Polyethylene Glycol Crowder's Effect on Enzyme Aggregation, Thermal Stability, and Residual Catalytic Activity

Low-cost food-grade alternatives for serum albumins in FBS-free cell culture media

Cultivated meat may be an ethical, environmentally friendly, antibiotic-free meat alternative of the future. As of now, one of the main limiting factors for bringing cultivated meat to the market is the high cost of the cell culture media and their great dependency on serum albumins, production of which is predicted to become a major bottleneck of this industry. Here, using bovine muscle stem cells, we optimized serum free B8/B9 medium. We identified several food grade, low-price medium stabilizers, exhibiting comparable or even superior stabilization of the B8 medium in short- and long-term cultivations, as compared to recombinant human serum albumin. We show transferability of our approach to other satellite cells (porcine, chicken) and CHO cells, though significant cell-line specific differences in response to stabilizers were observed. Thus, we provide an alternative to serum albumin, enabling up to an overall 73% reduction of medium price for certain cell lines.

Decorating channel walls in ordered macroporous ZIF-8 with hydrophilic PEG to immobilize lipase for efficient chiral resolution

The development of efficient immobilization support for the enhancement of enzyme activity and recyclability is a highly desirable objective. Single-crystalline ordered macro-microporous ZIF-8 (SOM-ZIF-8), has emerged as a highly effective matrix for enzyme immobilization, however, the inherent hydrophobic nature limits its further advancement. Herein, we have customized the immobilization of the Pseudomonas cepacia lipase (LP) in the modification-channels of SOM-ZIF-8 by functionalizing the inner surface-properties with polyethylene glycol (PEG) (LP@SOM-ZIF-8-PEG), and significant enhancement of the activity and (thermal, solvent and cyclic) stability can be realized. The incorporation of PEG into SOM-ZIF-8 regulates its inner surface charge and hydrophobic properties, thereby enhancing enzyme loading, facilitating enzyme conformational adjustments, and achieving a uniform dispersion of LP in SOM-ZIF-8-PEG. LP@SOM-ZIF-8-PEG not only demonstrates a pronounced elevation in enzyme loading and activity over LP@SOM-ZIF-8 but also shows an enzyme activity that is impressively three times greater than LP@ZIF-8. It can completely resolve the 1-phenylethanol racemate in 60 min, with a conversion close to 50 % and an enantioselectivity of 99.8 %. After nine cycles of reuse, the LP@SOM-ZIF-8-PEG still holds onto 95 % of its initial activity. The excellent catalytic performance and stability of LP@SOM-ZIF-8-PEG, along with the universality of the PEG modification strategy for other enzymes, make this work promising in industrial applications.

Unstructured protein domains stabilize RNA binding and mediate RNA folding by AUF1

AUF1 is an RNA-binding protein that targets AU-rich elements, cis-acting regulatory sequences commonly enriched in mRNAs encoding inflammatory mediators and oncoproteins. AUF1 post-transcriptionally regulates gene expression by modulating the stability and/or translational efficiency of mRNA targets in a context-specific manner; however, the mechanisms by which AUF1 directly engages RNA substrates and mediates regulatory outcomes remain largely unknown. The purpose of this study was to define the biochemical basis for RNA recognition by AUF1 using the smallest protein isoform (p37AUF1) as a model. AUF1 contains two tandem RNA recognition motifs (RRMs), common RNA-binding domains that stabilize the formation of many ribonucleoprotein complexes. Using quantitative fluorescence anisotropy-based assays, we observed that p37AUF1's tandem RRM domain only weakly binds AU-rich element substrates. Testing a panel of protein mutants revealed that the N- and C-terminal flanking domains each make modest but similar contributions to stabilization of both the initial RNA:protein complex and a subsequent protein-binding event. However, focused protein truncations showed that residues immediately N-terminal of the RRMs were vital for high affinity binding, but only in the context of the C-terminal domain. The C-terminal domain was also required for protein-induced RNA remodeling; both this function and its ribonucleoprotein-stabilizing role involve nonbase-specific contacts with RNA upstream of the AU-rich motif. Finally, our data suggest that the C-terminal domain is intrinsically disordered but may undergo a conformational change upon interaction with RNA ligands. Together, these findings reveal distinct roles for flanking protein domains in RNA binding and remodeling by AUF1.

