Pressure effects on intra- and intermolecular interactions within proteins

AAontology: An Ontology of Amino Acid Scales for Interpretable Machine Learning

Amino acid scales are crucial for protein prediction tasks, many of them being curated in the AAindex database. Despite various clustering attempts to organize them and to better understand their relationships, these approaches lack the fine-grained classification necessary for satisfactory interpretability in many protein prediction problems. To address this issue, we developed AAontology-a two-level classification for 586 amino acid scales (mainly from AAindex) together with an in-depth analysis of their relations-using bag-of-word-based classification, clustering, and manual refinement over multiple iterations. AAontology organizes physicochemical scales into 8 categories and 67 subcategories, enhancing the interpretability of scale-based machine learning methods in protein bioinformatics. Thereby it enables researchers to gain a deeper biological insight. We anticipate that AAontology will be a building block to link amino acid properties with protein function and dysfunctions as well as aid informed decision-making in mutation analysis or protein drug design.

Stabilization of galactose oxidase by high hydrostatic pressure: Insights on the role of cavities size

High hydrostatic pressure stabilized galactose oxidase (GaOx) at 70.0-80.0°C against thermal inactivation. The pseudo-first-order rate constant of inactivation kinact decreased by a factor of 8 at 80°C and by a factor of 44 at 72.5°C. The most pronounced effect of pressure was at the lowest studied temperature of 70.0°C with an activation volume of inactivation ΔV‡ of 78.8 cm3 mol-1. The optimal pressure against thermal inactivation was between 200 and 300 MPa. Unlike other enzymes, as temperature increased the ΔV‡ of inactivation decreased, and as pressure increased the activation energy of inactivation Eai increased. Combining the results for GaOx with earlier research on the pressure-induced stabilization of other enzymes suggests that ΔV‡ of inactivation correlates with the total molar volume of cavities larger than ~100 Å3 in enzyme monomers for enzymes near the optimal pH and whose thermal unfolding is not accompanied by oligomer dissociation.

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.

Effect of high pressure pretreatment on the inhibition of ice nucleation and biochemical changes in pork loins during supercooling preservation

In this study, the effect of high pressure (HP) pretreatment on the stability of pork loins during supercooling (SC) preservation was investigated, and the freshness and postmortem metabolism of pork loins preserved by SC was evaluated. Based on the differential scanning calorimetry (DSC), the peak enthalpies of 200 MPa treatment were lower than those of 50 MPa treatment (P < 0.05). For the nuclear magnetic resonance (NMR) relaxometry, extramyofibrillar water in pork loins was decreased with increasing intermyofibrillar water at >100 MPa (P < 0.05). Compared to unpressurized control all HP treatment had less α-helix structure while random coil was dominated from the Fourier transform infrared (FTIR) spectroscopy (P < 0.05). A 200 MPa was selected to estimate the relationship between HP pretreatment and stability of SC preservation of pork loins. The HP-treated pork loins showed high stability during SC preservation under the relatively low temperature algorithm. Compared to fresh control, HP pretreatment caused physicochemical changes of pork loins which did not recover even after 2 weeks of preservation. Nevertheless, HP followed by SC preservation was able to reduce property changes better than pork loins preserved by normal refrigeration. According to the analyses of transmission electron microscopy (TEM), the HP pretreatment influenced the postmortem biochemical metabolism of pork loins, however, it did not affect the freshness and quality parameters of pork loins due to the subsequently applied low preservation temperature of SC. Therefore, this study demonstrated that moderate HP pretreatment was a potential pretreatment for SC preservation of pork loins.

High-Pressure Pasteurization of Oat Okara

The issue of the short microbiological shelf life of residues from the plant-based beverage industry creates a large food waste problem. Today, the oat beverage residue, in this study referred to as oat okara, is generally converted to energy or used as animal feed. High-pressure pasteurization (200 MPa, 400 MPa, and 600 MPa) was applied to oat okara to investigate the effect on shelf life and microbiological activity. A 4-week microbiological storage study was performed and thermal properties, viscosity, and water and oil holding capacities were analyzed. The total aerobic count, including yeast and mold, was significantly reduced (p < 0.05) by 600 MPa after four weeks of storage at 4 °C. The content of lactic acid bacteria after four weeks of storage was low for untreated oat okara (3.2 log CFU/g) but, for 600 MPa, the content remained at the detection limit (2.3 log CFU/g). Conversely, the treatments of 200 MPa and 400 MPa increased the microbial content of the total aerobic count significantly (p < 0.05) after two weeks in comparison to untreated oat okara. The thermal properties of untreated and high-pressure-treated oat okara demonstrated an increase in protein denaturation of the 12S globulin, avenalin, when higher pressure was applied (400-600 MPa). This was also confirmed in the viscosity measurements where a viscosity peak for avenalin was only present for untreated and 200 MPa treated oat okara. The water holding capacity did not change as a function of high-pressure treatment (3.5-3.8 mL/g) except for the treatment at 200 MPa, which was reduced (2.7 mL/g). The oil holding capacity was constant (1.2-1.3 mL/g) after all treatments. High-pressure pasteurization of 600 MPa reduced the microbial content in oat okara resulting in a shelf life of 2-4 weeks. However, more research is required to identify the microorganisms in oat okara to achieve a microbiologically safe product that can be used for food applications.

