Pressure-temperature phase diagrams of biomolecules

Thermally optimized subcritical water hydrolysis for green extraction of bioactive compounds from sea cucumber Stichopus japonicus

This study investigated the bioactive compounds in Stichopus japonicus extracts obtained using subcritical water hydrolysis (SWH) at nine temperatures (115 °C-235 °C at 15 °C intervals). Increasing temperature enhanced the extraction efficiency and decreased the average molecular weight, extracts had abundant amino acids and phenolic compounds. Maximum protein (832.66 ± 15.00 mg BSA/g) and polysachchrides (32.02 ± 0.88 mg glucose/g) contents were achieved at 175 °C, while the highest phenolic content (23.93 ± 0.16 mg GAE/g) and antioxidant activity were observed at 220 °C. The highest α-amylase (18.62 % ± 1.17 %) and α-glucosidase (24.31 % ± 1.43 %) activities were observed at 115 °C. However, there was no significant trend between temperature and anti-inflammatory or anticholesterol activities. GC-MS analysis confirmed the presence of bioactive compounds with antioxidant, anti-inflammatory, antidiabetic, and anticholesterol potential. In conclusion, our results indicate that SWH is a sustainable approach for extracting bioactive compounds from S. japonicus, with promising applications in functional foods and therapeutics.

Understanding the Relationship between Pressure and Temperature Unfolding of Proteins

Proteins unfold under different environmental insults, among which are heat, cold, high pressure, and chaotropic agents. Understanding the mechanisms that determine unfolding under each of these conditions is an important problem that directly relates to the physical forces that determine the three-dimensional structure of a protein. Here, we studied a residue-specific description of the unfolding transitions of marginally stable yeast protein Yfh1 using high-pressure nuclear magnetic resonance. We compared the cold, heat, and pressure unfolded states and demonstrated what has up to now been only a hypothesis: the pressure-unfolded spectrum at room temperature shares features in common with that at low but not at high temperature and room pressure, suggesting a tighter similarity of the mechanisms and a similar role of hydration in these two processes. By exploring the phase diagram of the protein and mapping unfolding onto the three-dimensional structure of the protein, we also show that the pressure-induced unfolding pathways at low and high temperatures differ, suggesting a synergic mechanism between pressure- and temperature-induced denaturation. Our observations help us to reconstruct the structural events determining unfolding and distinguish the mechanisms that rule the different processes of unfolding.

Two-dimensional (P/T) studies of secondary/tertiary conformational dynamics in nucleic acids: pressure induced melting and Maxwell relations at the single molecule level

A predictive understanding of conformational folding of nucleic acids depends crucially on the underlying competition between enthalpic and entropic contributions to overall free energy changes. In extreme environments (e.g. deep ocean vents), such free energy changes are in turn impacted by both pressure and temperature as strongly coupled intensive variables, emphasizing the importance of a detailed molecular level understanding of the underlying thermodynamics. In this work, single-molecule fluorescence energy resonance transfer (smFRET) microscopy methods are implemented for quantitative kinetic study of secondary structure (i.e., DNA hybridization) and tertiary structure (i.e., RNA Mn2+ riboswitch folding) equilibria as a function of both pressure (P = 1 to 1000 bar) and temperature (T = 21 to 27 °C). Temperature dependent studies at a series of fixed pressures reveal the single molecule DNA and RNA constructs to be stabilized and destabilized, respectively, with increasing T. Interestingly, results for the Mn2+ riboswitch indicate a positive entropy change (ΔS > 0) for achieving the native tertiary conformation at all external pressures. This is contrary to more common physical expectations of increased order and thus an entropically penalty for tertiary folding of the RNA. On the other hand, pressure dependent scans for a series of constant temperature conditions confirm that both the DNA hairpin and RNA riboswitch constructs destabilize ("melt") under increasing pressure, which by van't Hoff analysis implies a positive volume change (ΔV0 > 0) for both secondary and tertiary folding into the native state. Furthermore, slices through these two-dimensional free energy surfaces permit parameters for isobaric thermal expansion in both secondary and tertiary conformational folding coordinates to be extracted. Finally, experimental control of multiple variables allows determination of the folding free energies as a two-dimensional function of pressure and temperature (ΔG(P, T)). To the best of our knowledge, this facilitates a first experimental confirmation of the underlying Maxwell relation (∂ΔS/∂P)T = -(∂ΔV/∂T)P for the exact free energy differential dG(P, V, S, T) at the single molecule level.

Effects of pressure on the survival and viability of cancer cells in vitro: An analytical study

Intense cancer research is underway to discover possible therapies but no major breakthrough appears to be in sight in terms of its cure when diagnosed late. The cytostatic and growth inhibitory effect of high pressure on cells is well documented. In the present study, two cancer cell lines viz. MDA-MB-231 (breast carcinoma) and A549 (lung carcinoma) and one normal cell line (Vero) were subjected to increased pressure of 18 psi in a specially constructed pressure chamber. It was found that a pressure of 18 psi induced a significant change in the growth parameters of both cancer cell lines versus normal cells. Exposure to increased pressure greatly increased the proportion of MDA-MB-231 cells in the S phase while concurrently reducing the number of cells in the G0/G1 phase as compared to their untreated counterparts. SEM and AFM analysis revealed presence of characteristic 'pores' and 'pits' on the cell surface of pressure-treated versus untreated cancer cells. TEM analysis also revealed significant intracellular differences between pressure-treated and untreated cancer cells. Hyperbaric nitrogen therapy is proposed as a novel cancer-treatment modality involving administration of N2 at the tumor site in murine models of breast and lung cancer. This would eventually pave the way for development of a device effective treatment strategy for human tumors in future.

