Macromolecular Crowding Enhances Catalytic Efficiency and Stability of α-Amylase

On the behavior of Hoechst 33258 in DNA-PEG mixtures

Most of the studies on the interaction of fluorescent dyes with DNA have been performed under conditions radically different from those occurring in situ. Among others, this includes diluteness of experimental solutions, their homogeneity, and presence of a large amount of free water. To a certain extent, some model systems can help to approach the biological conditions. Thus, since some features of liquid-crystalline-like packaging of DNA were found in a number of living systems, to shed light on the behavior of Hoechst 33258 in biological-like conditions, we performed a detailed study of its properties in DNA-PEG mixtures, and, in particular, in the dispersed mesophases formed via polymer and salt induced (psi-) condensation. Being in complex with DNA, Hoechst 33258 shows a high sensitivity to the changes in osmotic conditions - the addition of PEG leads to a release of the dye molecules. However, this effect nonlinearly depends on osmolality. Individually, neither PEG nor NaCl at the studied concentrations significantly affect its complex with nucleic acid. The effect is caused precisely by their synergistic action. In cases of the dispersed systems formation, significant fraction of Hoechst 33258 molecules is retained within the resulting particles and is protected even from further increase in osmolality. This is partly due to competition between the processes of the dye releasing and formation of the dispersed particles.

The effect of konjac glucomannan on enzyme kinetics and fluorescence spectrometry of digestive enzymes: An in vitro research from the perspective of macromolecule crowding

Konjac glucomannan (KGM) can significantly prolong gastrointestinal digestion. However, it is still worth investigating whether the macromolecular crowding (MMC) induced by KGM is correlated with digestion. In this paper, the MMC effect was quantified by fluorescence resonance energy transfer and microrheology, and the digests of starch, protein, and oil were determined. The digestive enzymes were analyzed by enzyme reaction kinetic and fluorescence quenching. The results showed that higher molecular weight (604.85 ∼ 1002.21 kDa) KGM created a larger MMC (>0.8), and influenced the digestion of macronutrients; the digests of starch, protein, and oil all decreased significantly. MMC induced by KGM decreased the Michaelis-Menten constants (Km and Vmax) of pancreatic α-amylase (PPA), pepsin (PEP), and pancreatic lipase (PPL). The larger MMC (>0.8) induced by KGM resulted in the decrease of fluorescence quenching constants (Ksv) in PPA and PPL, and the increase of Ksv in PEP. Therefore, varying degrees of MMC induced by KGM could play a role in regulating digestion and the inhibitory effect on digestion was more significant in a relatively more crowded environment induced by KGM. This study provides theoretical support for the strategies of nutrient digestion regulation from the perspective of MMC caused by dietary fiber.

Sodium caseinate medium promotes the in vitro digestion of starch: An insight into the macromolecular crowding effect

The macromolecular crowding effects of polysaccharides can alter the activity of digestive enzymes; however, whether protein crowding affects the digestive properties of starch remains unknown. Herein, the interaction of sodium caseinate (NaCas) with starch and pig pancreas α-amylase (PPA) and their effects on enzyme activity and starch digestion were studied. NaCas delayed gelatinization and reduced the leaching amount of amylose and increased the relative content of easily digestible starch. The ratio of the ordered structure (α-helix and β-sheet) to disordered structure (β-turns) of PPA increased with NaCas concentration, indicating that NaCas maintained the conformational stability of the enzyme and thereby accelerated the rate of enzymatic hydrolysis. This study demonstrates the detailed mechanism of NaCas-induced enhancement of starch digestibility and suggests a nonnegligible macromolecular crowding effect should be considered when evaluating the function of food macromolecules.