Influence of elevated pressure and pressurized fluids on microenvironment and activity of enzymes

Enzymes have great potential in bioprocess engineering due to their green and mild reaction conditions. However, there are challenges to their application, such as enzyme extraction and purification costs, enzyme recovery, and long reaction time. Enzymatic reaction rate enhancement and enzyme immobilization have the potential to overcome some of these challenges. Application of high pressure (e.g., hydrostatic pressure, supercritical carbon dioxide) has been shown to increase the activity of some enzymes, such as lipases and cellulases. Under high pressure, enzymes undergo multiple alterations simultaneously. High pressure reduces the bond lengths of molecules of reaction components and causes a reduction in the activation volume of enzyme-substrate complex. Supercritical CO2 interacts with enzyme molecules, catalyzes structural changes, and removes some water molecules from the enzyme's hydration layer. Interaction of scCO2 with the enzyme also leads to an overall change in secondary structure content. In the extreme, such changes may lead to enzyme denaturation, but enzyme activation and stabilization have also been observed. Immobilization of enzymes onto silica and zeolite-based supports has been shown to further stabilize the enzyme and provide resistance towards perturbation under subjection to high pressure and scCO2.

High-pressure processing of beef increased the in vitro protein digestibility in an infant digestion model

Beef is an ideal protein source for use as a complementary food in infants. Considering the limited protein-digesting capacity of infants, it is required to enhance protein digestibility while minimizing the deterioration of beef quality. Thus, this study aimed to determine the effects of high-pressure processing (HPP) on the physicochemical properties and in vitro digestibility of beef proteins in an infant digestion model. HPP at 200 and 300 MPa decreased the tryptophan fluorescence intensity of the myosin and actin fractions relative to that at 0.1 MPa (P < 0.05). Compared to treatment at 0.1 and 100 MPa, HPP at 300 MPa decreased α-helix and β-turn contents in the myosin and actin fractions (P < 0.05), whilst increasing the β-sheet content (P < 0.05). Beef actomyosin content decreased (P < 0.05) during HPP at 200 and 300 MPa (c.f., 0.1 and 100 MPa). After in vitro digestion of beef, HPP at 200 and 300 MPa increased the α-amino group content and the abundance of proteins below 3 kDa in the digesta (P < 0.05). However, due to the considerable lipid oxidation at 300 MPa, HPP at 200 MPa is ideal for improving the protein digestibility of beef when incorporated into complementary foods for infants.

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.

Technologies for Vitrification Based Cryopreservation

Cryopreservation is a unique and practical method to facilitate extended access to biological materials. Because of this, cryopreservation of cells, tissues, and organs is essential to modern medical science, including cancer cell therapy, tissue engineering, transplantation, reproductive technologies, and bio-banking. Among diverse cryopreservation methods, significant focus has been placed on vitrification due to low cost and reduced protocol time. However, several factors, including the intracellular ice formation that is suppressed in the conventional cryopreservation method, restrict the achievement of this method. To enhance the viability and functionality of biological samples after storage, a large number of cryoprotocols and cryodevices have been developed and studied. Recently, new technologies have been investigated by considering the physical and thermodynamic aspects of cryopreservation in heat and mass transfer. In this review, we first present an overview of the physiochemical aspects of freezing in cryopreservation. Secondly, we present and catalog classical and novel approaches that seek to capitalize on these physicochemical effects. We conclude with the perspective that interdisciplinary studies provide pieces of the cryopreservation puzzle to achieve sustainability in the biospecimen supply chain.