Life and death of Yfh1: how cool is cold denaturation

Yeast frataxin (Yfh1) is a small natural protein from yeast that has the unusual property of undergoing cold denaturation at temperatures above the freezing point of water when under conditions of low ionic strength. This peculiarity, together with remarkable resilience, allows the determination, for the whole protein as well as for individual residues, of the stability curve, that is the temperature dependence of the free energy difference between the unfolded and folded forms. The ease of measuring stability curves without the need to add denaturants or introduce ad hoc destabilizing mutations makes this protein an ideal 'tool' for investigating the influence of many environmental factors on protein stability. The present review aims at recapitulating all the open questions that Yfh1 has helped to address, including understanding the differences and commonalities of the cold, heat and pressure unfolded states. This protein thus offers a unique tool for studying aspects of protein stability so far been considered difficult to assess and provides important guidelines that could allow the identification of other similar systems.

Effect of hydrostatic pressure on the supramolecular assembly of surfactant-cyclodextrin inclusion complexes

The supramolecular assembly of simple colloids into complex, hierarchical structures arises from a delicate interplay of short-range directional and isotropic long-range forces. These assemblies are highly sensitive to environmental changes, such as temperature variations and the presence of specific molecules, making them promising candidates for nanomachine design. In this study, we investigate the effect of hydrostatic pressure, up to 1800 bar, on the supramolecular assemblies of cyclodextrin/surfactant complexes. Using small-angle neutron scattering, we demonstrate that while the overall structure of the supramolecular aggregates remains largely stable under pressure, the stiffness of the planar lattice formed by the inclusion complexes, the basic structural unit of the supramolecular assemblies, shows a fourfold increase between 250 and 1000 bar. These findings suggest that high-pressure studies can be exploited to better understand the mechanisms of supramolecular assembly processes, thereby aiding in the design of more robust and functional systems.

Proteome-Wide Assessment of Protein Structural Perturbations Under High Pressure

One of the planet's more understudied ecosystems is the deep biosphere, where organisms can experience high hydrostatic pressures (30-110 MPa); yet, by current estimates, these subsurface and deep ocean zones host the majority of the Earth's microbial and animal life. The extent to which terrestrially relevant pressures up to 100 MPa deform most globular proteins - and which kinds - has not been established. Here, we report the invention of an experimental apparatus that enables structural proteomic methods to be carried out at high pressures for the first time. The method, called high-pressure limited proteolysis (Hi-P LiP), involves performing pulse proteolysis on whole cell extracts brought to high pressure. The resulting sites of proteolytic susceptibility induced by pressure are subsequently read out by sequencing the peptide fragments with tandem liquid chromatography-mass spectrometry. The method sensitively detects pressure-induced structural changes with residue resolution and on whole proteomes, providing a deep and broad view of the effect of pressure on protein structure. When applied to a piezo-sensitive thermophilic bacterium, Thermus thermophilus, we find that ca. 40% of its soluble proteome is structurally perturbed at 100 MPa. Proteins with lower charge density are more resistant to pressure-induced deformation, as expected; however, contrary to expectations, proteins with lower packing density (i.e., more voids) are also more resistant to deformation. Furthermore, high pressure has previously been shown to preferentially alter conformations around active sites. Here, we show this is also observed in Hi-P LiP, suggesting that the method could provide a generic and unbiased modality to detect binding sites on a proteome scale. Hence, datasets of this kind could prove useful for training emerging AI models to predict cryptic binding sites with greater accuracy.

Advances in sample environments for neutron scattering for colloid and interface science

This review describes recent advances in sample environments across the full complement of applicable neutron scattering techniques to colloid and interface science. Temperature, pressure, flow, tensile testing, ultrasound, chemical reactions, IR/visible/UV light, confinement, humidity and electric and magnetic field application, as well as tandem X-ray methods, are all addressed. Consideration for material choices in sample environments and data acquisition methods are also covered as well as discussion of current and potential future use of machine learning and artificial intelligence.

Thermoresponsive Polymers under Pressure with a Focus on Poly(N-isopropylacrylamide) (PNIPAM)

Pressure is a key variable in the phase behavior of responsive polymers, both for applications and from a fundamental point of view. In this feature article, we review recent developments, particularly applications of neutron techniques such as small-angle neutron scattering (SANS) and quasi-elastic neutron scattering (QENS), across the temperature-pressure phase diagram. These are complemented by kinetic SANS experiments following pressure jumps. In the prototype system poly(N-isopropylacrylamide) (PNIPAM), QENS revealed the pressure-dependent characteristics of hydration water around the lower critical solution temperature transition. The size, water content, and inner structure of the mesoglobules formed in the two-phase region depend strongly on pressure, as shown by SANS. Beside these changes at the phase transition, the mesoglobule formation at low pressure is determined by kinetic factors, namely the formation of a polymer-rich, rigid shell, which hampers further growth by coalescence. At high pressure, in contrast, the growth proceeds by diffusion-limited coalescence without any kinetic hindrance. The disintegration of the mesoglobules evolves either via chain release from their surface or via swelling, depending on the osmotic pressure of the water. Moreover, we report on the profound influence of pressure on the cononsolvency effect. In the temperature-pressure frame, the one-phase region is hugely expanded upon the addition of the cosolvent methanol. SANS experiments unveil the enthalpic and entropic contributions to the effective Flory-Huggins interaction parameter between the segments and the solvent mixture. QENS experiments demonstrate an increase in polymer associated water with pressure, whereas methanol is released. Correspondingly, the solvent phase becomes enriched in methanol, providing a mechanism for the breakdown of cononsolvency at a high pressure. Finally, we outline future opportunities for high-pressure studies of thermoresponsive polymers, with a focus on neutron methods.

