High-Pressure Chemical Biology and Biotechnology

Exploring high hydrostatic pressure effects on anthocyanin binding to serum albumin and food-derived transferrins

This study investigated the effects of high hydrostatic pressure (HHP) on the binding interactions of cyanindin-3-O-glucoside (C3G) to bovine serum albumin, human serum albumin (HSA), bovine lactoferrin, and ovotransferrin. Fluorescence quenching revealed that HHP reduced C3G-binding affinity to HSA, while having a largely unaffected role for the other proteins. Notably, pretreating HSA at 500 MPa significantly increased its dissociation constant with C3G from 24.7 to 34.3 μM. Spectroscopic techniques suggested that HSA underwent relatively pronounced tertiary structural alterations after HHP treatments. The C3G-HSA binding mechanisms under pressure were further analyzed through molecular dynamics simulation. The localized structural changes in HSA under pressure might weaken its interaction with C3G, particularly polar interactions such as hydrogen bonds and electrostatic forces, consequently leading to a decreased binding affinity. Overall, the importance of pressure-induced structural alterations in proteins influencing their binding with anthocyanins was highlighted, contributing to optimizing HHP processing for anthocyanin-based products.

Fabrication and characterization of curcumin-loaded composite nanoparticles based on high-hydrostatic-pressure-treated zein and pectin: Interaction mechanism, stability, and bioaccessibility

We successfully designed curcumin (Cur)-loaded composite nanoparticles consisting of high-hydrostatic-pressure-treated (HHP-treated) zein and pectin with a pressure of 150 MPa (zein-150 MPa-P-Cur), showing nano-spherical structure with high zeta-potential (-36.72 ± 1.14 mV) and encapsulation efficiency (95.64 ± 1.23 %). We investigated the interaction mechanism of the components in zein-150 MPa-P-Cur using fluorescence spectroscopy, molecular dynamics simulation, Fourier-transform infrared spectrometry and scanning electron microscopy techniques. Compared with zein-P-Cur, the binding sites and binding energy (-53.68 kcal/mol vs. - 44.22 kcal/mol) of HHP-treated zein and Cur were increased. Meanwhile, the interaction force among HHP-treated zein, pectin, and Cur was significantly enhanced, which formed a tighter and more stable particle structure to further improve package performance. Additionally, Cur showed the best chemical stability in zein-150 MPa-P-Cur. And the bioavailability of Cur was increased to 65.53 ± 1.70 %. Collectively, composite nanoparticles based on HHP-treated zein and pectin could be used as a promising Cur delivery system.

Enabling High Activation of Glucose-6-Phosphate Dehydrogenase Activity Through Liquid Condensate Formation and Compression

Droplet formation via liquid-liquid phase separation is thought to be involved in the regulation of various biological processes, including enzymatic reactions. We investigated a glycolytic enzymatic reaction, the conversion of glucose-6-phosphate to 6-phospho-D-glucono-1,5-lactone with concomitant reduction of NADP+ to NADPH both in the absence and presence of dynamically controlled liquid droplet formation. Here, the nucleotide serves as substrate as well as the scaffold required for the formation of liquid droplets. To further expand the process parameter space, temperature and pressure dependent measurements were performed. Incorporation of the reactants in the liquid droplet phase led to a boost in enzymatic activity, which was most pronounced at medium-high pressures. The crowded environment of the droplet phase induced a marked increase of the affinity of the enzyme and substrate. An increase in turnover number in the droplet phase at high pressure contributed to a further strong increase in catalytic efficiency. Enzyme systems that are dynamically coupled to liquid condensate formation may be the key to deciphering many biochemical reactions. Expanding the process parameter space by adjusting temperature and pressure conditions can be a means to further increase the efficiency of industrial enzyme utilization and help uncover regulatory mechanisms adopted by extremophiles.

H2 production under stress: [FeFe]‑hydrogenases reveal strong stability in high pressure environments

Hydrogenases are a diverse group of metalloenzymes that catalyze the conversion of H2 into protons and electrons and the reverse reaction. A subgroup is formed by the [FeFe]‑hydrogenases, which are the most efficient enzymes of microbes for catalytic H2 conversion. We have determined the stability and activity of two [FeFe]‑hydrogenases under high temperature and pressure conditions employing FTIR spectroscopy and the high-pressure stopped-flow methodology in combination with fast UV/Vis detection. Our data show high temperature stability and an increase in activity up to the unfolding temperatures of the enzymes. Remarkably, both enzymes reveal a very high pressure stability of their structure, even up to pressures of several kbars. Their high pressure-stability enables high enzymatic activity up to 2 kbar, which largely exceeds the pressure limit encountered by organisms in the deep sea and sub-seafloor on Earth.

Cellular transfection using rapid decrease in hydrostatic pressure

Of all methods exercised in modern molecular biology, modification of cellular properties through the introduction or removal of nucleic acids is one of the most fundamental. As such, several methods have arisen to promote this process; these include the condensation of nucleic acids with calcium, polyethylenimine or modified lipids, electroporation, viral production, biolistics, and microinjection. An ideal transfection method would be (1) low cost, (2) exhibit high levels of biological safety, (3) offer improved efficacy over existing methods, (4) lack requirements for ongoing consumables, (5) work efficiently at any scale, (6) work efficiently on cells that are difficult to transfect by other methods, and (7) be capable of utilizing the widest array of existing genetic resources to facilitate its utility in research, biotechnical and clinical settings. To address such issues, we describe here Pressure-jump-poration (PJP), a method using rapid depressurization to transfect even difficult to modify primary cell types such as embryonic stem cells. The results demonstrate that PJP can be used to introduce an array of genetic modifiers in a safe, sterile manner. Finally, PJP-induced transfection in primary versus transformed cells reveals a surprising dichotomy between these classes which may provide further insight into the process of cellular transformation.