Development of a novel regenerative therapy for malignant bone tumors using an autograft containing tumor inactivated by high hydrostatic pressurization (HHP)

Surgical resection of malignant bone tumors leads to significant defects in the normal surrounding tissues that should be reconstructed to avoid amputation. Our research aimed to inactivate osteosarcoma (OS)-affected bone to obtain autologous bone grafts for bone defect reconstruction using a novel therapy called high hydrostatic pressurization (HHP) therapy. The key points are complete tumor death and preservation of the non-denatured native extracellular matrix (ECM) and bone tissue by HHP. Previously, we found that HHP at 200 MPa for 10 min can completely inactivate cells in normal skin and skin tumors, including malignant melanoma and squamous cell carcinoma while maintaining their original biochemical properties and biological components. Based on our previous research, this study used HHP at 200 MPa for 10 min to eradicate OS. We prepared an OS cell line (LM8), pressurized it at 200 MPa for 10 min, and confirmed its inactivation through morphological observation, WST-8 assay, and live/dead assay. We then injected OS cells with or without HHP into the bone marrow of the murine tibia, after which we implanted tumor tissues with or without HHP into the anterior surface of the tibia. After HHP, OS cells did not proliferate and were assessed using a live/dead assay. The pressurized cells and tumors did not grow after implantation. The pressurized bone was well prepared as tumor-free autologous bone tissues, resulting in the complete eradication of OS. This straightforward and short-pressing treatment was proven to process the tumor-affected bone to make a transplantable and tumor-free autologous bone substitute.

Marine enzymes: Classification and application in various industries

Oceans are regarded as a plentiful and sustainable source of biological compounds. Enzymes are a group of marine biomaterials that have recently drawn more attention because they are produced in harsh environmental conditions such as high salinity, extensive pH, a wide temperature range, and high pressure. Hence, marine-derived enzymes are capable of exhibiting remarkable properties due to their unique composition. In this review, we overviewed and discussed characteristics of marine enzymes as well as the sources of marine enzymes, ranging from primitive organisms to vertebrates, and presented the importance, advantages, and challenges of using marine enzymes with a summary of their applications in a variety of industries. Current biotechnological advancements need the study of novel marine enzymes that could be applied in a variety of ways. Resources of marine enzyme can benefit greatly for biotechnological applications duo to their biocompatible, ecofriendly and high effectiveness. It is beneficial to use the unique characteristics offered by marine enzymes to either develop new processes and products or improve existing ones. As a result, marine-derived enzymes have promising potential and are an excellent candidate for a variety of biotechnology applications and a future rise in the use of marine enzymes is to be anticipated.

High hydrostatic pressure induces slow contraction in mouse cardiomyocytes

Cardiomyocytes are contractile cells that regulate heart contraction. Ca2+ flux via Ca2+ channels activates actomyosin interactions, leading to cardiomyocyte contraction, which is modulated by physical factors (e.g., stretch, shear stress, and hydrostatic pressure). We evaluated the mechanism triggering slow contractions using a high-pressure microscope to characterize changes in cell morphology and intracellular Ca2+ concentration ([Ca2+]i) in mouse cardiomyocytes exposed to high hydrostatic pressures. We found that cardiomyocytes contracted slowly without an acute transient increase in [Ca2+]i, while a myosin ATPase inhibitor interrupted pressure-induced slow contractions. Furthermore, transmission electron microscopy showed that, although the sarcomere length was shortened upon the application of 20 MPa, this pressure did not collapse cellular structures such as the sarcolemma and sarcomeres. Our results suggest that pressure-induced slow contractions in cardiomyocytes are driven by the activation of actomyosin interactions without an acute transient increase in [Ca2+]i.

Conformational Rearrangements in the Redox Cycling of NADPH-Cytochrome P450 Reductase from Sorghum bicolor Explored with FRET and Pressure-Perturbation Spectroscopy

Simple Summary

NADPH-cytochrome P450 reductase (CPR) enzymes are known to undergo an ample conformational transition between the closed and open states in the process of their redox cycling. To explore the conformational landscape of CPR from the potential biofuel crop Sorghum bicolor (SbCPR), we incorporated a FRET donor/acceptor pair into the enzyme and employed rapid scanning stop-flow and pressure perturbation spectroscopy to characterize the equilibrium between its open and closed states at different stages of the redox cycle. Our results suggest the presence of several open conformational sub-states differing in the system volume change associated with the opening transition (ΔV⁰). Although the closed conformation always predominates in the conformational landscape, the population of the open conformations increases by order of magnitude upon the two-electron reduction and the formation of the disemiquinone state of the enzyme. In addition to elucidating the functional choreography of plant CPRs, our study demonstrates the high exploratory potential of a combination of the pressure-perturbation approach with the FRET-based monitoring of protein conformational transitions.