Understanding the Impacts of Molecular and Macromolecular Crowding Agents on Protein-Polymer Complex Coacervates

Complex coacervation refers to the liquid-liquid phase separation (LLPS) process occurring between charged macromolecules. The study of complex coacervation is of great interest due to its implications in the formation of membraneless organelles (MLOs) in living cells. However, the impacts of the crowded intracellular environment on the behavior and interactions of biomolecules involved in MLO formation are not fully understood. To address this knowledge gap, we investigated the effects of crowding on a model protein-polymer complex coacervate system. Specifically, we examined the influence of sucrose as a molecular crowder and polyethylene glycol (PEG) as a macromolecular crowder. Our results reveal that the presence of crowders led to the formation of larger coacervate droplets that remained stable over a 25-day period. While sucrose had a minimal effect on the physical properties of the coacervates, PEG led to the formation of coacervates with distinct characteristics, including higher density, increased protein and polymer content, and a more compact internal structure. These differences in coacervate properties can be attributed to the effects of crowders on individual macromolecules, such as the conformation of model polymers, and nonspecific interactions among model protein molecules. Moreover, our results show that sucrose and PEG have different partition behaviors: sucrose was present in both the coacervate and dilute phases, while PEG was observed to be excluded from the coacervate phase. Collectively, our findings provide insights into the understanding of crowding effects on complex coacervation, shedding light on the formation and properties of coacervates in the context of MLOs.

Crowding-induced morphological changes in synthetic lipid vesicles determined using smFRET

Lipid vesicles are valuable mesoscale molecular confinement vessels for studying membrane mechanics and lipid-protein interactions, and they have found utility among bio-inspired technologies, including drug delivery vehicles. While vesicle morphology can be modified by changing the lipid composition and introducing fusion or pore-forming proteins and detergents, the influence of extramembrane crowding on vesicle morphology has remained under-explored owing to a lack of experimental tools capable of capturing morphological changes on the nanoscale. Here, we use biocompatible polymers to simulate molecular crowding in vitro, and through combinations of FRET spectroscopy, lifetime analysis, dynamic light scattering, and single-vesicle imaging, we characterize how crowding regulates vesicle morphology. We show that both freely diffusing and surface-tethered vesicles fluorescently tagged with the DiI and DiD FRET pair undergo compaction in response to modest concentrations of sorbitol, polyethylene glycol, and Ficoll. A striking observation is that sorbitol results in irreversible compaction, whereas the influence of high molecular weight PEG-based crowders was found to be reversible. Regulation of molecular crowding allows for precise control of the vesicle architecture in vitro, with vast implications for drug delivery and vesicle trafficking systems. Furthermore, our observations of vesicle compaction may also serve to act as a mechanosensitive readout of extramembrane crowding.

Particle-Based Simulation Reveals Macromolecular Crowding Effects on the Michaelis-Menten Mechanism

Many computational models for analyzing and predicting cell physiology rely on in vitro data collected in dilute and controlled buffer solutions. However, this can mislead models because up to 40% of the intracellular volume—depending on the organism, the physiology, and the cellular compartment—is occupied by a dense mixture of proteins, lipids, polysaccharides, RNA, and DNA. These intracellular macromolecules interfere with the interactions of enzymes and their reactants and thus affect the kinetics of biochemical reactions, making in vivo reactions considerably more complex than the in vitro data indicates. In this work, we present a new, to our knowledge, type of kinetics that captures and quantifies the effect of volume exclusion and other spatial phenomena on the kinetics of elementary reactions. We further developed a framework that allows for the efficient parameterization of these kinetics using particle simulations. Our formulation, entitled generalized elementary kinetics, can be used to analyze and predict the effect of intracellular crowding on enzymatic reactions and was herein applied to investigate the influence of crowding on phosphoglycerate mutase in Escherichia coli, which exhibits prototypical reversible Michaelis-Menten kinetics. Current research indicates that many enzymes are reaction limited and not diffusion limited, and our results suggest that the influence of fractal diffusion is minimal for these reaction-limited enzymes. Instead, increased association rates and decreased dissociation rates lead to a strong decrease in the effective maximal velocities V_max and the effective Michaelis-Menten constants K_M under physiologically relevant volume occupancies. Finally, the effects of crowding were explored in the context of a linear pathway, with the finding that crowding can have a redistributing effect on the effective flux responses in the case of twofold enzyme overexpression. We suggest that this framework, in combination with detailed kinetics models, will improve our understanding of enzyme reaction networks under nonideal conditions.

