

We review here several niche downstream purification processes that are not covered by other articles in this special issue. The first is the use of activated carbon to capture contaminants and clarify culture medium for purification of proteins, including antibodies. Flow-through operation of the activated carbon filter showed over 80 % recovery of antibodies with 10--fold reduction of host cell proteins and effective lipopolysaccharide and virus removal. The second is salt or arginine-tolerant column chromatography, in which the respective resins, such as hydroxyapatite and mixed-mode resins, can bind proteins in the presence of salt or arginine at high concentrations. Effective use of arginine was also suggested in size exclusion and affinity chromatography. The last is the isolation of proteins using gel electrophoresis and simple extraction procedure. These technologies offer simple and cost-effective methods for purifying proteins and protein complexes in the native state.

Sodium dodecyl sulfate (SDS) is one of the most widely used detergents. Here, we discuss current knowledge regarding applications of SDS and its modes of interaction with proteins, particularly at low concentrations. SDS at 1-2 %, which is well above the critical micelle concentration, is commonly used to extract fully denatured and dissociated proteins and SDS polyacrylamide gel electrophoresis (SDS-PAGE) in various applications, especially proteomics. In contrast, low concentration SDS may have been relatively underutilized. Here, we demonstrate the use of 0.1 % SDS for decellularization and protein fractionation. Why is 0.1 % SDS unique? The interaction between SDS and proteins is complex and depends on both the conditions and the proteins involved. At 0.1 %, the effects of SDS appear to be intermediate between negligible and extensive binding, highlighting its potential for novel applications. Two milder anionic detergents, Sarkosyl and sodium N-lauroyglutamate, whose effects are similar in certain applications to those of low concentration SDS, were briefly discussed.

In this study, we examined the effects of arginine (L-ArgHCl) on ultrafiltration performance, a process with practical significance for not only research but also pharmaceutical applications. Specifically, we assessed the yield and filtration rate of ultrafiltration using rabbit and goat polyclonal antibodies (neutral to basic isoelectric points) as well as model proteins, BSA (acidic) and lysozyme (basic). When a 1 mg/mL protein solution was concentrated approximately 10-fold using a standard commercially available centrifugal ultrafiltration device, the addition of L-ArgHCl significantly improved yield at near-neutral buffer pH. The observed order of improvement was: 20 mM L-ArgHCl >100 mM L-ArgHCl ≈0.5 M NaCl > no addition. A similar trend was observed with BSA, whereas lysozyme achieved slightly higher yields at 100 mM L-ArgHCl. In a 40-fold concentration of rabbit polyclonal antibody from 1 mg/mL, 20 mM L-ArgHCl enhanced yield at pH 6 and 7, but had minimal or no effect at pH 7.5. Notably, at pH 8, high yields were achieved without arginine. L-ArgHCl also accelerated the concentration rate at all pH levels, with greater enhancements observed at higher arginine concentrations. These findings suggest that L-ArgHCl mitigates protein precipitation and solubility loss by reducing protein-protein interactions and nonspecific binding to the ultrafiltration membrane. At pH 8, the increased surface charge of the antibody reduced hydrophobicity, further improving solubility. In summary, the addition of L-ArgHCl, particularly near pH 7, effectively enhanced ultrafiltration performance. This provides a practical strategy for improving protein concentration processes.

