Combined co-solvent and pressure effect on kinetics of a peptide hydrolysis: an activity-based approach

Effects of Crowding and Cosolutes on Biomolecular Function at Extreme Environmental Conditions

The extent of the effect of cellular crowding and cosolutes on the functioning of proteins and cells is manifold and includes the stabilization of the biomolecular systems, the excluded volume effect, and the modulation of molecular dynamics. Simultaneously, it is becoming increasingly clear how important it is to take the environment into account if we are to shed light on biological function under various external conditions. Many biosystems thrive under extreme conditions, including the deep sea and subseafloor crust, and can take advantage of some of the effects of crowding. These relationships have been studied in recent years using various biophysical techniques, including neutron and X-ray scattering, calorimetry, FTIR, UV-vis and fluorescence spectroscopies. Combining knowledge of the structure and conformational dynamics of biomolecules under extreme conditions, such as temperature, high hydrostatic pressure, and high salinity, we highlight the importance of considering all results in the context of the environment. Here we discuss crowding and cosolute effects on proteins, nucleic acids, membranes, and live cells and explain how it is possible to experimentally separate crowding-induced effects from other influences. Such findings will contribute to a better understanding of the homeoviscous adaptation of organisms and the limits of life in general.

Life in Multi-Extreme Environments: Brines, Osmotic and Hydrostatic Pressure─A Physicochemical View

Elucidating the details of the formation, stability, interactions, and reactivity of biomolecular systems under extreme environmental conditions, including high salt concentrations in brines and high osmotic and high hydrostatic pressures, is of fundamental biological, astrobiological, and biotechnological importance. Bacteria and archaea are able to survive in the deep ocean or subsurface of Earth, where pressures of up to 1 kbar are reached. The deep subsurface of Mars may host high concentrations of ions in brines, such as perchlorates, but we know little about how these conditions and the resulting osmotic stress conditions would affect the habitability of such environments for cellular life. We discuss the combined effects of osmotic (salts, organic cosolvents) and hydrostatic pressures on the structure, stability, and reactivity of biomolecular systems, including membranes, proteins, and nucleic acids. To this end, a variety of biophysical techniques have been applied, including calorimetry, UV/vis, FTIR and fluorescence spectroscopy, and neutron and X-ray scattering, in conjunction with high pressure techniques. Knowledge of these effects is essential to our understanding of life exposed to such harsh conditions, and of the physical limits of life in general. Finally, we discuss strategies that not only help us understand the adaptive mechanisms of organisms that thrive in such harsh geological settings but could also have important ramifications in biotechnological and pharmaceutical applications.

Extremophilic behavior of catalytic amyloids sustained by backbone structuring

Enzyme function relies on the placement of chemistry defined by solvent and self-associative hydrogen bonding displayed by the protein backbone. Amyloids, long-range multi-peptide and -protein materials, can mimic enzyme functions while having a high proportion of stable self-associative backbone hydrogen bonds. Though catalytic amyloid structures have exhibited a degree of temperature and solvent stability, defining their full extremophilic properties and the molecular basis for such extreme activity has yet to be realized. Here we demonstrate that, like thermophilic enzymes, catalytic amyloid activity persists across high temperatures with an optimum activity at 81 °C where they are 30-fold more active than at room temperature. Unlike thermophilic enzymes, catalytic amyloids retain both activity and structure well above 100 °C as well as in the presence of co-solvents. Changes in backbone vibrational states are resolved in situ using non-linear 2D infrared spectroscopy (2DIR) to reveal that activity is sustained by reorganized backbone hydrogen bonds in extreme environments, evidenced by an emergent vibrational mode centered at 1612 cm^-1. Restructuring also occurs in organic solvents, and facilitates complete retention of hydrolysis activity in co-solvents of lesser polarity. We support these findings with molecular modeling, where the displacement of water by co-solvents leads to shorter, less competitive, bonding lifetimes that further stabilize self-associative backbone interactions. Our work defines amyloid properties that counter classical proteins, where extreme environments induce mechanisms of restructuring to support enzyme-like functions necessary for synthetic applications.