Abstract

NADPH-cytochrome P450 reductase (CPR) from Sorghum bicolor (SbCPR) serves as an electron donor for cytochrome P450 essential for monolignol and lignin production in this biofuel crop. The CPR enzymes undergo an ample conformational transition between the closed and open states in their functioning. This transition is triggered by electron transfer between the FAD and FMN and provides access of the partner protein to the electron-donating FMN domain. To characterize the electron transfer mechanisms in the monolignol biosynthetic pathway better, we explore the conformational transitions in SbCPR with rapid scanning stop-flow and pressure-perturbation spectroscopy. We used FRET between a pair of donor and acceptor probes incorporated into the FAD and FMN domains of SbCPR, respectively, to characterize the equilibrium between the open and closed states and explore its modulation in connection with the redox state of the enzyme. We demonstrate that, although the closed conformation always predominates in the conformational landscape, the population of open state increases by order of magnitude upon the formation of the disemiquinone state. Our results are consistent with several open conformation sub-states differing in the volume change (ΔV⁰) of the opening transition. While the ΔV⁰ characteristic of the oxidized enzyme is as large as −88 mL/mol, the interaction of the enzyme with the nucleotide cofactor and the formation of the double-semiquinone state of CPR decrease this value to −34 and −18 mL/mol, respectively. This observation suggests that the interdomain electron transfer in CPR increases protein hydration, while promoting more open conformation. In addition to elucidating the functional choreography of plant CPRs, our study demonstrates the high exploratory potential of a combination of the pressure-perturbation approach with the FRET-based monitoring of protein conformational transitions.

Effects of high-pressure processing on the functional properties of pork batters containing Artemisia sphaerocephala krasch gum

Here, the effect of high-pressure conditions (0.1-400 MPa) on the water-loss, texture, gel strength, color, dynamic rheological property, and water migration of pork batters containing 0.1% (W/W) Artemisia sphaerocephala krasch gum (PB-AG) is studied. Results indicated that the cooking yield, water-holding capacity, texture, gel strength, L^* values, and G' values increased with the increase in pressure (0.1-300 MPa) (p < 0.05). Dynamic rheological results (G') revealed that the thermal gelling ability of the PB-AG gel gradually increased with pressure (0.1-300 MPa). The minimum of T₂₂ content was observed and the proportion of immobilized water decreased at 300 MPa by low-filed nuclear magnetic resonance. However, excessive high-pressure processing treatments (400 MPa) resulted in lower gel strength, WHC, texture, and G'. The scanning electron microscopy results shown that a denser network structure with small cavities was observed at 300 MPa. Therefore, moderate pressure treatment (≤300 MPa) may improve gelation properties of PB-AG gel, while excessive pressure treatment (400 MPa) may weaken the gelation properties. PRACTICAL APPLICATION: High-pressure processing combining Artemisia sphaerocephala krasch gum could enhance the gelation properties of pork batters. To do so, establishing knowledge on gelation properties of pork batters with Artemisia sphaerocephala krasch gum at different pressure levels treatment would be of paramount importance, because this contributes furnishing engineering data pertinent to the technical progress for the processing of emulsion-type meat with high quality.

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.

Non-thermal emerging technologies as alternatives to chemical additives to improve the quality of wheat flour for breadmaking: a review

Wheat flour is the main ingredient used in the preparation of bread. Factors such as low gluten content and the addition of nontraditional ingredients in baking affect the quality of wheat flour and may limit its use in baking. With the increasing trend of "clean label" products, it may be interesting to develop and use physical processes to improve the quality of wheat flour and avoid the use of chemical additives. High hydrostatic pressure, non-thermal plasma, ultrasound, ozonation, ultraviolet light, and pulsed light treatments are non-thermal emerging technologies (NTETs) that have been studied for this purpose. They were originally developed to inactivate microorganisms and enzymes in foods. Additionally, these technologies can be used at low temperatures to modify the most important component of wheat flour, i.e., gluten and its fractions, which are responsible for the rheological properties of wheat flour dough. Thus, this review focuses on the effects of these NTETs by considering the following factors: (1) the technological properties of gluten, (2) gluten-starch interactions, (3) possible effects of NTETs on minor components of flours, and (4) the quality of wheat flour and the resulting final products.

Thermostable adenosine 5'-monophosphate phosphorylase from Thermococcus kodakarensis forms catalytically active inclusion bodies

Catalytically active inclusion bodies (CatIBs) produced in Escherichia coli are an interesting but currently underexplored strategy for enzyme immobilization. They can be purified easily and used directly as stable and reusable heterogenous catalysts. However, very few examples of CatIBs that are naturally formed during heterologous expression have been reported so far. Previous studies have revealed that the adenosine 5′-monophosphate phosphorylase of Thermococcus kodakarensis (TkAMPpase) forms large soluble multimers with high thermal stability. Herein, we show that heat treatment of soluble protein from crude extract induces aggregation of active protein which phosphorolyse all natural 5′-mononucleotides. Additionally, inclusion bodies formed during the expression in E. coli were found to be similarly active with 2–6 folds higher specific activity compared to these heat-induced aggregates. Interestingly, differences in the substrate preference were observed. These results show that the recombinant thermostable TkAMPpase is one of rare examples of naturally formed CatIBs.