Biological functions at high pressure: transcriptome response of Shewanella oneidensis MR-1 to hydrostatic pressure relevant to Titan and other icy ocean worlds

High hydrostatic pressure (HHP) is a key driver of life's evolution and diversification on Earth. Icy moons such as Titan, Europa, and Enceladus harbor potentially habitable high-pressure environments within their subsurface oceans. Titan, in particular, is modeled to have subsurface ocean pressures ≥ 150 MPa, which are above the highest pressures known to support life on Earth in natural ecosystems. Piezophiles are organisms that grow optimally at pressures higher than atmospheric (0.1 MPa) pressure and have specialized adaptations to the physical constraints of high-pressure environments - up to ~110 MPa at Challenger Deep, the highest pressure deep-sea habitat explored. While non-piezophilic microorganisms have been shown to survive short exposures at Titan relevant pressures, the mechanisms of their survival under such conditions remain largely unelucidated. To better understand these mechanisms, we have conducted a study of gene expression for Shewanella oneidensis MR-1 using a high-pressure experimental culturing system. MR-1 was subjected to short-term (15 min) and long-term (2 h) HHP of 158 MPa, a value consistent with pressures expected near the top of Titan's subsurface ocean. We show that MR-1 is metabolically active in situ at HHP and is capable of viable growth following 2 h exposure to 158 MPa, with minimal pressure training beforehand. We further find that MR-1 regulates 264 genes in response to short-term HHP, the majority of which are upregulated. Adaptations include upregulation of the genes argA, argB, argC, and argF involved in arginine biosynthesis and regulation of genes involved in membrane reconfiguration. MR-1 also utilizes stress response adaptations common to other environmental extremes such as genes encoding for the cold-shock protein CspG and antioxidant defense related genes. This study suggests Titan's ocean pressures may not limit life, as microorganisms could employ adaptations akin to those demonstrated by terrestrial organisms.

Modulation of protein-saccharide interactions by deep-sea osmolytes under high pressure stress

Deep-sea organisms must cope with high hydrostatic pressures (HHP) up to the kbar regime to control their biomolecular processes. To alleviate the adverse effects of HHP on protein stability most organisms use high amounts of osmolytes. Little is known about the effects of these high concentrations on ligand binding. We studied the effect of the deep-sea osmolytes trimethylamine-N-oxide, glycine, and glycine betaine on the binding between lysozyme and the tri-saccharide NAG3, employing experimental and theoretical tools to reveal the combined effect of osmolytes and HHP on the conformational dynamics, hydration changes, and thermodynamics of the binding process. Due to their different chemical makeup, these cosolutes modulate the protein-sugar interaction in different ways, leading to significant changes in the binding constant and its pressure dependence. These findings suggest that deep-sea organisms may down- and up-regulate reactions in response to HHP stress by altering the concentration and type of the intracellular osmolyte.

The structure of anthocyanins and the copigmentation by common micromolecular copigments: A review

Under natural physiological conditions, anthocyanins can keep bright and stable color for a long time due to the relatively stable acid-base environment of plant vacuoles and the copigmentation from various copigment substances, such as polyphenols, nucleotides, metallic ions and other substances. Therefore, the copigmentation caused by copigments is considered an effective way to stabilize anthocyanins against adverse environmental conditions. This is attributed to the covalent and noncovalent interactions between colored forms of anthocyanins (flavylium ions and quinoidal bases) and colorless or pale yellow organic molecules (copigments). These interactions are usually manifested in both hyperchromic effect and bathochromic shifts. In addition to making anthocyanins more stable, the copigmentation also could make an important contribution to the diversification of their tone. Based on the molecular structure of anthocyanins, this review focuses on the interaction mode of auxochrome groups or copigments with anthocyanins and their effects on the chemical and color stability of anthocyanins.

Leveraging liquid-liquid phase separation and volume modulation to regulate the enzymatic activity of formate dehydrogenase

Engineering of reaction media is an exciting alternative for modulating kinetic properties of biocatalytic reactions. We addressed the combined effect of an aqueous two-phase system (ATPS) and high hydrostatic pressure on the kinetics of the Candida boidinii formate dehydrogenase-catalyzed oxidation of formate to CO2. Pressurization was found to lead to an increase of the binding affinity (decrease of KM, respectively) and a decrease of the turnover number, kcat. The experimental approach was supported using thermodynamic modeling with the electrolyte Perturbed-Chain Statistical Associating Fluid Theory (ePC-SAFT) equation of state to predict the liquid-liquid phase separation and the molecular crowding effect of the ATPS on the kinetic properties. The ePC-SAFT was able to quantitatively predict the KM-values of the substrate in both phases at 1 bar as well as up to a pressure of 1000 bar. The framework presented enables significant advances in bioprocess engineering, including the design of processes with significantly fewer experiments and trial-and-error approaches.

Reversible disassembly-reassembly of C-phycocyanin in pressurization-depressurization cycles of high hydrostatic pressure

Hydrostatic pressure can reversibly modulate protein-protein and protein-chromophore interactions of C-phycocyanin (C-PC) from Spirulina platensis. Small-angle X-ray scattering combined with UV-Vis spectrophotometry and protein modeling was used to explore the color and structural changes of C-PC under high pressure conditions at different pH levels. It was revealed that pressures up to 350 MPa were enough to fully disassemble C-PC from trimers to monomers at pH 7.0, or from monomers to detached subunits at pH 9.0. These disassemblies were accompanied by protein unfolding that caused these high-pressure induced structures to be more extended. These changes were reversible following depressurization. The trimer-to-monomer transition proceeded through a collection of previously unrecognized, L-shaped intermediates resembling C-PC dimers. Additionally, pressurized C-PC showed decayed Q-band absorption and fortified Soret-band absorption. This was evidence that the folded tetrapyrroles, which had folded at ambient pressure, formed semicyclic unfolded conformations at a high pressure. Upon depressurization, the peak intensity and shift all recovered stepwise, showing pressure can precisely manipulate C-PC's structure as well as its color. Overall, a protein-chromophore regulatory theory of C-PC was unveiled. The pressure-tunability could be harnessed to modify and stabilize C-PC's structure and photochemical properties for designing new delivery and optical materials.