Incubation of Horseradish Peroxidase near 50 Hz AC Equipment Promotes Its Disaggregation and Enzymatic Activity

Low-frequency electromagnetic fields, induced by alternating current (AC)-based equipment such as transformers, are known to influence the physicochemical properties and function of enzymes, including their catalytic activity. Herein, we have investigated how incubation near a 50 Hz AC autotransformer influences the physicochemical properties of horseradish peroxidase (HRP), by atomic force microscopy (AFM) and spectrophotometry. We found that a half-hour-long incubation of the enzyme above the coil of a loaded autotransformer promoted the adsorption of the monomeric form of HRP on mica, enhancing the number of adsorbed enzyme particles by two orders of magnitude in comparison with the control sample. Most interestingly, the incubation of HRP above the switched-off transformer, which was unplugged from the mains power supply, for the same period of time was also found to cause a disaggregation of the enzyme. Notably, an increase in the activity of HRP against ABTS was observed in both cases. We hope that the interesting effects reported will emphasize the importance of consideration of the influence of low-frequency electromagnetic fields on enzymes in the design of laboratory and industrial equipment intended for operation with enzyme systems. The effects revealed in our study indicate the importance of proper shielding of AC-based transformers in order to avoid the undesirable influence of low-frequency electromagnetic fields induced by these transformers on humans.

Phenylacetylcarbinol biotransformation by disrupted yeast cells using ultrasonic treatment in conjunction with a dipropylene glycol mediated biphasic emulsion system

Biotransformation of a pharmaceutical precursor, phenylacetylcarbinol (PAC), could be achieved by frozen-thawed Candida tropicalis whole cells (FT-WHC). The treatment of FT-WHC, which contained intracellular pyruvate decarboxylase (PDC) enzyme, using high-power ultrasonication with varying amplitudes were compared with glass bead attrition (GBA) as well as control for the release of PDC. Ultrasonication at 20% amplitude (Ult20) proved to be the most effective, resulting in the highest volumetric and specific PDC activities of 0.210 ± 0.004 U/mL and 0.335 ± 0.033 U/mg protein, respectively. Disrupted FT-WHC using Ult20 exhibited a statistically significant (p ≤ 0.05) higher initial PAC production rate (3.26 ± 0.04 mM). The comparison of three organic phases, namely, vegetable oil (Vg-Oil), Vg-Oil + dipropylene glycol (DPG), and octanol in the two-phase emulsion system for PAC biotransformation revealed the highest statistically significant (p ≤ 0.05) overall PAC concentration of 28.9 ± 0.1 mM in Vg-Oil + DPG system. The novel addition of DPG helped facilitating the partitioning of PAC into aqueous phase, stabilizing specific PDC activity, and specific PAC productivity in combination with ultrasonication treatment.

Purification of a Fc-Fusion Protein with [Bathophenathroline:metal] Complexes

In this study, we assess an alternative Fc-fusion protein purification method that does not rely on chromatographic media or ligands. Recombinant human acetylcholinesterase, fused to the Fc domain of human IgG1 (henceforth, AChE-Fc), was purified with precipitated aromatic complexes composed of the bathophenanthroline (henceforth, batho) chelator with either Zn2+ or Cu2+ ions (i.e., [(batho)3:Zn2+] or [(batho)2:Cu2+]) in the presence of polyethylene glycol 6000 (PEG-6000). In a three-step purification process conducted at pH 7, AChE-Fc was captured by the aromatic complexes (Step 1); unbound or weakly bound protein impurities were removed with 20 mM NaCl (Step 2); and AChE-Fc was then extracted at pH 7 (Step 3) using 100 mM Na citrate buffer in 250 mM NaCl. Purified AChE-Fc was not aggregated (as determined by dynamic light scattering (DLS) and Native PAGE). However, full enzymatic activity was only preserved with the [(batho)3:Zn2+] complex. Interaction between AChE-Fc and [(batho)3:Zn2+] led to ~83-88% overall protein yield. Thirty-fold process upscaling by volume required only proportional increase in the amounts of [(batho)3:Zn2+] and PEG-6000. Efficient (95-97%) chelator recycling was achieved by recrystallization. Chelator leaching into purified AchE-Fc was estimated to be ~0.3% relative to the total amount used. Taken together, this novel procedure has the potential to provide an economical and practical avenue for the industrial purification of Fc-fusion proteins.