Effects of High Hydrostatic Pressure on the Conformational Structure and Gel Properties of Myofibrillar Protein and Meat Quality: A Review

In meat processing, changes in the myofibrillar protein (MP) structure can affect the quality of meat products. High hydrostatic pressure (HHP) has been widely utilized to change the conformational structure (secondary, tertiary and quaternary structure) of MP so as to improve the quality of meat products. However, a systematic summary of the relationship between the conformational structure (secondary and tertiary structure) changes in MP, gel properties and product quality under HHP is lacking. Hence, this review provides a comprehensive summary of the changes in the conformational structure and gel properties of MP under HHP and discusses the mechanism based on previous studies and recent progress. The relationship between the spatial structure of MP and meat texture under HHP is also explored. Finally, we discuss considerations regarding ways to make HHP an effective strategy in future meat manufacturing.

Effects of high-pressure treatment on the muscle structure of salmon (Salmo salar)

High pressure (HP) is a non-thermal treatment that is generally used to reduce the microbiological contamination of food products, such as Atlantic salmon (Salmo salar). However, HP is known to alter the stability of proteins and can therefore affect the quality of salmon flesh. In this study, the effects of HP treatment for 5 min at 200, 400 and 600 MPa on the structure of Atlantic salmon were investigated. Transversal histological sections revealed a decrease in the fibre size from 200 MPa associated with an expansion of the extracellular spaces. Connective tissue was found to be modified from 400 MPa, resulting in an increase in its surface area. Fourier transform infrared (FT-IR) microspectroscopy revealed a reduction in the α-helix content and an increase in the aggregated β-sheet structure content with increasing pressure, reflecting a change in the secondary structure of proteins from 200 MPa.

The Effects of Temperature and Pressure on Protein-Ligand Binding in the Presence of Mars-Relevant Salts

Simple Summary

Interactions of ligands with proteins are central to all reactions in the biological cell. How such reactions are affected by harsh environmental conditions, such as low temperatures, high pressures, and high concentrations of biologically destructive salts, is still largely unknown. Our work focused on specific salts found on Mars to understand whether the planet’s potentially liquid, water-rich subsurface harbors conditions that are theoretically favorable for life. Our data show that, while magnesium chloride and sulfate do not significantly alter protein–ligand interactions, the perchlorate ion strongly affects protein–ligand binding. However, the temperature and pressure conditions encountered on Mars do not necessarily preclude protein–ligand interactions of the type studied here.

Abstract

Protein–ligand interactions are fundamental to all biochemical processes. Generally, these processes are studied at ambient temperature and pressure conditions. We investigated the binding of the small ligand 8-anilinonaphthalene-1-sulfonic acid (ANS) to the multifunctional protein bovine serum albumin (BSA) at ambient and low temperatures and at high pressure conditions, in the presence of ions associated with the surface and subsurface of Mars, including the chaotropic perchlorate ion. We found that salts such as magnesium chloride and sulfate only slightly affect the protein–ligand complex formation. In contrast, magnesium perchlorate strongly affects the interaction between ANS and BSA at the single site level, leading to a change in stoichiometry and strength of ligand binding. Interestingly, both a decrease in temperature and an increase in pressure favor the ligand binding process, resulting in a negative change in protein–ligand binding volume. This suggests that biochemical reactions that are fundamental for the regulation of biological processes are theoretically possible outside standard temperature and pressure conditions, such as in the harsh conditions of the Martian subsurface.

Nano-architectural assembly of soy proteins: A promising strategy to fabricate nutraceutical nanovehicles

Use of protein-based nanovehicles has been well recognized to be one of the most effective strategies to improve water dispersibility, stability and bioavailability of nutraceuticals or bioactive ingredients. Thanks to their health-benefiting effects and unique assembly behavior, soy proteins seem to be the perfect food proteins for fabricating nanovehicles in this regard. This review presents the state-of-art knowledge about the assembly of soy proteins into nano-architectures, e. g., nanoparticles, nanocomplexes or nanogels, induced by different physicochemical strategies and approaches. The strategies to trigger the assembly of soy proteins into a variety of nano-architectures are highlighted and critically reviewed. Such strategies include heating, enzymatic hydrolysis, pH shift, urea or ethanol treatment, reduction, and static high pressure treatment. The self-assembly behavior of soy proteins (native or denatured) is also reviewed. Besides the assembly of proteins alone, soy proteins can co-assemble with polysaccharides to form versatile nano-architectures, through different processes, e.g., heating or ultrasonication. Finally, recent progress in the development of assembled soy protein nano-architectures as nanovehicles for hydrophobic nutraceuticals is briefly summarized. With the fast increasing health awareness for natural and safe functional foods, this review is of crucial relevance for providing an important strategy to develop a kind of novel soy protein-based functional foods with dual-function health effects from soy proteins and nutraceuticals.