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.

Targeting Biomolecular Condensation and Protein Aggregation against Cancer

Biomolecular condensates, membrane-less entities arising from liquid-liquid phase separation, hold dichotomous roles in health and disease. Alongside their physiological functions, these condensates can transition to a solid phase, producing amyloid-like structures implicated in degenerative diseases and cancer. This review thoroughly examines the dual nature of biomolecular condensates, spotlighting their role in cancer, particularly concerning the p53 tumor suppressor. Given that over half of the malignant tumors possess mutations in the TP53 gene, this topic carries profound implications for future cancer treatment strategies. Notably, p53 not only misfolds but also forms biomolecular condensates and aggregates analogous to other protein-based amyloids, thus significantly influencing cancer progression through loss-of-function, negative dominance, and gain-of-function pathways. The exact molecular mechanisms underpinning the gain-of-function in mutant p53 remain elusive. However, cofactors like nucleic acids and glycosaminoglycans are known to be critical players in this intersection between diseases. Importantly, we reveal that molecules capable of inhibiting mutant p53 aggregation can curtail tumor proliferation and migration. Hence, targeting phase transitions to solid-like amorphous and amyloid-like states of mutant p53 offers a promising direction for innovative cancer diagnostics and therapeutics.

Effects of high pressure synergistic enzymatic physical state and concentration on the denaturation of polyphenol oxidase

The synergistic effect of the initial state of the enzyme and pressure level on the denaturation of PPO has not been clear yet, but it significantly affects the application of high hydrostatic pressure (HHP) in the enzyme-containing food processing. Solid (S-) and low/high concentration liquid (LL-/HL-) polyphenol oxidase (PPO) was used as the study object, and the microscopic conformation, molecular morphology and macroscopic activity of PPO under HHP treatments (100-400 MPa, 25 °C/30 min) were investigated by spectroscopic techniques. The results show that the initial state has a significant effect on the activity, structure, active force and substrate channel of PPO under pressure. The effec can be ranked as follows: physical state > concentration > pressure, S-PPO > LL-PPO > HL-PPO. High concentration has a weakening effect on the pressure denaturation of the PPO solution. Under high pressure, the α-helix and concentration factors play a crucial role in stabilizing the structure.

Liquid-Droplet-Mediated ATP-Triggered Amyloidogenic Pathway of Insulin-Derived Chimeric Peptides: Unraveling the Microscopic and Molecular Processes

Disease-associated progression of protein dysfunction is typically determined by an interplay of transition pathways leading to liquid-liquid phase separation (LLPS) and amyloid fibrils. As LLPS introduces another layer of complexity into fibrillization of metastable proteins, a need for tunable model systems to study these intertwined processes has emerged. Here, we demonstrate the LLPS/fibrillization properties of a family of chimeric peptides, ACC1-13Kn, in which the highly amyloidogenic fragment of insulin (ACC1-13) is merged with oligolysine segments of various lengths (Kn, n = 8, 16, 24, 32, 40). LLPS and fibrillization of ACC1-13Kn are triggered by ATP through Coulombic interactions with Kn fragments. ACC1-13K8 and ACC1-13K16 form fibrils after a short lag phase without any evidence of LLPS. However, in the case of the three longest peptides, ATP triggers instantaneous LLPS followed by the disappearance of droplets occurring in-phase with the formation of amyloid fibrils. The kinetics of the phase transition and the stability of mature co-aggregates are highly sensitive to ionic strength, indicating that electrostatic interactions play a pivotal role in selecting the LLPS-fibrillization transition pathway. Densely packed ionic interactions that characterize ACC1-13Kn-ATP fibrils render them highly sensitive to hydrostatic pressure due to solvent electrostriction, as demonstrated by infrared spectroscopy. Using atomic force microscopy imaging of rapidly frozen samples, we demonstrate that early fibrils form within single liquid droplets, starting at the droplet/bulk interface through the formation of single bent fibers. A hypothetical molecular scenario underlying the emergence of the LLPS-to-fibrils pathway in the ACC1-13Kn-ATP system has been put forward.

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.

Water Leakage Pathway Leads to Internal Hydration of the p53 Core Domain

The gene encoding the p53 tumor suppressor protein is the most frequently mutated oncogene in cancer patients; yet, generalized strategies for rescuing the function of different p53 mutants remain elusive. This work investigates factors that may contribute to the low inherent stability of the wild-type p53 core domain (p53C) and structurally compromised Y220C mutant. Pressure-induced unfolding of p53C was compared to p63C, the p53 family member with the highest stability, the engineered superstable p53C hexamutant (p53C HM), and lower stability p53C Y220C cancer-associated mutant. The following pressure unfolding values (P50% bar) were obtained: p53C 3346, p53C Y220C 2217, p53C HM 3943, and p63C 4326. Molecular dynamics (MD) simulations revealed that p53C Y220C was most prone to water infiltration, followed by p53C, whereas the interiors of p53C HM and p63C remained comparably dry. A strong correlation (r² = 0.92) between P50% and extent of interior hydration was observed. The pathways of individual water molecule entry and exit were mapped and analyzed, revealing a common route preserved across the p53 family involving a previously reported pocket, along with a novel surface cleft, both of which appear to be targetable by small molecules. Potential determinants of propensity to water incursion were assessed, including backbone hydrogen bond protection and combined sequence and structure similarity. Collectively, our results indicate that p53C has an intrinsic susceptibility to water leakage, which is exacerbated in a structural class mutant, suggesting that there may be a common avenue for rescuing p53 function.