Behavior of enzymes under high pressure in food processing: mechanisms, applications, and developments

High pressure processing (HPP) offers the benefits of safety, uniformity, energy-efficient, and low waste, which is widely applied for microbial inactivation and shelf-life extension for foods. Over the past forty years, HPP has been extensively researched in the food industry, enabling the inactivation or activation of different enzymes in future food by altering their molecular structure and active site conformation. Such activation or inactivation of enzymes effectively hinders the spoilage of food and the production of beneficial substances, which is crucial for improving food quality. This paper reviews the mechanism in which high pressure affects the stability and activity of enzymes, concludes the roles of key enzymes in the future food processed using high pressure technologies. Moreover, we discuss the application of modified enzymes based on high pressure, providing insights into the future direction of enzyme evolution under complex food processing conditions (e.g. high temperature, high pressure, high shear, and multiple elements). Finally, we conclude with prospects of high pressure technology and research directions in the future. Although HPP has shown positive effects in improving the future food quality, there is still a pressing need to develop new and effective combined processing methods, upgrade processing modes, and promote sustainable lifestyles.

Pressure Tuning Studies of Four-Stranded Nucleic Acid Structures

Four-stranded folded structures, such as G-quadruplexes and i-motifs in the genome, have attracted a growing interest nowadays since they have been discovered in the telomere and in several oncogene promoter regions. Their biological relevance is undeniable since their existence in living cells has been observed. In vivo they take part in the regulation of gene expression, in vitro they are used in the analytical biochemistry. They are attractive and promising targets for cancer therapy. Pressure studies can reveal specific aspects of the molecular processes. Pressure tuning experiments allow the determination of the volumetric parameters of the folded structures and of the folding-unfolding processes. Here, we review the thermodynamic parameters with a special focus on the volumetric ones, which were determined using pressure tuning spectroscopic experiments on the G-quadruplex and i-motif nucleic acid forms.

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.

Effects of External Perturbations on Protein Systems: A Microscopic View

Protein folding can be viewed as the origami engineering of biology resulting from the long process of evolution. Even decades after its recognition, research efforts worldwide focus on demystifying molecular factors that underlie protein structure-function relationships; this is particularly relevant in the era of proteopathic disease. A complex co-occurrence of different physicochemical factors such as temperature, pressure, solvent, cosolvent, macromolecular crowding, confinement, and mutations that represent realistic biological environments are known to modulate the folding process and protein stability in unique ways. In the current review, we have contextually summarized the substantial efforts in unveiling individual effects of these perturbative factors, with major attention toward bottom-up approaches. Moreover, we briefly present some of the biotechnological applications of the insights derived from these studies over various applications including pharmaceuticals, biofuels, cryopreservation, and novel materials. Finally, we conclude by summarizing the challenges in studying the combined effects of multifactorial perturbations in protein folding and refer to complementary advances in experiment and computational techniques that lend insights to the emergent challenges.

Conformational Stability and Denaturation Processes of Proteins Investigated by Electrophoresis under Extreme Conditions

The functional structure of proteins results from marginally stable folded conformations. Reversible unfolding, irreversible denaturation, and deterioration can be caused by chemical and physical agents due to changes in the physicochemical conditions of pH, ionic strength, temperature, pressure, and electric field or due to the presence of a cosolvent that perturbs the delicate balance between stabilizing and destabilizing interactions and eventually induces chemical modifications. For most proteins, denaturation is a complex process involving transient intermediates in several reversible and eventually irreversible steps. Knowledge of protein stability and denaturation processes is mandatory for the development of enzymes as industrial catalysts, biopharmaceuticals, analytical and medical bioreagents, and safe industrial food. Electrophoresis techniques operating under extreme conditions are convenient tools for analyzing unfolding transitions, trapping transient intermediates, and gaining insight into the mechanisms of denaturation processes. Moreover, quantitative analysis of electrophoretic mobility transition curves allows the estimation of the conformational stability of proteins. These approaches include polyacrylamide gel electrophoresis and capillary zone electrophoresis under cold, heat, and hydrostatic pressure and in the presence of non-ionic denaturing agents or stabilizers such as polyols and heavy water. Lastly, after exposure to extremes of physical conditions, electrophoresis under standard conditions provides information on irreversible processes, slow conformational drifts, and slow renaturation processes. The impressive developments of enzyme technology with multiple applications in fine chemistry, biopharmaceutics, and nanomedicine prompted us to revisit the potentialities of these electrophoretic approaches. This feature review is illustrated with published and unpublished results obtained by the authors on cholinesterases and paraoxonase, two physiologically and toxicologically important enzymes.