Optical characterization of molecular interaction strength in protein condensates

Biomolecular condensates have been identified as a ubiquitous means of intracellular organization, exhibiting very diverse material properties. However, techniques to characterize these material properties and their underlying molecular interactions are scarce. Here, we introduce two optical techniques-Brillouin microscopy and quantitative phase imaging (QPI)-to address this scarcity. We establish Brillouin shift and linewidth as measures for average molecular interaction and dissipation strength, respectively, and we used QPI to obtain the protein concentration within the condensates. We monitored the response of condensates formed by fused in sarcoma (FUS) and by the low-complexity domain of hnRNPA1 (A1-LCD) to altering temperature and ion concentration. Conditions favoring phase separation increased Brillouin shift, linewidth, and protein concentration. In comparison to solidification by chemical cross-linking, the ion-dependent aging of FUS condensates had a small effect on the molecular interaction strength inside. Finally, we investigated how sequence variations of A1-LCD, that change the driving force for phase separation, alter the physical properties of the respective condensates. Our results provide a new experimental perspective on the material properties of protein condensates. Robust and quantitative experimental approaches such as the presented ones will be crucial for understanding how the physical properties of biological condensates determine their function and dysfunction.

Optical characterization of molecular interaction strength in protein condensates

Biomolecular condensates have been identified as a ubiquitous means of intracellular organization, exhibiting very diverse material properties. However, techniques to characterize these material properties and their underlying molecular interactions are scarce. Here, we introduce two optical techniques - Brillouin microscopy and quantitative phase imaging (QPI) - to address this scarcity. We establish Brillouin shift and linewidth as measures for average molecular interaction and dissipation strength, respectively, and we used QPI to obtain the protein concentration within the condensates. We monitored the response of condensates formed by FUS and by the low-complexity domain of hnRNPA1 (A1-LCD) to altering temperature and ion concentration. Conditions favoring phase separation increased Brillouin shift, linewidth, and protein concentration. In comparison to solidification by chemical crosslinking, the ion-dependent aging of FUS condensates had a small effect on the molecular interaction strength inside. Finally, we investigated how sequence variations of A1-LCD, that change the driving force for phase separation, alter the physical properties of the respective condensates. Our results provide a new experimental perspective on the material properties of protein condensates. Robust and quantitative experimental approaches such as the presented ones will be crucial for understanding how the physical properties of biological condensates determine their function and dysfunction.

Harnessing Water Competition to Drive Enzyme Crosstalk

In nature, enzymatic pathways often involve compartmentalization effects that can modify the intrinsic activity and specificity of the different enzymes involved. Consequently, extensive research has focused on replicating and studying the compartmentalization effects on individual enzymes and on multistep enzyme "cascade" reactions. This study explores the influence of compartmentalization achieved using molecular crowding on the glucose oxidase/horseradish peroxidase (GOx/HRP) cascade reaction. The crowder tested is methoxy poly(ethylene glycol) (mPEG) that can, depending on conditions, promote GOx and HRP coassociation at the nanoscale and extend their contact time. Low-molecular-weight mPEG (0.35 kDa), but not mPEG of higher molecular weights (5 or 20 kDa), significantly enhanced the cascade reaction where up to a 20-fold increase in the rate of the cascade reaction was observed under some conditions. The combined analyses emphasize the particularity of low-molecular-weight mPEG and point toward mPEG-induced coassociation of HRP and GOx, producing nearest crowded neighbor effects of HRP on GOx, and vice versa. These altered the nanoscale environments of these enzymes, which influenced substrate affinity. Using mPEG to promote protein coassociation is simple and does not chemically modify the proteins studied. This approach could be of interest for more broadly characterizing nearest crowded neighbor effects (i.e., protein-protein interactions) for multiprotein systems (i.e., more than just two), thus making it an interesting tool for studying very complex systems, such as those found in nature.

Macromolecular Crowding Effect on Chitosan-Hyaluronic Acid Complexation and the Activity of Encapsulated Catalase

The associative phase separation of charged biomacromolecules plays a key role in many biophysical events that take place in crowded intracellular environments. Such natural polyelectrolyte complexation and phase separation often occur at nonstoichiometric charge ratios with the incorporation of bioactive proteins, which is not studied as extensively as those complexations at stoichiometric ratios. In this work, we investigated how the addition of a crowding agent (polyethylene glycol, PEG) affected the complexation between chitosan (CS) and hyaluronic acid (HA), especially at nonstoichiometric ratios, and the encapsulation of enzyme (catalase, CAT) by the colloidal complexes. The crowded environment promoted colloidal phase separation at low charge ratios, forming complexes with increased colloidal and dissolution stability, which resulted in a smaller size and polydispersity (PDI). The binding isotherms revealed that the addition of PEG greatly enhanced the ion-pairing strength (with increased ion-pairing equilibrium constant Ka from 4.92 × 104 without PEG to 1.08 × 106 with 200 g/L PEG) and switched the coacervation from endothermic to exothermic, which explained the promoted complexation and phase separation. At the stoichiometric charge ratio, the enhanced CS-HA interaction in crowded media generated a more solid-like coacervate phase with a denser network, slower chain relaxation, and higher modulus. Moreover, both crowding and complex encapsulation enhanced the activity and catalytic efficiency of CAT, represented by a 2-fold increase in catalytic efficiency (Kcat/Km) under 100 g/L PEG crowding and CS-HA complex encapsulation. This is likely due to the lower polarity in the microenvironment surrounding the enzyme molecules. By a systematic investigation of both nonstoichiometric and stoichiometric charge ratios under macromolecular crowding, this work provided new insights into the complexation between natural polyelectrolytes in a scenario closer to an intracellular environment.