Large cosolutes, small cosolutes, and dihydrofolate reductase activity

Protein enzymes are the main catalysts in the crowded and complex cellular interior, but their activity is almost always studied in dilute buffered solutions. Studies that attempt to recreate the cellular interior in vitro often utilize synthetic polymers as crowding agents. Here, we report the effects of the synthetic polymer cosolutes Ficoll, dextran, and polyvinylpyrrolidone, and their respective monomers, sucrose, glucose, and 1-ethyl-2-pyrrolidone, on the activity of the 18-kDa monomeric enzyme, Escherichia coli dihydrofolate reductase. At low concentrations, reductase activity increases relative to buffer and monomers, suggesting a macromolecular effect. However, the effect decreases at higher concentrations, approaching, and, in some cases, falling below buffer values. We also assessed activity in terms of volume occupancy, viscosity, and the overlap concentration (where polymers form an interwoven mesh). The trends vary with polymer family, but changes in activity are within threefold of buffer values. We also compiled and analyzed results from previous studies and conclude that alterations of steady-state enzyme kinetics in solutions crowded with synthetic polymers are idiosyncratic with respect to the crowding agent and enzyme.

Measuring macromolecular crowding in cells through fluorescence anisotropy imaging with an AIE fluorogen

We report a new strategy that allows spatiotemporal visualization of the macromolecular crowding effect in cells.

β-galactosidase stability at high substrate concentrations

Enzymatic synthesis of galacto-oligosaccharides is usually performed at high initial substrate concentrations since higher yields are obtained. We report here on the stability of β-galactosidase from Bacillus circulans at 25, 40, and 60°C in buffer, and in systems with initially 5.0 and 30% (w/w) lactose. In buffer, the half-life time was 220 h and 13 h at 25 and 40°C, respectively, whereas the enzyme was completely inactivated after two hours at 60°C. In systems with 5.0 and 30% (w/w) lactose, a mechanistic model was used to correct the oNPG converting activity for the presence of lactose, glucose, galactose, and oligosaccharides in the activity assay. Without correction, the stability at 5.0% (w/w) lactose was overestimated, while the stability at 30% (w/w) lactose was underestimated. The inactivation constant k d was strongly dependent on temperature in buffer, whereas only a slight increase in k d was found with temperature at high substrate concentrations. The enzyme stability was found to increase strongly with the initial substrate concentrations. The inactivation energy E a appeared to be lower at high initial substrate concentrations.

Effects of carbohydrates on the oNPG converting activity of β-galactosidases

The effects of high concentrations of carbohydrates on the o-nitrophenyl β-d-galactopyranoside (oNPG) converting activity of β-galactosidase from Bacillus circulans are studied to get a better understanding of the enzyme behavior in concentrated and complicated systems in which enzymatic synthesis of galacto-oligosaccharides is usually performed. The components that were tested were glucose, galactose, lactose, sucrose, trehalose, raffinose, Vivinal GOS, dextran-6000, dextran-70,000, and sarcosine. Small carbohydrates act as acceptors in the reaction. This speeds up the limiting step, which is binding of the galactose residue with the acceptor and release of the product. Simultaneously, both inert and reacting additives seem to cause some molecular crowding, which results in a higher enzyme affinity for the substrate. The effect of molecular crowding on the enzyme activity is small compared to the effect of carbohydrates acting in the reactions as acceptors. The effects of reactants on β-galactosidases from B. circulans, A. oryzae, and K. lactis are compared.