Conceptual density functional theory under pressure: Part I. XP-PCM method applied to atoms

High pressure chemistry offers the chemical community a range of possibilities to control chemical reactivity, develop new materials and fine-tune chemical properties. Despite the large changes that extreme pressure brings to the table, the field has mainly been restricted to the effects of volume changes and thermodynamics with less attention devoted to electronic effects at the molecular scale. This paper combines the conceptual DFT framework for analyzing chemical reactivity with the XP-PCM method for simulating pressures in the GPa range. Starting from the new derivatives of the energy with respect to external pressure, an electronic atomic volume and an atomic compressibility are found, comparable to their enthalpy analogues, respectively. The corresponding radii correlate well with major known sets of this quantity. The ionization potential and electron affinity are both found to decrease with pressure using two different methods. For the electronegativity and chemical hardness, a decreasing and increasing trend is obtained, respectively, and an electronic volume-based argument is proposed to rationalize the observed periodic trends. The cube of the softness is found to correlate well with the polarizability, both decreasing under pressure, while the interpretation of the electrophilicity becomes ambiguous at extreme pressures. Regarding the electron density, the radial distribution function shows a clear concentration of the electron density towards the inner region of the atom and periodic trends can be found in the density using the Carbó quantum similarity index and the Kullback-Leibler information deficiency. Overall, the extension of the CDFT framework with pressure yields clear periodic patterns.

A High-Pressure, High-Temperature Flow Reactor Simulating the Hadean Earth Environment, with Application to the Pressure Dependence of the Cleavage of Avocado Viroid Hammerhead Ribozyme

The RNA world hypothesis suggests that chemical networks consisting of functional RNA molecules could have constructed a primitive life-like system leading a first living system. The chemical evolution scenario of RNA molecules should be consistent with the Hadean Earth environment. We have demonstrated the importance of the environment at both high temperature and high pressure, using different types of hydrothermal flow reactor systems and high-pressure equipment. In the present study, we have attempted to develop an alternative easy-to-implement method for high-pressure measurements and demonstrate that the system is applicable as an efficient research tool for high-pressure experiments at pressures up to 30 MPa. We demonstrate the usefulness of the system by detecting the high-pressure influence for the self-cleavage of avocado hammerhead ribozyme (ASBVd(−):HHR) at 45–65 °C. A kinetic analysis of the high-pressure behavior of ASBVd(−):HHR shows that the ribozyme is active at 30 MPa and its activity is sensitive to pressures between 0.1–30 MPa. The surprising finding that such a short ribozyme is effective for self-cleavage at a high pressure suggests the importance of pressure as a factor for selection of adaptable RNA molecules towards an RNA-based life-like system in the Hadean Earth environment deep in the ocean.

High-Pressure, Low-Temperature Induced Unfolding and Aggregation of Monoclonal Antibodies: Role of the Fc and Fab Fragments

The effects of high pressure and low temperature on the stability of two different monoclonal antibodies (MAbs) were examined in this work. Fluorescence and small-angle neutron scattering were used to monitor the in situ effects of pressure to infer shifts in tertiary structure and characterize aggregation prone intermediates. Partial unfolding was observed for both MAbs, to different extents, under a range of pressure/temperature conditions. Fourier transform infrared spectroscopy was also used to monitor ex situ changes in secondary structure. Preservation of native secondary structure after incubation at elevated pressures and subzero ° C temperatures was independent of the extent of tertiary unfolding and reversibility. Several combinations of pressure and temperature were also used to discern the respective contributions of the isolated Ab fragments (Fab and Fc) to unfolding and aggregation. The fragments for each antibody showed significantly different partial unfolding profiles and reversibility. There was not a simple correlation between stability of the full MAb and either the Fc or Fab fragment stabilities across all cases, demonstrating a complex relationship to full MAb unfolding and aggregation behavior. That notwithstanding, the combined use of spectroscopic and scattering techniques provides insights into MAb conformational stability and hysteresis in high-pressure, low-temperature environments.

The Effects of High-Pressure Processing on pH, Thiobarbituric Acid Value, Color and Texture Properties of Frozen and Unfrozen Beef Mince

In this study, beef mince (approximately 4% fat longissmus costarum muscle of approximately 2-year-old Holstein cattle) was used as a material. High-pressure processing (HPP) was applied to frozen and unfrozen, vacuum-packed minced meat samples. The pH and thiobarbituric acid (TBA) values of the samples were examined during 45 days of storage. Color values (L*, a* and b*) and texture properties were examined during 30 days of storage. After freezing and HPP (350 MPa, 10 min, 10 °C), the pH value of minced meat increased (p > 0.05) and its TBA value decreased (p < 0.05). The increase in pH may be due to increased ionization during HPP. Some meat peptides, which are considered antioxidant compounds, increased the oxidative stability of meat, so a decrease in TBA may have been observed after freezing and HPP. While the color change in unpressurized samples was a maximum of 3.28 units during storage, in the pressurized sample, it exceeded the limit of 10 units on the first day of storage and exceeded the limit of 10 units on the third day of storage in the frozen and pressurized sample. Freezing and HPP caused the color of beef mince to be retained longer. The hardness, gumminess, chewability, adherence, elasticity, flexibility values of the pressurized and pressurized after freezing samples were higher than those of the unpressurized samples during storage. On the other hand, the opposite was the case for the adhesiveness values. In industrial applications, meat must be pressurized after being vacuum packed. If HPP is applied to frozen beef mince, some of its properties such as TBA, color, and texture can be preserved for a longer period of time without extreme change.