Using Intrinsic Fluorescence to Measure Protein Stability Upon Thermal and Chemical Denaturation

Understanding how point mutations affect the performance of protein stability has been the focus of several studies all over the years. Intrinsic fluorescence is commonly used to follow protein unfolding since during denaturation, progressive redshifts on tryptophan fluorescence emission are observed. Since the unfolding process (achieved by chemical or physical denaturants) can be considered as two-state N➔D, it is possible to utilize the midpoint unfolding curves (fU = 50%) as a parameter to evaluate if the mutation destabilizes wild-type protein. The idea is to determine the [D]_1/2 or T_m values from both wild type and mutant and calculate the difference between them. Positive values indicate the mutant is less stable than wild type.

Harnessing Pressure-Axis Experiments to Explore Volume Fluctuations, Conformational Substates, and Solvation of Biomolecular Systems

Intrinsic thermodynamic fluctuations within biomolecules are crucial for their function, and flexibility is one of the strategies that evolution has developed to adapt to extreme environments. In this regard, pressure perturbation is an important tool for mechanistically exploring the causes and effects of volume fluctuations in biomolecules and biomolecular assemblies, their role in biomolecular interactions and reactions, and how they are affected by the solvent properties. High hydrostatic pressure is also a key parameter in the context of deep-sea and subsurface biology and the study of the origin and physical limits of life. We discuss the role of pressure-axis experiments in revealing intrinsic structural fluctuations as well as high-energy conformational substates of proteins and other biomolecular systems that are important for their function and provide some illustrative examples. We show that the structural and dynamic information obtained from such pressure-axis studies improves our understanding of biomolecular function, disease, biological evolution, and adaptation.

Inline small-angle X-ray scattering-coupled chromatography under extreme hydrostatic pressure

As continuing discoveries highlight the surprising abundance and resilience of deep ocean and subsurface microbial life, the effects of extreme hydrostatic pressure on biological structure and function have attracted renewed interest. Biological small-angle X-ray scattering (BioSAXS) is a widely used method of obtaining structural information from biomolecules in solution under a wide range of solution conditions. Due to its ability to reduce radiation damage, remove aggregates, and separate monodisperse components from complex mixtures, size-exclusion chromatography-coupled SAXS (SEC-SAXS) is now the dominant form of BioSAXS at many synchrotron beamlines. While BioSAXS can currently be performed with some difficulty under pressure with non-flowing samples, it has not been clear how, or even if, continuously flowing SEC-SAXS, with its fragile media-packed columns, might work in an extreme high-pressure environment. Here we show, for the first time, that reproducible chromatographic separations coupled directly to high-pressure BioSAXS can be achieved at pressures up to at least 100 MPa and that pressure-induced changes in folding and oligomeric state and other properties can be observed. The apparatus described here functions at a range of temperatures (0°C-50°C), expanding opportunities for understanding biomolecular rules of life in deep ocean and subsurface environments.

Evolutionary Role of Water-Accessible Cavities in Src Homology 2 (SH2) Domains

Protein excited states are fundamental in the understanding of biological function, despite the fact they are hardly observed using traditional biophysical methodologies. Pressure perturbation coupled with nuclear magnetic resonance (NMR) spectroscopy is a powerful physicochemical tool to glance at these low-populated high-energy states on a residue-by-residue basis and underpin mechanistic insights into protein functionalities. Here we performed pressure titrations using NMR spectroscopy and relaxation dispersion experiments to identify the low-lying energetic states of the c-Abl SH2 domain. By showing that the SH2 excited state contains a hydrated hydrophobic cavity, fast-exchange motions, and highly conserved residues facing the water-accessible hole, we discuss the implications of water-protein interactions in SH2 modules achieving high-affinity binding and promiscuous phospho-Tyr peptide recognition.

Effect of high hydrostatic pressure processing on the structure, functionality, and nutritional properties of food proteins: A review

Proteins are important food ingredients that possess both functional and nutritional properties. High hydrostatic pressure (HHP) is an emerging nonthermal food processing technology that has been subject to great advancements in the last two decades. It is well established that pressure can induce changes in protein folding and oligomerization, and consequently, HHP has the potential to modify the desired protein properties. In this review article, the research progress over the last 15 years regarding the effect of HHP on protein structures, as well as the applications of HHP in modifying protein functionalities (i.e., solubility, water/oil holding capacity, emulsification, foaming and gelation) and nutritional properties (i.e., digestibility and bioactivity) are systematically discussed. Protein unfolding generally occurs during HHP treatment, which can result in increased conformational flexibility and the exposure of interior residues. Through the optimization of HHP and environmental conditions, a balance in protein hydrophobicity and hydrophilicity may be obtained, and therefore, the desired protein functionality can be improved. Moreover, after HHP treatment, there might be greater accessibility of the interior residues to digestive enzymes or the altered conformation of specific active sites, which may lead to modified nutritional properties. However, the practical applications of HHP in developing functional protein ingredients are underutilized and require more research concerning the impact of other food components or additives during HHP treatment. Furthermore, possible negative impacts on nutritional properties of proteins and other compounds must be also considered.

Suppression of Liquid‐Liquid Phase Separation and Aggregation of Antibodies by Modest Pressure Application

The high colloidal stability of antibody (immunoglobulin) solutions is important for pharmaceutical applications. Inert cosolutes, excipients, are generally used in therapeutic protein formulations to minimize physical instabilities, such as liquid–liquid phase separation (LLPS), aggregation and precipitation, which are often encountered during manufacturing and storage. Despite their widespread use, a detailed understanding of how excipients modulate the specific protein‐protein interactions responsible for these instabilities is still lacking. In this work, we demonstrate the high sensitivity to pressure of globulin condensates as a suitable means to suppress LLPS and subsequent aggregation of concentrated antibody solutions. The addition of excipients has only a minor effect. The high pressure sensitivity observed is due to the fact that these flexible Y‐shaped molecules create a considerable amount of void volume in the condensed phase, leading to an overall decrease in the volume of the system upon dissociation of the droplet phase by pressure already at a few tens of to hundred bar. Moreover, we show that immunoglobulin molecules themselves are highly resistant to unfolding under pressure, and can even sustain pressures up to about 6 kbar without conformational changes. This implies that immunoglobulins are resistant to the pressure treatment of foods, such as milk, in high‐pressure food‐processing technologies, thereby preserving their immunological activity.