Assessing the Influence of Betaine-Based Natural Deep Eutectic Systems on Horseradish Peroxidase

To validate the use of horseradish peroxidase (HRP) in natural deep eutectic systems (NADES), five different betaine-based NADES were characterized in terms of water content, water activity, density, and viscosity experimentally and by thermodynamic modeling. The results show that the NADES under study have a water activity of about 0.4 at 37 °C for water contents between 14 and 22 wt %. The densities of the studied NADES had values between 1.2 and 1.3 g^.cm^-3 at 20 °C. The density was modeled with a state-of-the-art equation of state; an excellent agreement with the experimental density data was achieved, allowing reasonable predictions for water activities. The system betaine:glycerol (1:2) was found to be the most viscous with a dynamic viscosity of ∼600 mPa^.s at 40 °C, while all the other systems had viscosities <350 mPa^.s at 40 °C. The impact of the NADES on the enzymatic activity, as well as on, conformational and thermal stability was assessed. The system betaine/sorbitol:water (1:1:3) showed the highest benefit for enzymatic activity, increasing it by two-folds. Moreover, upon NADES addition, thermal stability was increased followed by an increment in a-helix secondary structure content.

Make or break: the thermodynamic equilibrium of polyphosphate kinase-catalysed reactions

Polyphosphate kinases (PPKs) have become popular biocatalysts for nucleotide 5'-triphosphate (NTP) synthesis and regeneration. Two unrelated families are described: PPK1 and PPK2. They are structurally unrelated and use different catalytic mechanisms. PPK1 enzymes prefer the usage of adenosine 5'-triphosphate (ATP) for polyphosphate (polyP) synthesis while PPK2 enzymes favour the reverse reaction. With the emerging use of PPK enzymes in biosynthesis, a deeper understanding of the enzymes and their thermodynamic reaction course is of need, especially in comparison to other kinases. Here, we tested four PPKs from different organisms under the same conditions without any coupling reactions. In comparison to other kinases using phosphate donors with comparably higher phosphate transfer potentials that are characterised by reaction yields close to full conversion, the PPK-catalysed reaction reaches an equilibrium in which about 30% ADP is left. These results were obtained for PPK1 and PPK2 enzymes, and are supported by theoretical data on the basic reaction. At high concentrations of substrate, the different kinetic preferences of PPK1 and PPK2 can be observed. The implications of these results for the application of PPKs in chemical synthesis and as enzymes for ATP regeneration systems are discussed.

Boosting the kinetic efficiency of formate dehydrogenase by combining the effects of temperature, high pressure and co-solvent mixtures

The application of co-solvents and high pressure has been shown to be an efficient means to modify the kinetics of enzyme-catalyzed reactions without compromising enzyme stability, which is often limited by temperature modulation. In this work, the high-pressure stopped-flow methodology was applied in conjunction with fast UV/Vis detection to investigate kinetic parameters of formate dehydrogenase reaction (FDH), which is used in biotechnology for cofactor recycling systems. Complementary FTIR spectroscopic and differential scanning fluorimetric studies were performed to reveal pressure and temperature effects on the structure and stability of the FDH. In neat buffer solution, the kinetic efficiency increases by one order of magnitude by increasing the temperature from 25° to 45 °C and the pressure from ambient up to the kbar range. The addition of particular co-solvents further doubled the kinetic efficiency of the reaction, in particular the compatible osmolyte trimethylamine-N-oxide and its mixtures with the macromolecular crowding agent dextran. The thermodynamic model PC-SAFT was successfully applied within a simplified activity-based Michaelis-Menten framework to predict the effects of co-solvents on the kinetic efficiency by accounting for interactions involving substrate, co-solvent, water, and FDH. Especially mixtures of the co-solvents at high concentrations were beneficial for the kinetic efficiency and for the unfolding temperature.