The Pressure Dependence of the Stability of the G-quadruplex Formed by d(TGGGGT)

The G-quadruplex (GQ), a tetrahelix formed by guanine-rich nucleic acid sequences, is a potential drug target for several diseases. Monomolecular GQs are stabilized by guanine tetrads and non-guanine regions that form loops. Hydrostatic pressure destabilizes the folded, monomolecular GQ structures. In this communication, we present data on the effect of pressure on the conformational stability of the tetramolecular GQ, d[5′-TGGGGT-3′]₄. This molecule does not have loops linking the tetrads; thus, its physical properties presumably reflect those of the tetrads alone. Understanding the properties of the tetrads will aid in understanding the contribution of the other structural components to the stability of GQ DNA. By measuring UV light absorption, we have studied the effect of hydrostatic pressure on the thermal stability of the tetramolecular d[5′-TGGGGT-3′]₄ in the presence of sodium ions. Our data show that, unlike monomolecular GQ, the temperature at which d[5′-TGGGGT-3′]₄ dissociates to form the constituent monomers is nearly independent of pressure up to 200 MPa. This implies that there is no net molar volume difference (∆V) between the GQ and the unfolded random-coil states. This finding further suggests that the large negative ∆V values for the unfolding of monomolecular GQ are due to the presence of the loop regions in those structures.

Biomolecules under Pressure: Phase Diagrams, Volume Changes, and High Pressure Spectroscopic Techniques

Pressure is an equally important thermodynamical parameter as temperature. However, its importance is often overlooked in the biophysical and biochemical investigations of biomolecules and biological systems. This review focuses on the application of high pressure (>100 MPa = 1 kbar) in biology. Studies of high pressure can give insight into the volumetric aspects of various biological systems; this information cannot be obtained otherwise. High-pressure treatment is a potentially useful alternative method to heat-treatment in food science. Elevated pressure (up to 120 MPa) is present in the deep sea, which is a considerable part of the biosphere. From a basic scientific point of view, the application of the gamut of modern spectroscopic techniques provides information about the conformational changes of biomolecules, fluctuations, and flexibility. This paper reviews first the thermodynamic aspects of pressure science, the important parameters affecting the volume of a molecule. The technical aspects of high pressure production are briefly mentioned, and the most common high-pressure-compatible spectroscopic techniques are also discussed. The last part of this paper deals with the main biomolecules, lipids, proteins, and nucleic acids: how they are affected by pressure and what information can be gained about them using pressure. I I also briefly mention a few supramolecular structures such as viruses and bacteria. Finally, a subjective view of the most promising directions of high pressure bioscience is outlined.

Characterization of Structural Changes of Casein Micelles at Different PH Using Microscopy and Spectroscopy Techniques

This study aimed to evaluate the influence of pH changes on morphometric parameters of casein micelles and a general overview of their conformational structure through microscopy techniques, Raman spectroscopy and multivariate analysis. It was found that casein micelles morphology and protein secondary structure depend strongly upon pH. The changes of arithmetic average roughness (Ra), size, and shape of casein micelles at different pH are properly characterized by atomic force and cryo-transmission electron microscopy. Morphometric changes of casein micelles were correlated correctly with folding and unfolding of casein molecules as evaluated by Raman spectroscopy when the pH was varied. The novelty of this contribution consists in demonstrating that there is a close structure-functionality relationship between the morphometric parameters of proteins and their secondary structure. Knowledge about casein micelles can help improve their use of its diverse applications.

Atomistic Simulations of Thermal Unfolding

This tutorial will provide a practical overview of the use of atomistic simulations to study thermal unfolding of biomolecules, in particular small proteins and RNA oligomers. The tutorial focuses on the use of atomistic, all atom simulations of biomolecules in explicit solvent, to study (reversible) thermal unfolding. The simulation methods described here have also been applied to study biomolecules using implicit solvent and coarse-grained models. We do not intend to provide an up-to-date review of the vast literature of biomolecular dynamics, enhanced sampling methods, force field developments, and applications of these methods. The purpose of this tutorial is to provide basic guidelines into the use of these methods to the starting scientist.

Pressure Perturbation Studies of Noncanonical Viral Nucleic Acid Structures

G-quadruplexes are noncanonical structures formed by guanine-rich sequences of the genome. They are found in crucial loci of the human genome, they take part in the regulation of important processes like cell proliferation and cell death. Much less is known about the subjects of this work, the viral G-quadruplexes. We have chosen three potentially G-quadruplex-forming sequences of hepatitis B. We measured the stability and the thermodynamic parameters of these quadruplexes. We also investigated the potential stabilization of these G-quadruplexes by binding a special ligand that was originally developed for cancer therapy. Fluorescence and infrared spectroscopic measurements were performed over wide temperature and pressure ranges. Our experiments indicate the small unfolding volume change of all three oligos. We found a difference between the unfolding of the 2-quartet and the 3-quartet G-quadruplexes. All three G-quadruplexes were stabilized by TMPyP4, which is a cationic porphyrin developed for stabilizing the human telomere.

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.

A comprehensive review on impact of non-thermal processing on the structural changes of food components

Non-thermal food processing is a viable alternative to traditional thermal processing to meet customer needs for high-quality, convenient and minimally processed foods. They are designed to eliminate elevated temperatures during processing and avoid the adverse effects of heat on food products. Numerous thermal and novel non-thermal technologies influence food structure at the micro and macroscopic levels. They affect several properties such as rheology, flavour, process stability, texture, and appearance at microscopic and macroscopic levels. This review presents existing knowledge and advances on the impact of non-thermal technologies, for instance, cold plasma treatment, irradiation, high-pressure processing, ultrasonication, pulsed light technology, high voltage electric field and pulsed electric field treatment on the structural changes of food components. An extensive review of the literature indicates that different non-thermal processing technologies can affect the food components, which significantly affects the structure of food. Applications of novel non-thermal technologies have shown considerable impact on food structure by altering protein structures via free radicals or larger or smaller molecules. Lipid oxidation is another process responsible for undesirable effects in food when treated with non-thermal techniques. Non-thermal technologies may also affect starch properties, reduce molecular weight, and change the starch granule's surface. Such modification of food structure could create novel food textures, enhance sensory properties, improve digestibility, improve water-binding ability and improve mediation of gelation processes. However, it is challenging to determine these technologies' influence on food components due to differences in their primary operation and equipment design mechanisms and different operating conditions. Hence, to get the most value from non-thermal technologies, more in-depth research about their effect on various food components is required.