Human growth hormone inclusion bodies present native-like secondary and tertiary structures which can be preserved by mild solubilization for refolding

BACKGROUND

Native-like secondary structures and biological activity have been described for proteins in inclusion bodies (IBs). Tertiary structure analysis, however, is hampered due to the necessity of mild solubilization conditions. Denaturing reagents used for IBs solubilization generally lead to the loss of these structures and to consequent reaggregation due to intermolecular interactions among exposed hydrophobic domains after removal of the solubilization reagent. The use of mild, non-denaturing solubilization processes that maintain existing structures could allow tertiary structure analysis and increase the efficiency of refolding.

RESULTS

In this study we use a variety of biophysical methods to analyze protein structure in human growth hormone IBs (hGH-IBs). hGH-IBs present native-like secondary and tertiary structures, as shown by far and near-UV CD analysis. hGH-IBs present similar λmax intrinsic Trp fluorescence to the native protein (334 nm), indicative of a native-like tertiary structure. Similar fluorescence behavior was also obtained for hGH solubilized from IBs and native hGH at pH 10.0 and 2.5 kbar and after decompression. hGH-IBs expressed in E. coli were extracted to high yield and purity (95%) and solubilized using non-denaturing conditions [2.4 kbar, 0.25 M arginine (pH 10), 10 mM DTT]. After decompression, the protein was incubated at pH 7.4 in the presence of the glutathione-oxidized glutathione (GSH-GSSG) pair which led to intramolecular disulfide bond formation and refolded hGH (81% yield).

CONCLUSIONS

We have shown that hGH-IBs present native-like secondary and tertiary structures and that non-denaturing methods that aim to preserve them can lead to high yields of refolded protein. It is likely that the refolding process described can be extended to different proteins and may be particularly useful to reduce the pH required for alkaline solubilization.

Deep sea osmolytes in action: their effect on protein-ligand binding under high pressure stress

Because organisms living in the deep sea and in the sub-seafloor must be able to cope with hydrostatic pressures up to 1000 bar and more, their biomolecular processes, including ligand-binding reactions, must be adjusted to keep the associated volume changes low in order to function efficiently. Almost all organisms use organic cosolvents (osmolytes) to protect their cells from adverse environmental conditions. They counteract osmotic imbalance, stabilize the structure of proteins and maintain their function. We studied the binding properties of the prototypical ligand proflavine to two serum proteins with different binding pockets, BSA and HSA, in the presence of two prominent osmolytes, trimethylamine-N-oxide (TMAO) and glycine betaine (GB). TMAO and GB play an important role in the regulation and adaptation of life in deep-sea organisms. To this end, pressure dependent fluorescence spectroscopy was applied, supplemented by circular dichroism (CD) spectroscopy and computer modeling studies. The pressure-dependent measurements were also performed to investigate the intimate nature of the complex formation in relation to hydration and packing changes caused by the presence of the osmolytes. We show that TMAO and GB are able to modulate the ligand binding process in specific ways. Depending on the chemical make-up of the protein's binding pocket and thus the thermodynamic forces driving the binding process, there are osmolytes with specific interaction sites and binding strengths with water that are able to mediate efficient ligand binding even under external stress conditions. In the binding of proflavine to BSA and HSA, the addition of both compatible osmolytes leads to an increase in the binding constant upon pressurization, with TMAO being the most efficient, rendering the binding process also insensitive to pressurization even up to 2 kbar as the volume change remains close to zero. This effect can be corroborated by the effects the cosolvents impose on the strength and dynamics of hydration water as well as on the conformational dynamics of the protein.

Proposed Role for Internal Lens Pressure as an Initiator of Age-Related Lens Protein Aggregation Diseases

The process that initiates lens stiffness evident in age-related lens protein aggregation diseases is thought to be mainly the result of oxidation. While oxidation is a major contributor, the exposure of lens proteins to physical stress over time increases susceptibility of lens proteins to oxidative damage, and this is believed to play a significant role in initiating these diseases. Accordingly, an overview of key physical stressors and molecular factors known to be implicated in the development of age-related lens protein aggregation diseases is presented, paying particular attention to the consequence of persistent increase in internal lens pressure.

Recombinant PilS: Cloning, Expression and Biochemical Characterization of a Pil-Fimbriae Subunit

Pil-fimbriae is a type IV pili member, which is a remarkably versatile component with a wide variety of functions, including motility, attachment to different surfaces, electrical conductance, DNA acquisition, and secretion of a broad range of structurally distinct protein substrates. Despite the previous functional characterization of Pil, more studies are required to understand the regulation of Pil expression and production, since the exact mechanisms involved in these steps are still unknown. Therefore it is extremely important to have a protein with the correct secondary and tertiary structure that will enable an accurate characterization and a specific antisera generation. For this reason, the aim of this work was to generate potential tools for further investigations to comprehend the mechanisms involved in Pil regulation and its role in pathogenic E. coli infections with the obtaining of a precise native-like recombinant PilS and the corresponding antisera. The pilS gene was successfully cloned into an expression vector, and recombinant PilS (rPilS) was efficiently solubilized and purified by metal affinity chromatography. Protein characterization analyses indicated that rPilS presented native-like secondary and tertiary structures after the refolding process. The generated anti-rPilS sera efficiently recognized recombinant and native proteins from atypical enteropathogenic E. coli strains.