Enzyme stability in polymer hydrogel-enzyme hybrid nanocarrier containing phosphorylcholine group

Enzymes are biological catalysts with good biocompatibility and high efficiency and have been widely used in many fields, such as wastewater treatment, biosensors, and the medical industry. However, their inherently low stability under conditions of practical use limits further applications. Zwitterionic polymers possessing a pair of oppositely charged groups in their repeating units can increase protein stability because of their good biocompatibility and high water content. In this study, zwitterionic copolymer nanogels comprising poly(2-methacryloyloxyethyl phosphorylcholine (MPC)-co-methacrylic acid-N-hydroxy succinimide ester (MNHS)) (PMS) were synthesized via reversible addition-fragmentation chain-transfer polymerization (RAFT). β-Galactosidase (β-gal) was post-modified within zwitterionic polymer nanogels with a covalently-bound spacer and the activity was compared with that of directly immobilized β-gal and free β-gal. Compared with direct immobilization, covalent immobilization with a spacer could reduce the structural change of β-gal, as confirmed by the circular dichroism spectra. Although the activity of β-gal decreased after immobilization, the hybrids of the β-gal immobilized nanogels, termed hybrid nanogel-enzymes, demonstrated superior stability compared to the free enzymes. The hybrid nanogel-enzymes maintained their function against inactivation by organic solvents and proteinases owing to their high water content, anti-biofouling properties, and limited mass transfer. They can also withstand protein aggregation at high temperatures and maintain their activity. Compared to direct immobilization, immobilization with a spacer resulted in a dramatic increase in the enzyme activity and a slight decrease in the stability. These results indicate that polymer nanogels containing phosphorylcholine units are promising materials for enzyme immobilization, expanding the scope of enzyme applications.

Effects of osmolytes under crowding conditions on the properties of muscle glycogen phosphorylase b

The study of the relationship between the activity and stability of enzymes under crowding conditions in the presence of osmolytes is important for understanding the functioning of a living cell. The effect of osmolytes (trehalose and betaine) on the secondary and tertiary structure and activity of muscle glycogen phosphorylase b (Phb) under crowding conditions created by PEG 2000 and PEG 20000 was investigated using dynamic light scattering, differential scanning calorimetry, circular dichroism spectroscopy, fluorimetry and enzymatic activity assay. At 25 °C PEGs increased Phb activity, but PEG 20000 to a greater extent. Wherein, PEG 20000 significantly destabilized its tertiary and secondary structure, in contrast to PEG 2000. Trehalose removed the effects of PEGs on Phb, while betaine significantly reduced the activating effect of PEG 20000 without affecting the action of PEG 2000. Under heat stress at 48 °C, the protective effect of osmolytes under crowding conditions was more pronounced than at room temperature, and the Phb activity in the presence of osmolytes was higher in these conditions than in diluted solutions. These results provide important insights into the complex mechanism, by which osmolytes affect the structure and activity of Phb under crowding conditions.

Fluorescent protein lifetimes report densities and phases of nuclear condensates during embryonic stem-cell differentiation

Fluorescent proteins (FP) are frequently used for studying proteins inside cells. In advanced fluorescence microscopy, FPs can report on additional intracellular variables. One variable is the local density near FPs, which can be useful in studying densities within cellular bio-condensates. Here, we show that a reduction in fluorescence lifetimes of common monomeric FPs reports increased levels of local densities. We demonstrate the use of this fluorescence-based variable to report the distribution of local densities within heterochromatin protein 1α (HP1α) in mouse embryonic stem cells (ESCs), before and after early differentiation. We find that local densities within HP1α condensates in pluripotent ESCs are heterogeneous and cannot be explained by a single liquid phase. Early differentiation, however, induces a change towards a more homogeneous distribution of local densities, which can be explained as a liquid-like phase. In conclusion, we provide a fluorescence-based method to report increased local densities and apply it to distinguish between homogeneous and heterogeneous local densities within bio-condensates.