Oriented Soft DNA Curtains for Single-Molecule Imaging

Over the past 20 years, single-molecule methods have become extremely important for biophysical studies. These methods, in combination with new nanotechnological platforms, can significantly facilitate experimental design and enable faster data acquisition. A nanotechnological platform, which utilizes a flow-stretch of immobilized DNA molecules, called DNA Curtains, is one of the best examples of such combinations. Here, we employed new strategies to fabricate a flow-stretch assay of stably immobilized and oriented DNA molecules using a protein template-directed assembly. In our assay, a protein template patterned on a glass coverslip served for directional assembly of biotinylated DNA molecules. In these arrays, DNA molecules were oriented to one another and maintained extended by either single- or both-end immobilization to the protein templates. For oriented both-end DNA immobilization, we employed heterologous DNA labeling and protein template coverage with the antidigoxigenin antibody. In contrast to single-end immobilization, both-end immobilization does not require constant buffer flow for keeping DNAs in an extended configuration, allowing us to study protein-DNA interactions at more controllable reaction conditions. Additionally, we increased the immobilization stability of the biotinylated DNA molecules using protein templates fabricated from traptavidin. Finally, we demonstrated that double-tethered Soft DNA Curtains can be used in nucleic acid-interacting protein (e.g., CRISPR-Cas9) binding assay that monitors the binding location and position of individual fluorescently labeled proteins on DNA.

Increased activity of alcohol oxidase at high hydrostatic pressure

Alcohol oxidase (AOx) from P. pastoris has potential applications in the production of carbonyl compounds and for the detection and quantification of alcohols. However, AOx's poor stability and low activity have hindered its practical application. There are two fractions of AOx in P. pastoris with different thermal stability. High hydrostatic pressure (HHP) increased the activity of the labile (L) + resistant (R) combined fractions but not of the R fraction alone. The activity of the L + R fractions increased 2.4-fold at 160 MPa and 30 °C compared to the activity at 0.1 MPa. At higher temperatures, the increase in activity with pressure was greater due to the combined stabilization and activation effects. The reaction rate of the R fraction at 50 °C was 17.9 ± 3.6 or 17.7 ± 0.8 μM min^-1 at 80 or 160 MPa, respectively, and was not significantly different from the activity of the L + R fractions under the same conditions (18.4 ± 2.7 μM min^-1). The activation energy of the R fraction was not significantly different between 80 MPa (41.5 ± 10.5 kJ mol^-1) and 160 MPa (43.8 ± 7.8 kJ mol^-1). The combined increase in the stability of the R fraction at HHP enables the use of the enzyme at 50 °C with little loss of activity and an increased catalytic rate.

Combinations of Radiotherapy with Vaccination and Immune Checkpoint Inhibition Differently Affect Primary and Abscopal Tumor Growth and the Tumor Microenvironment

Radiotherapy (RT) is known to have immune-modulatory properties. We hypothesized that RT and inactivated whole tumor cell vaccines generated with high hydrostatic pressure (HHP) synergize to retard the tumor growth which can be additionally improved with anti-PD-1 treatment. In abscopal tumor models, we injected mice with B16-F10 melanoma or TS/A mammary tumors. To evaluate the efficiency of RT in combination with HHP vaccines, we locally irradiated only one tumor with 2 × 8 Gy or 3 × 8 Gy. HHP vaccines further retarded the growth of locally irradiated (2 × 8 Gy) tumors. However, HHP vaccination combined with RT failed to induce abscopal anti-tumor immune responses, namely those to non-irradiated tumors, and even partly abrogated those which were induced with RT plus anti-PD-1. In the latter group, the abscopal effects were accompanied by an elevated infiltration of CD8+ T cells, monocytes/macrophages, and dendritic cells. 3 × 8 Gy failed to induce abscopal effects in association with increased expression of immunosuppressive checkpoint molecules compared to 2 × 8 Gy. We conclude that HHP vaccines induce anti-tumor effects, but only if the tumor microenvironment was previously modulated by hypofractionated RT with not too many fractions, but failed to improve RT plus anti-PD-induced abscopal responses that are characterized by distinct immune alterations.