Solution-State Hydrostatic Pressure Chemistry: Application to Molecular, Supramolecular, Polymer, and Biological Systems

ConspectusPressure (P), as one of the most inherent state quantities, has become an academic subject of study and has attracted attention for a long time for the minute control of reaction equilibria and rates, not only in the gas phase, based on the gas state equation, but also in the solution state. In the latter case, the pressure applied to the solutions is classified as hydrostatic pressure, which is a type of isotropic mechanical force. For instance, deep-sea organisms are exposed to hydrostatic pressure environments of up to 100 MPa, implying that hydrostatic pressurization plays a role in homeostatic functions at physiological levels. The pressure control of such complicated biological behavior can be addressed by thermodynamics or kinetics. In fact, the spontaneity (ΔG) of a reaction that is governed by weak interactions (approximately 10 kcal/mol), such as electrostatic, van der Waals, hydrophobic, hydrogen bonding, and π-π stacking, is determined by the exquisite balance of enthalpy (ΔH) and entropy changes (ΔS), in accordance with the fundamental thermodynamic equation ΔG = ΔH - TΔS. The mutually correlated ΔH-ΔS relationship is known as the enthalpy-entropy compensation law, in which a more negative enthalpic change (more exothermic) causes further entropic loss based on a more negative entropy change. Namely, changing the temperature (T) as the state quantity, except for P, is highly likely to be equal to controlling the entropy term. The solution-state entropy term is relatively vague, mainly based on solvation, and thus unpredictable, even using high-cost quantum mechanical calculations because of the vast number of solvation molecules. Hence, such entropy control is not always feasible and must be demonstrated on a trial-and-error basis. Furthermore, the above-mentioned equation can be rearranged as ΔG = ΔF + PΔV, enabling us to control solution-state reactions by simply changing P as hydrostatic pressure based on the volume change (ΔV). The volume term is strongly relevant to conformational changes, solvation changes, and molecular recognition upon complexation and thus is relatively predictable, that is, volumetrically compact or not, compared to the complicated entropy term. These extrathermodynamic and kinetic observations prompted us to use hydrostatic pressure as a controlling factor over a long period. Hydrostatic pressure chemistry in the solution phase has developed over the past six decades and then converged and passed the fields of mechanochemistry and mechanobiology, which are new but challenging and current hot topics in multidisciplinary science. In this Account, we fully summarize our achievements in solution-state hydrostatic pressure chemistry for smart/functional molecular, supramolecular, polymer, and biological systems. We hope that the phenomena, mechanistic outcomes, and methodologies that we introduced herein for hydrostatic-pressure-controlling dynamics can provide guidance for both theoretical and experimental chemists working in supramolecular and (bio)macromolecular chemistry, mechanoscience, materials science, and technology.

Advances in drying techniques for retention of antioxidants in agro produces

Antioxidants are compounds that are essential for the human body which prevents cell from disease causing free radicals. Antioxidants are present in a wide range of fruits, vegetables, and spices. However, a considerable amount of antioxidants is lost during the post-harvest drying operation of agro produces for their shelf-life enhancement. Hence, retention of antioxidants becomes utmost importance in preserving the nutritional aspects of fruits and vegetables. Compared to conventional hot air drying, methods like freeze drying, vacuum drying, and dehumidified drying helps in the retention of antioxidants. However, the drawbacks prevalent in current drying practices, such as high-power consumption and high capital cost, could be eliminated by adopting novel drying mechanisms. This review focuses on various pretreatment methods like ultra-sonication, high pressure processing, pulsed electric field and ethanol treatment prior to drying operation helps in enhancing the drying efficiency with maximum retention of antioxidants. In addition, hybrid drying technologies such as microwave assisted drying, IR-radiated drying and electro-magnetic assisted drying methods also could significantly improve the retention of antioxidants.HIGHLIGHTSDrying is the most commonly adopted unit operation for enhancing the shelf life of perishable agro produces.However, drying is accompanied by loss of bioactive, color, texture, and sensory attributes.Compared to conventional drying techniques like hot air drying, methods like freeze drying, vacuum drying and dehumidified drying helps in the retention of antioxidants present in agro/food produces.Pretreatment methods like Ozonation, ultra-sonication, and UV radiation prior to drying are also found to improve the drying performance with good retention of antioxidants.Recent developments like microwave-assisted and IR-assisted drying methods perform well in the retention of antioxidants with less energy consumption.

High Hydrostatic Pressure-Based Combination Strategies for Microbial Inactivation of Food Products: The Cases of Emerging Combination Patterns

The high demand for fresh-like characteristics of vegetables and fruits (V&F) boosts the industrial implementation of high hydrostatic pressure (HHP), due to its capability to simultaneously maintain original organoleptic characteristics and to achieve preservative effect of the food. However, there remains great challenges for assuring complete microbial inactivation only relying on individual HHP treatments, including pressure-resistant strains and regrowth of injured microbes during the storage process. Traditional HHP-assisted thermal processing may compromise the nutrition and functionalities due to accelerated chemical kinetics under high pressure conditions. This work summarizes the recent advances in HHP-based combination strategies for microbial safety, as exemplified by several emerging non-thermally combined patterns with high inactivation efficiencies. Considerations and requirements about future process design and development of HHP-based combination technologies are also given.