Carbonic Anhydrase Enhanced UV-Crosslinked PEG-DA/PEO Extruded Hydrogel Flexible Filaments and Durable Grids for CO2 Capture

In this study, poly (ethylene glycol) diacrylate/poly (ethylene oxide) (PEG-DA/PEO) interpenetrating polymer network hydrogels (IPNH) were extruded into 1D filaments and 2D grids. The suitability of this system for enzyme immobilization and CO₂ capture application was validated. IPNH chemical composition was verified spectroscopically using FTIR. The extruded filament had an average tensile strength of 6.5 MPa and elongation at break of 80%. IPNH filament can be twisted and bent and therefore is suitable for further processing using conventional textile fabrication methods. Initial activity recovery of the entrapped carbonic anhydrase (CA) calculated from esterase activity, showed a decrease with an increase in enzyme dose, while activity retention of high enzyme dose samples was over 87% after 150 days of repeated washing and testing. IPNH 2D grids that were assembled into spiral roll structured packings exhibited increased CO₂ capture efficiency with increasing enzyme dose. Long-term CO₂ capture performance of the CA immobilized IPNH structured packing was tested in a continuous solvent recirculation experiment for 1032 h, where 52% of the initial CO₂ capture performance and 34% of the enzyme contribution were retained. These results demonstrate the feasibility of using rapid UV-crosslinking to form enzyme-immobilized hydrogels by a geometrically-controllable extrusion process that uses analogous linear polymers for both viscosity enhancement and chain entanglement purposes, and achieves high activity retention and performance stability of the immobilized CA. Potential uses for this system extend to 3D printing inks and enzyme immobilization matrices for such diverse applications as biocatalytic reactors and biosensor fabrication.

Resolving the enthalpy of protein stabilization by macromolecular crowding

Proteins in the cellular milieu reside in environments crowded by macromolecules and other solutes. Although crowding can significantly impact the protein folded state stability, most experiments are conducted in dilute buffered solutions. To resolve the effect of crowding on protein stability, we use 19 F nuclear magnetic resonance spectroscopy to follow the reversible, two-state unfolding thermodynamics of the N-terminal Src homology 3 domain of the Drosophila signal transduction protein drk in the presence of polyethylene glycols (PEGs) of various molecular weights and concentrations. Contrary to most current theories of crowding that emphasize steric protein-crowder interactions as the main driving force for entropically favored stabilization, our experiments show that PEG stabilization is accompanied by significant heat release, and entropy disfavors folding. Using our newly developed model, we find that stabilization by ethylene glycol and small PEGs is driven by favorable binding to the folded state. In contrast, for larger PEGs, chemical or soft PEG-protein interactions do not play a significant role. Instead, folding is favored by excluded volume PEG-protein interactions and an exothermic nonideal mixing contribution from release of confined PEG and water upon folding. Our results indicate that crowding acts through molecular interactions subtler than previously assumed and that interactions between solution components with both the folded and unfolded states must be carefully considered.

Atomistic Simulation of Lysozyme in Solutions Crowded by Tetraethylene Glycol: Force Field Dependence

The behavior of biomolecules in crowded environments remains largely unknown due to the accuracy of simulation models and the limited experimental data for comparison. Here we chose a small crowder of tetraethylene glycol (PEG-4) to investigate the self-crowding of PEG-4 solutions and molecular crowding effects on the structure and diffusion of lysozyme at varied concentrations from dilute water to pure PEG-4 liquid. Two Amber-like force fields of Amber14SB and a99SB-disp were examined with TIP3P (fast diffusivity and low viscosity) and a99SB-disp (slow diffusivity and high viscosity) water models, respectively. Compared to the Amber14SB protein simulations, the a99SB-disp model yields more coordinated water and less PEG-4 molecules, less intramolecular hydrogen bonds (HBs), more protein-water HBs, and less protein-PEG HBs as well as stronger interactions and more hydrophilic and less hydrophobic contacts with solvent molecules. The a99SB-disp model offers comparable protein-solvent interactions in concentrated PEG-4 solutions to that in pure water. The PEG-4 crowding leads to a slow-down in the diffusivity of water, PEG-4, and protein, and the decline in the diffusion from atomistic simulations is close to or faster than the hard sphere model that neglects attractive interactions. Despite these differences, the overall structure of lysozyme appears to be maintained well at different PEG-4 concentrations for both force fields, except a slightly large deviation at 370 K at low concentrations with the a99SB-disp model. This is mainly attributed to the strong intramolecular interactions of the protein in the Amber14SB force field and to the large viscosity of the a99SB-disp water model. The results indicate that the protein force fields and the viscosity of crowder solutions affect the simulation of biomolecules under crowding conditions.