Refolding of protein from denatured structure caused by sodium dodecyl sulfate (SDS) was examined using agarose native gel electrophoresis and circular dichroism (CD). Refolding of protein from SDS complex was induced with the addition of non-ionic and zwitterionic detergents followed by agarose native gel electrophoresis. The native gel electrophoresis was done without both SDS and non-ionic detergents in the agarose gel and running buffer. The electrophoretic mobility of bovine serum albumin (BSA) drastically increased with the addition of 1% SDS to the samples indicative of SDS-BSA complex formation. The SDS-denatured BSA returned to the native mobility by the addition of non-ionic Tween 20 and Triton X-100 and zwitterionic CHAPS as a function of detergent concentration. Refolding, at least partially, was confirmed by CD, which was done in the presence of both SDS and non-ionic detergents, a condition different from the native gel electrophoresis done in their absence. When BSA was denatured by both 1% SDS and a disulfide-reducing dithiothreitol, even 10% Tween 20 was insufficient to restore the native BSA mobility on agarose native gel electrophoresis. When BSA was denatured by 1% Sarkosyl and sodium lauroyl-glutamate, Tween 20 restored the native structure at Tween 20 concentration lower than the Tween 20 concentration used for SDS denaturation. A similar refolding by non-ionic detergents was also observed for a rabbit monoclonal IgG, but not for lysozyme. The results with lysozyme suggest strong SDS binding and difficulty in dissociating the bound SDS by non-ionic detergents due to high isoelectric point of the protein and thereby more SDS binding.

Protein and nucleic acid play central roles in biology and pharmaceuticals. Both share a similar architecture made of a backbone and side chains. Protein has a peptide backbone and various side chains, whereas nucleic acid has a phosphate backbone and aromatic side chains. However, they are significantly different in the chemical properties of the backbone and side chains. The protein backbone is uncharged, while nucleic acid backbone is negatively charged. The protein side chains comprise widely different chemical properties. On the other hand, the nucleic acid side chains comprise a uniform chemical property of aromatic bases. Such differences lead to fundamentally different folding, molecular interactions and co-solvent interactions, which are the focus of this review. In regular protein secondary structures, the peptide groups form polar hydrogen bonds, making the interior hydrophilic. The side chains of different chemical properties are exposed on the outside of the protein secondary structures and participate in molecular and co-solvent interactions. On the other hand, hydrophobic/aromatic nucleobase side chains are located inside the typical double helix or quadruplex structures. The charged phosphate groups of the nucleic acid backbone are located outside, participating in electrostatic interactions. The nucleobases are also involved in molecular interactions, when exposed in breaks, hairpins, kinks and loops. These structural differences between protein and nucleic acid confer different interactions with commonly used co-solvents, such as denaturants, organic solvents and polymers.

Abstract: Currently, antibodies are major therapeutic modalities in biopharmaceutical research and development. Because of required high dose for certain clinical applications, antibodies are formulated at high protein concentration for convenience of administration, shipping and storage. We will describe the inter-molecular interactions that can occur in such a crowded environment of high protein concentration. Two types of repulsive interactions, i.e., electrostatic and excluded volume effects, and three types of attractive interactions, i.e., hydrophobic, electrostatic and cross-linking, need to be considered in such a crowded environments. We then show consequences of such inter-molecular interactions, leading to high viscosity, opalescence and phase separation of antibody solutions. Co-solvents are used to control the stability, structure and molecular interactions and thereby to alleviate these solution problems. Among various co-solvents, arginine has been extensively used to suppress protein-protein interactions at high protein concentration. Arginine weakly but extensively interacts with aromatic/hydrophobic groups as well as charged groups on proteins, leading to effective suppression of viscosity, opalescence and phase separation of antibody solution.

Gel electrophoresis and size exclusion chromatography (SEC) are vital techniques in biochemical research, employing gel matrix structures made of polysaccharides or synthetic polymers like polyacrylamide for the analysis and separation of macromolecules. Polysaccharides, such as agarose, offer safer alternatives to acrylamide. Polysaccharide gels, notably agarose, facilitate the analysis and purification of proteins and nucleic acids through a molecular sieving mechanism. Gel electrophoresis for proteins is mainly divided into denaturing and native methods. Denaturing electrophoresis with sodium dodecyl sulfate (SDS) simplifies protein migration but disrupts molecular interactions. Conversely, native gel electrophoresis, without SDS, allows proteins to migrate based on the running pH and the isoelectric point of the proteins, while nucleic acids consistently migrate toward the anode. The electrophoresis of proteins with variable charges presents complexes. This review focuses on the use of polysaccharides, particularly agarose, for native gel electrophoresis, highlighting their applications in separating macromolecules. It also discusses the applications and limitations of agarose gels when used as a matrix for electrophoresis. Such information should help in designing electrophoresis experiments using polysaccharides.