High-pressure small-angle X-ray scattering cell for biological solutions and soft materials

Pressure is a fundamental thermodynamic parameter controlling the behavior of biological macromolecules. Pressure affects protein denaturation, kinetic parameters of enzymes, ligand binding, membrane permeability, ion trans-duction, expression of genetic information, viral infectivity, protein association and aggregation, and chemical processes. In many cases pressure alters the molecular shape. Small-angle X-ray scattering (SAXS) is a primary method to determine the shape and size of macromolecules. However, relatively few SAXS cells described in the literature are suitable for use at high pressures and with biological materials. Described here is a novel high-pressure SAXS sample cell that is suitable for general facility use by prioritization of ease of sample loading, temperature control, mechanical stability and X-ray background minimization. Cell operation at 14 keV is described, providing a q range of 0.01 < q < 0.7 Å-1, pressures of 0-400 MPa and an achievable temperature range of 0-80°C. The high-pressure SAXS cell has recently been commissioned on the ID7A beamline at the Cornell High Energy Synchrotron Source and is available to users on a peer-reviewed proposal basis.

Pressure tolerance of deep-sea enzymes can be evolved through increasing volume changes in protein transitions: a study with lactate dehydrogenases from abyssal and hadal fishes

We explore the principles of pressure tolerance in enzymes of deep-sea fishes using lactate dehydrogenases (LDH) as a case study. We compared the effects of pressure on the activities of LDH from hadal snailfishes Notoliparis kermadecensis and Pseudoliparis swirei with those from a shallow-adapted Liparis florae and an abyssal grenadier Coryphaenoides armatus. We then quantified the LDH content in muscle homogenates using mass-spectrometric determination of the LDH-specific conserved peptide LNLVQR. Existing theory suggests that adaptation to high pressure requires a decrease in volume changes in enzymatic catalysis. Accordingly, evolved pressure tolerance must be accompanied with an important reduction in the volume change associated with pressure-promoted alteration of enzymatic activity ( Δ V PP ∘ ). Our results suggest an important revision to this paradigm. Here, we describe an opposite effect of pressure adaptation-a substantial increase in the absolute value of Δ V PP ∘ in deep-living species compared to shallow-water counterparts. With this change, the enzyme activities in abyssal and hadal species do not substantially decrease their activity with pressure increasing up to 1-2 kbar, well beyond full-ocean depth pressures. In contrast, the activity of the enzyme from the tidepool snailfish, L. florae, decreases nearly linearly from 1 to 2500 bar. The increased tolerance of LDH activity to pressure comes at the expense of decreased catalytic efficiency, which is compensated with increased enzyme contents in high-pressure-adapted species. The newly discovered strategy is presumably used when the enzyme mechanism involves the formation of potentially unstable excited transient states associated with substantial changes in enzyme-solvent interactions.

Advanced Tenderization of Brine Injected Pork Loin as Affected by Ionic Strength and High Pressure

This study investigated the effects of brine injection and high hydrostatic pressure (HHP) on the quality characteristics of pork loin. Brine with ionic strength conditions (0.7% vs 1.5% NaCl, w/v) were injected into pork loins, and the meat was pressurized up to 500 MPa for 3 min. As a quality indicator, moisture content, color, cooking loss and texture profile analysis (TPA) of pork loins were estimated. Based on the results, brine with low ionic strength (0.7% NaCl) resulted in low injection efficiency and high cooking loss, although, it improved tenderness of pork loin at moderate pressure level (~200 MPa). While high ionic strength condition (1.5% NaCl injection) lowered the hardness of pork loins at relatively high HHP level (400-500 MPa), it also caused high cooking loss. To commercialize the brine injected pork loins, it was necessary to regulate brine compositions, which was not evaluated in this study. Nevertheless, the present study demonstrated that brine injection followed by moderate pressure (200 MPa) could improve the tenderness of pork loins without causing other major quality losses.

Production of protein hydrolysate from Protaetia brevitarsis seulensis (Kolbe) larvae by enzyme treatment under high pressure

To improve the industrial use of health-functional materials based on edible insects, the objective of this study was to establish optimal conditions for improving the quality of Protaetia brevitarsis seulensis larval (PBSL) hydrolysates. PBSL was extracted using four methodologies: atmospheric pressure 50 °C-water extraction, atmospheric pressure 95 °C-water extraction, atmospheric pressure 50 °C-water enzymatic hydrolysis, and enzyme treatment under high pressure (HPE). The quality characteristics of soluble solid content, extraction yield, total protein content, protein yield, protein content with low molecular weight (LMW) (< 1kD), and the amino acid composition of hydrolysates were compared based on the different methods. All of the quality characteristics were found to be higher for HPE extracts than for the other extracts. Under optimized HPE conditions, extraction yield, protein yield, protein content with LMW, amino acid content and the content of essential amino acids increased by 3.4, 4.4 1.4 1.5, and 1.3 times respectively, compared to the other methods.