Implicit water model within the Zimm-Bragg approach to analyze experimental data for heat and cold denaturation of proteins

Studies of biopolymer conformations essentially rely on theoretical models that are routinely used to process and analyze experimental data. While modern experiments allow study of single molecules in vivo, corresponding theories date back to the early 1950s and require an essential update to include the recent significant progress in the description of water. The Hamiltonian formulation of the Zimm-Bragg model we propose includes a simplified, yet explicit model of water-polypeptide interactions that transforms into the equivalent implicit description after performing the summation of solvent degrees of freedom in the partition function. Here we show that our model fits very well to the circular dichroism experimental data for both heat and cold denaturation and provides the energies of inter- and intra-molecular H-bonds, unavailable with other processing methods. The revealed delicate balance between these energies determines the conditions for the existence of cold denaturation and thus clarifies its absence in some proteins.

On the liquid demixing of water + elastin-like polypeptide mixtures: bimodal re-entrant phase behaviour

Water + elastin-like polypeptides (ELPs) exhibit a transition temperature below which the chains transform from collapsed to expanded states, reminiscent of the cold denaturation of proteins. This conformational change coincides with liquid-liquid phase separation. A statistical-thermodynamics theory is used to model the fluid-phase behavior of ELPs in aqueous solution and to extrapolate the behavior at ambient conditions over a range of pressures. At low pressures, closed-loop liquid-liquid equilibrium phase behavior is found, which is consistent with that of other hydrogen-bonding solvent + polymer mixtures. At pressures evocative of deep-sea conditions, liquid-liquid immiscibility bounded by two lower critical solution temperatures (LCSTs) is predicted. As pressure is increased further, the system exhibits two separate regions of closed-loop of liquid-liquid equilibrium (LLE). The observation of bimodal LCSTs and two re-entrant LLE regions herald a new type of binary global phase diagram: Type XII. At high-ELP concentrations the predicted phase diagram resembles a protein pressure denaturation diagram; possible "molten-globule"-like states are observed at low concentration.

Negative volume changes of human G-quadruplexes at unfolding

G-quadruplexes are tetrahelical structures. They are important targets for anti-cancer drugs, since they are situated at crucial positions within the genome. We studied the volumetric properties of the unfolding of three G-quadruplexes in the presence of potassium ion. The unfolding volume changes were determined using high-pressure fluorescence spectroscopy. The c-MYC, KIT, and VEGF sequences unfold with the transition volume of -17, -6 and -18 cm³/mol, respectively. The small magnitude of the unfolding volume of KIT could be explained by its unique structure and the lower amount of void volume. Since the cell interior is highly crowded, the available volume is restricted. Therefore the volumetric changes during the conformational transformations gain biological importance.

Combining High-Pressure Perturbation with NMR Spectroscopy for a Structural and Dynamical Characterization of Protein Folding Pathways

High-hydrostatic pressure is an alternative perturbation method that can be used to destabilize globular proteins. Generally perfectly reversible, pressure exerts local effects on regions or domains of a protein containing internal voids, contrary to heat or chemical denaturant that destabilize protein structures uniformly. When combined with NMR spectroscopy, high pressure (HP) allows one to monitor at a residue-level resolution the structural transitions occurring upon unfolding and to determine the kinetic properties of the process. The use of HP-NMR has long been hampered by technical difficulties. Owing to the recent development of commercially available high-pressure sample cells, HP-NMR experiments can now be routinely performed. This review summarizes recent advances of HP-NMR techniques for the characterization at a quasi-atomic resolution of the protein folding energy landscape.

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.

Squeezing Oil into Water under Pressure: Inverting the Hydrophobic Effect

The molecular structure of dense homogeneous fluid water-methane mixtures has been determined for the first time using high-pressure neutron-scattering techniques at 1.7 and 2.2 GPa. A mixed state with a fully H-bonded water network is revealed. The hydration shell of the methane molecules is, however, revealed to be pressure-dependent with an increase in the water coordination between 1.7 and 2.2 GPa. In parallel, ab initio molecular dynamics simulations have been performed to provide insight into the microscopic mechanisms associated with the phenomenon of mixing. These calculations reproduce the observed phase change from phase separation to mixing with increasing pressure. The calculations also reproduce the experimentally observed structural properties. Unexpectedly, the simulations show mixing is accompanied by a subtle enhancement of the polarization of methane. Our results highlight the key role played by fine electronic effects on miscibility and the need to readjust our fundamental understanding of hydrophobicity to account for these.

On the extraordinary pressure stability of the Thermotoga maritima arginine binding protein and its folded fragments - a high-pressure FTIR spectroscopy study

The arginine binding protein from T. maritima (ArgBP) exhibits several distinctive biophysical and structural properties. Here we show that ArgBP is also endowed with a ramarkable pressure stability as it undergoes minor structural changes only, even at 10 kbar. A similar stability is also observed for its folded fragments (truncated monomer and individual domains). A survey of literature data on the pressure stability of proteins highlights the uncommon behavior of ArgBP.