In this study, we conducted Ferguson plot analyses using both agarose and polyacrylamide gels in native electrophoresis and SDS-PAGE. The results revealed intriguing differences in the behavior of bovine serum albumin (BSA) and other model proteins. Specifically, BSA exhibited Ferguson plot slopes that were dependent on the oligomer size in agarose native gel electrophoresis, while such size-dependent behavior was not observed in native-PAGE or SDS-PAGE. These findings suggest that Ferguson plot analysis is a suitable approach when using agarose gel under the electrophoretic conditions employed in this study. Furthermore, our investigation extended to model proteins with acidic isoelectric points and larger molecular weights, namely Ferritin and caseinolytic peptidase B (ClpB). Notably, these proteins displayed distinct Ferguson plot slopes when subjected to agarose gel electrophoresis. Intriguingly, when polyacrylamide gel was employed, ClpB exhibited multiple bands, each with its unique Ferguson plot slope, deviating from the expected behavior based on molecular size. This divergence in Ferguson plot characteristics between agarose and polyacrylamide gels points to an interesting and complex interplay between protein properties and gel electrophoresis conditions.

In this study, we review the properties of three anionic detergents, sodium dodecyl sulfate (SDS), Sarkosyl, and sodium lauroylglutamate (SLG), as they play a critical role in molecular biology research. SDS is widely used in electrophoresis and cell lysis for proteomics. Sarkosyl and, more frequently, SDS are used for the characterization of neuropathological protein fibrils and the solubilization of proteins. Many amyloid fibrils are resistant to SDS or Sarkosyl to different degrees and, thus, can be readily isolated from detergent-sensitive proteins. SLG is milder than the above two detergents and has been used in the solubilization and refolding of proteins isolated from inclusion bodies. Here, we show that both Sarkosyl and SLG have been used for protein refolding, that the effects of SLG on the native protein structure are weaker for SLG, and that SLG readily dissociates from the native proteins. We propose that SLG may be effective in cell lysis for functional proteomics due to no or weaker binding of SLG to the native proteins.

We have studied binding properties of three detergents, i.e., sodium dodecyl sulfate (SDS), Sarkosyl and sodium lauroyl glutamate (SLG), to model proteins based on their effects on electrophoretic mobilities of the proteins using agarose native gel electrophoresis and circular dichroism (CD). This simple technology can evaluate the dissociative properties of bound detergents from the proteins and their effects on protein structure. SDS influenced the electrophoretic mobilities of all model proteins more strongly than the other two detergents, implying a stronger inclination for protein binding and subsequent alterations in protein structure or reductions in activity, which are supported by CD analysis. On the contrary, Sarkosyl and SLG showed weaker binding and interfered less with the structure and biological activities, indicating that these detergents may be useful for protein purification and analysis. It appeared that SLG was weaker in protein binding than Sarkosyl, although the effects of these two detergents appeared to depend on the proteins.

Protein aggregation is a major hurdle in developing biopharmaceuticals, in particular protein formulation area, but plays a pivotal role in food products. Co-solvents are used to suppress protein aggregation in pharmaceutical proteins. On the contrary, aggregation is encouraged in the process of food product making. Thus, it is expected that co-solvents play a contrasting role in biopharmaceutical formulation and food products. Here, we show several examples that utilize co-solvents, e.g., salting-out salts, sugars, polyols and divalent cations in promoting protein-protein interactions. The mechanisms of co-solvent effects on protein aggregation and solubility have been studied on aqueous protein solution and applied to develop pharmaceutical formulation based on the acquired scientific knowledge. On the contrary, co-solvents have been used in food industries based on empirical basis. Here, we will review the mechanisms of co-solvent effects on protein-protein interactions that can be applied to both pharmaceutical and food industries and hope to convey knowledge acquired through research on co-solvent interactions in aqueous protein solution and formulation to those involved in food science and provide those involved in protein solution research with the observations on aggregation behavior of food proteins.