Thermodynamics and Kinetics of Glycolytic Reactions. Part I: Kinetic Modeling Based on Irreversible Thermodynamics and Validation by Calorimetry

In systems biology, material balances, kinetic models, and thermodynamic boundary conditions are increasingly used for metabolic network analysis. It is remarkable that the reversibility of enzyme-catalyzed reactions and the influence of cytosolic conditions are often neglected in kinetic models. In fact, enzyme-catalyzed reactions in numerous metabolic pathways such as in glycolysis are often reversible, i.e., they only proceed until an equilibrium state is reached and not until the substrate is completely consumed. Here, we propose the use of irreversible thermodynamics to describe the kinetic approximation to the equilibrium state in a consistent way with very few adjustable parameters. Using a flux-force approach allowed describing the influence of cytosolic conditions on the kinetics by only one single parameter. The approach was applied to reaction steps 2 and 9 of glycolysis (i.e., the phosphoglucose isomerase reaction from glucose 6-phosphate to fructose 6-phosphate and the enolase-catalyzed reaction from 2-phosphoglycerate to phosphoenolpyruvate and water). The temperature dependence of the kinetic parameter fulfills the Arrhenius relation and the derived activation energies are plausible. All the data obtained in this work were measured efficiently and accurately by means of isothermal titration calorimetry (ITC). The combination of calorimetric monitoring with simple flux-force relations has the potential for adequate consideration of cytosolic conditions in a simple manner.

High pressures increase α-chymotrypsin enzyme activity under perchlorate stress

Deep subsurface environments can harbour high concentrations of dissolved ions, yet we know little about how this shapes the conditions for life. We know even less about how the combined effects of high pressure influence the way in which ions constrain the possibilities for life. One such ion is perchlorate, which is found in extreme environments on Earth and pervasively on Mars. We investigated the interactions of high pressure and high perchlorate concentrations on enzymatic activity. We demonstrate that high pressures increase α-chymotrypsin enzyme activity even in the presence of high perchlorate concentrations. Perchlorate salts were shown to shift the folded α-chymotrypsin phase space to lower temperatures and pressures. The results presented here may suggest that high pressures increase the habitability of environments under perchlorate stress. Therefore, deep subsurface environments that combine these stressors, potentially including the subsurface of Mars, may be more habitable than previously thought.

Gault et al. show that high pressures increase α-chymotrypsin enzyme activity in the presence of high perchlorate concentrations. These perchlorate salts shift the folded enzyme phase space to lower temperatures and pressure and may move the optimum enzyme activity towards lower temperatures in addition to higher pressures, which has implications for Martian habitability.

Modulation of enzymatic activity by aqueous two-phase systems and pressure – rivalry between kinetic constants

Both, pressure and aqueous two-phase systems are able to modulate the kinetic parameters of enzymatic reactions.

The multifaceted effects of DMSO and high hydrostatic pressure on the kinetic constants of hydrolysis reactions catalyzed by α-chymotrypsin

The cosolvent DMSO and high pressure have antagonistic effects on the kinetic constants of α-chymotrypsin-catalyzed hydrolysis reactions.

Monitoring the changes in low molecular weight carbohydrates in cocoa beans during spontaneous fermentation: A chemometric and kinetic approach

The low molecular weight carbohydrate (LMWC) profile has recently been investigated, showing considerable changes between fermented and unfermented cocoa beans. These differences are a consequence of the fermentation process, which is considered a crucial step in chocolate production. During fermentation, LMWC are involved in Maillard reaction, a crucial reaction for the development of aroma and taste precursors. However, there is a lack of information related to LMWC changes and of contextualization with changes in other physicochemical parameters (pH and dry matter) during spontaneous fermentation. The different approaches employed in this manuscript have allowed the identification of a sequential degradation of tetra-, tri- and disaccharides, as well as an increase in the monosaccharide content during fermentation. Moreover, a correlation was determined between some LMWC and physicochemical parameters. Besides that, the chemometric approach identified the fermentation period ranging between 48 and 96 h as determinant to produce noticeable changes in unfermented beans based on the indicators evaluated. Furthermore, different kinetic parameteres (reaction order, observed reaction rates (k_obs) and half-life values (t_1/2)) of different LMWC were determined, showing differences between them. The results showed in this manuscript provide unprecedented mechanistic details of spontaneous cocoa fermentation.