Protein adaptation to high hydrostatic pressure: Computational analysis of the structural proteome

Hydrostatic pressure has a vital role in the biological adaptation of the piezophiles, organisms that live under high hydrostatic pressure. However, the mechanisms by which piezophiles are able to adapt their proteins to high hydrostatic pressure is not well understood. One proposed hypothesis is that the volume changes of unfolding (ΔVTot ) for proteins from piezophiles is distinct from those of nonpiezophilic organisms. Since ΔVTot defines pressure dependence of stability, we performed a comprehensive computational analysis of this property for proteins from piezophilic and nonpiezophilic organisms. In addition, we experimentally measured the ΔVTot of acylphosphatases and thioredoxins belonging to piezophilic and nonpiezophilic organisms. Based on this analysis we concluded that there is no difference in ΔVTot for proteins from piezophilic and nonpiezophilic organisms. Finally, we put forward the hypothesis that increased concentrations of osmolytes can provide a systemic increase in pressure stability of proteins from piezophilic organisms and provide experimental thermodynamic evidence in support of this hypothesis.

Unveiling the Interstitial Pressure between Growing Ice Crystals during Ice-Templating Using a Lipid Lamellar Probe

What is the pressure generated by ice crystals during ice-templating? This work addresses this crucial question by estimating the pressure exerted by oriented ice columns on a supramolecular probe composed of a lipid lamellar hydrogel during directional freezing. This process, also known as freeze-casting, has emerged as a unique processing technique for a broad class of organic, inorganic, soft, and biological materials. Nonetheless, the pressure exerted during and after crystallization between two ice columns is not known, despite its importance with respect to the fragility of the frozen material, especially for biological samples. By using the lamellar period of a glycolipid lamellar hydrogel as a common probe, we couple data obtained from ice-templated-resolved in situ synchrotron small-angle X-ray scattering (SAXS) with data obtained from controlled adiabatic desiccation experiments. We estimate the pressure to vary between 1 ± 10% kbar at -15 °C and 3.5 ± 20% kbar at -60 °C.

Stability of the chaperonin system GroEL-GroES under extreme environmental conditions

The chaperonin system GroEL-GroES is present in all kingdoms of life and rescues proteins from improper folding and aggregation upon internal and external stress conditions, including high temperatures and pressures. Here, we set out to explore the thermo- and piezostability of GroEL, GroES and the GroEL-GroES complex in the presence of cosolvents, nucleotides and salts employing quantitative FTIR spectroscopy and small-angle X-ray scattering. Owing to its high biological relevance and lack of data, our focus was especially on the effect of pressure on the chaperonin system. The experimental results reveal that the GroEL-GroES complex is remarkably temperature stable with an unfolding temperature beyond 70 °C, which can still be slightly increased by compatible cosolutes like TMAO. Conversely, the pressure stability of GroEL and hence the GroEL-GroES complex is rather limited and much less than that of monomeric proteins. Whereas GroES is pressure stable up to ∼5 kbar, GroEl and the GroEl-GroES complex undergo minor structural changes already beyond 1 kbar, which can be attributed to a dissociation-induced conformational drift. Quite unexpectedly, no significant unfolding of GroEL is observed even up to 10 kbar, however, i.e., the subunits themselves are very pressure stable. As for the physiological relevance, the structural integrity of the chaperonin system is retained in a relatively narrow pressure range, from about 1 to 1000 bar, which is just the pressure range encountered by life on Earth.

Revealing unfolding steps and volume changes of human telomeric i-motif DNA

The i-motif structure of the human telomeric DNA was destabilized by pressure and unfolded with a negative volume change.

DNA Hairpin Hybridization under Extreme Pressures: A Single-Molecule FRET Study

Organisms have evolved to live in a variety of complex environments, which clearly has required cellular biology to accommodate to extreme conditions of hydraulic pressure and elevated temperature. In this work, we exploit single-molecule Forster resonance energy transfer (FRET) spectroscopy to probe structural changes in DNA hairpins as a function of pressure and temperature, which allows us to extract detailed thermodynamic information on changes in free energy (ΔG°), free volume (ΔV°), enthalpy (ΔH°), and entropy (ΔS°) associated with DNA loop formation and sequence-dependent stem hybridization. Specifically, time-correlated single-photon counting experiments on freely diffusing 40A DNA hairpin FRET constructs are performed in a 50 μm × 50 μm square quartz capillary cell pressurized from ambient pressure up to 3 kbar. By pressure-dependent van't Hoff analysis of the equilibrium constants, ΔV° for hybridization of the DNA hairpin can be determined as a function of stem length (n_stem = 7-10) with single base-pair resolution, which further motivates a simple linear deconstruction into additive stem (ΔV°_stem = ΔV°_bp x n_stem) and loop (ΔV°_loop) contributions. We find that increasing pressure destabilizes the DNA hairpin stem region [ΔV°_bp = +1.98(16) cm³/(mol bp)], with additional positive free volume changes [ΔV°_loop = +7.0(14) cm³/mol] we ascribe to bending and base stacking disruption of the 40-dA loop. From a van't Hoff temperature-dependent analysis of the DNA 40A hairpin equilibria, the data support a similar additive loop/stem deconstruction of enthalpic (ΔH° = ΔH°_loop + ΔH°_stem) and entropic (ΔS° = ΔS°_loop + ΔS°_stem) contributions, which permits insightful comparison with predictions from nearest-neighbor thermodynamic models for DNA duplex formation. In particular, the stem thermodynamics is consistent with exothermically favored (ΔH°_stem < 0) and entropically penalized (ΔS°_stem < 0) hydrogen bonding but with additional enthalpic (ΔH°_loop > 0) and entropic (ΔS°_loop > 0) contributions due to loop bending effects consistent with distortion of dA base stacking in the 40-dA linker.