Effects of different antioxidants combined with high hydrostatic pressure on the color and anthocyanin retention of a blueberry juice blend during storage

Blueberry juice has been found to undergo severe browning after treatment and cold storage, such as processing by high hydrostatic pressure (HHP) at 550 MPa/10 min/25°C followed storage at 4°C for 4 days. This browning may be due to the degradation of anthocyanin (AC) in the berries. Therefore, in this study, gallic acid (GA), ferulic acid (FA), ascorbic acid (VC), citric acid (CA), tea polyphenol (TP) and α-tocopherol (VE) were compared to determine their ability to improve the stability of the AC in HHP-treated blueberry juice. The juice was combined with the six abovementioned antioxidants at different concentrations, then treated by HHP at 550 MPa/10 min/25°C and stored at 4°C for 20 days. Thereafter, the pH levels, degrees °Brix (°Bx), color parameters, total AC content and polyphenol oxidase (PPO) activity of the blueberry juice blend were measured and compared. Gallic acid at 2 g/L was found to be the most effective antioxidant to protect against AC degradation. After storage at 4°C for 20 days, the AC content of the juice with no added antioxidants had decreased by 62.27% with a PPO relative activity of 50.78%, while the AC content of juice supplemented with 2 g/L GA had decreased by 13.42% with a PPO relative activity of 28.13%. The results of this study, thus, suggest that GA can stabilize the structure of AC in blueberry juice and reduce PPO activity, which may be beneficial in guiding the production of blueberry juice with high AC retention.

Molecular Dynamics Calculations of Partial Molar Volumes of Amino Acids in Aqueous Solutions

Partial molar volumes of amino acids in their zwitterionic and molecular forms have been calculated using molecular dynamics simulations of these systems in aqueous solutions. Calculations performed with the TIP4P, SPC (rigid and flexible), SPC/E, and polarizable water models show that the choice of water model can have a significant impact on the calculated volumes. The effect of treatment of long-range electrostatic interactions on the calculated results was also investigated. Volumes obtained in simulations with a properly chosen water model fit well the experimental data for both molecular and zwitterionic forms of amino acids.

A pressure-induced ratiometric signalling chemosensor: a case of helical anthracenes

One of the helical anthracenes, [4]HA, in which two fused anthracene ends are spatially arranged top and bottom, exhibits a ratiometric fluorescence response due to the hydrostatic pressure-dependent intramolecular [4+4] photocyclodimerization. This ratiometric signalling comes from the formation of an intramolecular stacked species and its subsequent photoreaction upon hydrostatic pressurization. The ratiometric indexes as a function of hydrostatic pressure may enable us to quantify an unknown pressure in solutions.

Effects of Cosolvents and Crowding Agents on the Stability and Phase Transition Kinetics of the SynGAP/PSD-95 Condensate Model of Postsynaptic Densities

The SynGAP/PSD-95 binary protein system serves as a simple mimicry of postsynaptic densities (PSDs), which are protein assemblies based largely on liquid-liquid phase separation (LLPS), that are located underneath the plasma membrane of excitatory synapses. Surprisingly, the LLPS of the SynGAP/PSD-95 system is much more pressure sensitive than typical folded states of proteins or nucleic acids. It was found that phase-separated SynGAP/PSD-95 droplets dissolve into a homogeneous solution at a pressure of tens to hundred bar. Since organisms in the deep sea are exposed to pressures of up to ∼1000 bar, this observation suggests that deep-sea organisms must counteract the high pressure sensitivity of PSDs to avoid neurological impairment. We demonstrate here that the compatible osmolyte trimethylamine-N-oxide (TMAO) as well as macromolecular crowding agents at moderate concentrations can mitigate the deleterious effect of pressure on SynGAP/PSD-95 droplet stability, extending stable LLPS up to almost a kbar level. Moreover, the formation of SynGAP/PSD-95 droplets is a very rapid process that can be switched on and off in seconds. In contrast with the marked effects of the cosolutes on droplet stability, at the cosolutes' respective biologically relevant concentrations, their impact on the phase transformation kinetics is rather small. Only a high TMAO concentration results in a significant kinetic retardation of LLPS. Taken together, these findings offer new biophysical insights into the neurological effects of hydrostatic pressure. In particular, our results indicate how pressure-induced neurological disorders might be alleviated by upregulating certain cosolutes in the cellular milieu.

Can Urea and Trimethylamine-N-oxide Prevent the Pressure-Induced Phase Transition of Lipid Membrane?

Organisms dwelling in ocean trenches are exposed to the high hydrostatic pressure of ocean water. Increasing pressure can alter the membrane packing density and fluidity and trigger the fluid-to-gel phase transition. To combat environmental stress, the organisms synthesize small polar solutes, which are known as osmolytes. Urea and trimethylamine-N-oxide (TMAO) are two such solutes found in deep-sea creatures. While TMAO stabilizes protein, urea induces protein denaturation. These solutes strongly influence the packing density and membrane fluidity of the lipid bilayer at different conditions. But can these solutes affect the pressure-induced phase transition of the lipid membrane? In the present work, we have studied the effect of these two solutes on pressure-induced fluid-to-gel phase transition based on the all-atom molecular dynamics (MD) simulation approach. A high-pressure-stimulated fluid-to-gel phase transition of the membrane is seen at 800 bar, which is consistent with previous experiments. We have also observed that in the low-pressure region (1-400 bar), urea slightly increases the membrane fluidity where TMAO decreases the same. However, the phase transition pressure remains almost unchanged on the addition of urea while TMAO shifts the phase transition toward a lower pressure. We have found that the hydrogen (H)-bond interaction between lipid and urea plays an important role in preserving the fluidity of the membrane in the low-pressure zone. However, at a higher pressure, both water and urea are excluded from the membrane surface. TMAO is also excluded from the interfacial region of the membrane at all pressures. Exclusion from the membrane surface further triggers the phase transition of the lipid membrane from the fluid to gel phase at a high pressure.

Influence of iron binding in the structural stability and cellular internalization of bovine lactoferrin

Lactoferrin (Lf) is an iron-binding glycoprotein and a component of many external secretions with a wide diversity of functions. Structural studies are important to understand the mechanisms employed by Lf to exert so varied functions. Here, we used guanidine hydrochloride and high hydrostatic pressure to cause perturbations in the structure of bovine Lf (bLf) in apo and holo (unsaturated and iron-saturated, respectively) forms, and analyzed conformational changes by intrinsic and extrinsic fluorescence spectroscopy. Our results showed that the iron binding promotes changes on tertiary structure of bLf and increases its structural stability. In addition, we evaluated the effects of bLf structural change on the kinetics of bLf internalization in Vero cells by confocal fluorescence microscopy, and observed that the holo form was faster than the apo form. This finding may indicate that structural changes promoted by iron binding may play a key role in the intracellular traffic of bLf. Altogether, our data improve the comprehension of bLf stability and uptake, adding knowledge to its potential use as a biopharmaceutical.

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.

Hydrostatic High-Pressure-Induced Denaturation of LH2 Membrane Proteins

The denaturation of globular proteins by high pressure is frequently associated with the release of internal voids and/or the exposure of the hydrophobic protein interior to a polar aqueous solvent. Similar evidence with respect to membrane proteins is not available. Here, we investigate the impact of hydrostatic pressures reaching 12 kbar on light-harvesting 2 integral membrane complexes of purple photosynthetic bacteria using two types of innate chromophores in separate strategic locations: bacteriochlorophyll-a in the hydrophobic interior and tryptophan at both protein-solvent interfacial gateways to internal voids. The complexes from mutant Rhodobacter sphaeroides with low resilience against pressure were considered in parallel with the naturally robust complexes of Thermochromatium tepidum. In the former case, a firm correlation was established between the abrupt blue shift of the bacteriochlorophyll-a exciton absorption, a known indicator of the breakage of tertiary structure pigment-protein hydrogen bonds, and the quenching of tryptophan fluorescence, a supposed result of further protein solvation. No such effects were observed in the reference complex. While these data may be naively taken as supporting evidence of the governing role of hydration, the analysis of atomistic model structures of the complexes confirmed the critical part of the structure in the pressure-induced denaturation of the membrane proteins studied.

Kinetic Study of the Avocado Sunblotch Viroid Self-Cleavage Reaction Reveals Compensatory Effects between High-Pressure and High-Temperature: Implications for Origins of Life on Earth

A high pressure apparatus allowing one to study enzyme kinetics under pressure was used to study the self-cleavage activity of the avocado sunblotch viroid. The kinetics of this reaction were determined under pressure over a range up to 300 MPa (1-3000 bar). It appears that the initial rate of this reaction decreases when pressure increases, revealing a positive ΔV≠ of activation, which correlates with the domain closure accompanying the reaction and the decrease of the surface of the viroid exposed to the solvent. Although, as expected, temperature increases the rate of the reaction whose energy of activation was determined, it appeared that it does not significantly influence the ΔV≠ of activation and that pressure does not influence the energy of activation. These results provide information about the structural aspects or this self-cleavage reaction, which is involved in the process of maturation of this viroid. The behavior of ASBVd results from the involvement of the hammerhead ribozyme present at its catalytic domain, indeed a structural motif is very widespread in the ancient and current RNA world.

Cryo-EM to visualize the structural organization of viruses

It is intriguing to think that over millions of years, groups of nucleic acids got the chance to hold together with groups of proteins to build up what today is called a virus. Their only goal is to guarantee a successful replication inside a host. If their genome information is preserved, the task is accomplished. Viruses have evolved to infect organisms and propagate with high degree of adaptation, as it is the case of the SARS-CoV-2, agent of the 2020 world pandemic. The technological progress observed in the field of structural biology, especially in cryo-EM, has offered scientists the possibility of a better understanding of virus origins, behavior, and structural organization. In this minireview we summarize few perspectives about the origins and organization of viruses and the advances of cryo-EM to aid structural virologists to sample the virosphere.

Unraveling the binding characteristics of small ligands to telomeric DNA by pressure modulation

Recently, non-canonical DNA structures, such as G-quadruplexes (GQs), were found to be highly pressure sensitive, suggesting that pressure modulation studies can provide additional mechanistic details of such biomolecular systems. Using FRET and CD spectroscopy as well as binding equilibrium measurements, we investigated the effect of pressure on the binding reaction of the ligand ThT to the quadruplex 22AG in solutions containing different ionic species and a crowding agent mimicking the intracellular milieu. Pressure modulation helped us to identify the different conformational substates adopted by the quadruplex at the different solution conditions and to determine the volumetric changes during complex formation and the conformational transitions involved. The magnitudes of the binding volumes are a hallmark of packing defects and hydrational changes upon ligand binding. The conformational substates of the GQ as well as the binding strength and the stoichiometry of complex formation depend strongly on the solution conditions as well as on pressure. High hydrostatic pressure can also impact GQs inside living cells and thus affect expression of genetic information in deep sea organisms. We show that sub-kbar pressures do not only affect the conformational dynamics and structures of GQs, but also their ligand binding reactions.

Biomolecular Condensates under Extreme Martian Salt Conditions

Biomolecular condensates formed by liquid-liquid phase separation (LLPS) are considered one of the early compartmentalization strategies of cells, which still prevail today forming nonmembranous compartments in biological cells. Studies of the effect of high pressures, such as those encountered in the subsurface salt lakes of Mars or in the depths of the subseafloor on Earth, on biomolecular LLPS will contribute to questions of protocell formation under prebiotic conditions. We investigated the effects of extreme environmental conditions, focusing on highly aggressive Martian salts (perchlorate and sulfate) and high pressure, on the formation of biomolecular condensates of proteins. Our data show that the driving force for phase separation of proteins is not only sensitively dictated by their amino acid sequence but also strongly influenced by the type of salt and its concentration. At high salinity, as encountered in Martian soil and similar harsh environments on Earth, attractive short-range interactions, ion correlation effects, hydrophobic, and π-driven interactions can sustain LLPS for suitable polypeptide sequences. Our results also show that salts across the Hofmeister series have a differential effect on shifting the boundary of immiscibility that determines phase separation. In addition, we show that confinement mimicking cracks in sediments and subsurface saline water pools in the Antarctica or on Mars can dramatically stabilize liquid phase droplets, leading to an increase in the temperature and pressure stability of the droplet phase.