Segmental Motions of Proteins under Non-native States Evaluated Using Quasielastic Neutron Scattering

Characterization of the dynamics of disordered polypeptide chains is required to elucidate the behavior of intrinsically disordered proteins and proteins under non-native states related to the folding process. Here we develop a method using quasielastic neutron scattering, combined with small-angle X-ray scattering and dynamic light scattering, to evaluate segmental motions of proteins as well as diffusion of the entire molecules and local side-chain motions. We apply this method to RNase A under the unfolded and molten-globule (MG) states. The diffusion coefficients arising from the segmental motions are evaluated and found to be different between the unfolded and MG states. The values obtained here are consistent with those obtained using the fluorescence-based techniques. These results demonstrate not only feasibility of this method but also usefulness to characterize the behavior of proteins under various disordered states.

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

The application of co-solvents and high pressure has been reported to be an efficient means to tune the kinetics of enzyme-catalyzed reactions. Co-solvents and pressure can lead to increased reaction rates without sacrificing enzyme stability, while temperature and pH operation windows are generally very narrow. Quantitative prediction of co-solvent and pressure effects on enzymatic reactions has not been successfully addressed in the literature. Herein, we are introducing a thermodynamic approach that is based on molecular interactions in the form of activity coefficients of substrate and of enzyme in the multi-component solution. This allowed us to quantitatively predict the combined effect of co-solvent and pressure on the kinetic constants, i.e. the Michaelis constant K_M and the catalytic constant k_cat, of an α-CT-catalyzed peptide hydrolysis reaction. The reaction was studied in the presence of different types of co-solvents and at pressures up to 2 kbar, and quantitative predictions could be obtained for K_M, k_cat, and finally even primary Michaelis-Menten plots using activity coefficients provided by the thermodynamic model PC-SAFT.

Self-crowding influences the temperature - pressure stability of the human telomere G-quadruplex

We measured the effect of crowded environment on G-quadruplex structures, formed by guanine rich DNA sequences. Fluorescence and infrared spectroscopy were used to determine the temperature stability of G-quadruplex structure formed by the human telomere sequence. We determined the T-p phase diagram of Htel aptamer up to 1 GPa at different self-crowding conditions. The unfolding volume change was determined from the pressure induced shift of the unfolding temperature of the quadruplex form. The unfolding volume change decreased in magnitude, and even its sign changed from negative (-19 ml/mol) to positive (7 ml/mol) under self-crowded conditions. The possible explanations are the appearance of the parallel GQ structure at high concentration or the fact that the volume decrease caused by the released central K⁺ ion during the unfolding is less significant in crowded environment.

Modeling counterion partition in composite gels of BSA with gelatin following high pressure treatment

We examine the morphology of hydrogels made of bovine serum albumin and gelatin following high pressure processing at 300 MPa for 15 min at 10 and 80 °C. Emphasis is on the distribution of added calcium counterions between the polymeric phases seen in changes in the structural properties of the composite gel. Protocol includes thermal and HPP treatments, dynamic oscillation rheology, ESEM, and modeling from the "synthetic polymer approach" to rationalize results. Pressurization at 10 °C produced continuous gelatin networks with dispersed BSA inclusions whereas pressurization at 80 °C yielded an inverse dispersion of BSA as the continuous phase supporting liquid gelatin inclusions. Lewis and Nielsen equations were adapted to predict the counterion distribution between the polymeric phases that profoundly affected the structural properties of the pressurized gels. The concept of counterion partition (p_c) is introduced to the literature to follow the phase behavior of the composites in the presence of added calcium counterions.

Thermodynamic properties of aqueous osmolyte solutions at high-pressure conditions

Living organisms can be encountered in nature under extreme conditions. At the seabed, pressure may reach 1000 bar. Yet microorganisms can be found that still function under these conditions. On the one hand, it is known that high pressure even has a positive effect on piezophile enzymes increasing their activity. On the other hand, such microorganisms might contain up to very high concentrations of osmolytes that counteract osmotic stress. To better understand high-pressure influences on biochemical systems, fundamental knowledge about pressure effects on thermodynamic properties of such osmolytes is important. However, literature data is scarce and experiments at high-pressure conditions are challenging. Hence, new high-pressure density data of aqueous osmolyte solutions were measured in this work at temperatures between 298.15 K and 318.15 K and at osmolyte concentrations up to 3 mol/kg water. Further, the thermodynamic model PC-SAFT has been applied recently to successfully model vapor pressures of water and density of water up to 10 kbar [M. Knierbein et al., Density variations of TMAO solutions in the kilobar range: experiments, PC-SAFT predictions, and molecular dynamics simulations, Biophysical chemistry, (2019)]. This allowed accurately predicting effects of temperature and osmolyte concentration on thermodynamic properties (especially mixture densities) up to very high pressures. Common osmolytes (trimethylamine-N-oxide, urea, ectoine, glycerol, glycine) as well as the dipeptides acetyl-N-methylglycine amide, acetyl-N-methylalanine amide, and acetyl-N-methylleucine amide were under investigation.