Comparative gene expression profiling of human primary endotheliocytes cultivated on polyurethane-based electrospun 3D matrices and natural decellularized vein

The formation of a continuous layer of normally functioning endothelium on the lumen surface of small diameter vascular grafts is considered a prerequisite of their long-term functioning without stenosis. Thus, materials supporting not only endothelialization but also the normal functioning state of endotheliocytes are demanded. In this study, we have evaluated the functional state of human umbilical vein endothelial cells (HUVEC) cultivated on the surface of autologous decellularized human umbilical vein and electrospun polyurethane-based matrices by next generation sequencing gene expression profiling. Three types of matrices produced by electrospinning from hexafluoroisopropanol solutions of pure TECOFLEX™ EG-80A polyurethane, polyurethane with gelatin and polyurethane with gelatin and bivalirudin were studied. Cells cultivated on different supports were subjected to RNA-Seq profiling on an Illumina HiSeq platform. The data demonstrated that the structure of 3D matrices and the chemical composition of the fibers have a significant effect on the gene expression profiles of HUVEC. The results suggest that protein-enriched polyurethane-based 3D matrices represent a convenient surface for obtaining a normally functioning endothelial layer.

Effective pressure and treatment duration of high hydrostatic pressure to prepare melanoma vaccines

Current therapeutic methods for melanoma have numerous limitations, and thus the improvement of such treatment methods are essential. One possible option is the vaccination of autologous inactivated tumor cells. The primary indispensable principles of a cell-based melanoma vaccine include: i) Entire inactivation of melanoma cells; ii) retaining the immunogenicity of melanoma cells; and iii) adherence to laws and ethical guidelines. However, traditional methods for the production of the vaccine, such as ultrasonic, chemotherapeutics and freeze-thawing, have some juridical or therapeutic constraints. Therefore, the present study used high hydrostatic pressure (HHP) to inactivate malignant cells, and treated B16-F10 tumor cells with different pressures (≥50 MPa) and different durations (≥1 min). It was identified that tumor cells in vitro lost their proliferative ability, but retained their immunogenicity following treatment. Furthermore, the vaccination of the melanoma cells significantly suppressed their oncogenesis. Collectively, the present results suggest that HHP treatment may be an economically viable and effective measure to develop a melanoma vaccine, when pressure was ≥200 MPa and the treatment duration was ≥30 min.

High-pressure tuning of primary photochemistry in bacterial photosynthesis: membrane-bound versus detergent-isolated reaction centers

While photosynthesis thrives at close to normal pressures and temperatures, it is presently well known that life is similarly commonplace in the hostile environments of the deep seas as well as around hydrothermal vents. It is thus imperative to understand how key biological processes perform under extreme conditions of high pressures and temperatures. Herein, comparative steady-state and picosecond time-resolved spectroscopic studies were performed on membrane-bound and detergent-purified forms of a YM210W mutant reaction center (RC) from Rhodobacter sphaeroides under modulating conditions of high hydrostatic pressure applied at ambient temperature. A previously established breakage of the lone hydrogen bond formed between the RC primary donor and the protein scaffold was shown to take place in the membrane-bound RC at an almost 3 kbar higher pressure than in the purified RC, confirming the stabilizing role of the lipid environment for membrane proteins. The main change in the multi-exponential decay of excited primary donor emission across the experimental 10 kbar pressure range involved an over two-fold continuous acceleration, the kinetics becoming increasingly mono-exponential. The fastest component of the emission decay, thought to be largely governed by the rate of primary charge separation, was distinctly slower in the membrane-bound RC than in the purified RC. The change in character of the emission decay with pressure was explained by the contribution of charge recombination to emission decreasing with pressure as a result of an increasing free energy gap between the charge-separated and excited primary donor states. Finally, it was demonstrated that, in contrast to a long-term experimental paradigm, adding a combination of sodium ascorbate and phenazine methosulfate to the protein solution potentially distorts natural photochemistry in bacterial RCs.

Compensation of high-pressure processing for the solubility of sodium-reduced chicken breast myosin with three anion types of potassium salts

The effect of high-pressure processing (200 MPa, 10 min) on the solubility of chicken breast myosin with 25% molar substitution of Na+ by 3 anion types of potassium salts (KCl, K-lactate, and K-citrate) was investigated. The results showed that the lower hydrophobic group and reactive sulfhydryl group of nonpressurized myosin with the replacement of organic K-lactate or K-citrate possibly contributed to the aggregation of myosin molecules compared with the KCl group and thus decreased the solubility of both. In the presence of lactate or citrate, the high-pressure processing caused an increase in the surface hydrophobicity and reactive sulfhydryl group, indicating the unfolding of myosin molecule. Meanwhile, the increased hydration state and the decreased apparent viscosity suggested the disruption of protein-protein interactions and the strengthening of myosin-water interactions in pressurized myosin, ultimately resulting in increased solubility of the pressurized myosin with both organic potassium salts. The compensation of high-pressure processing is interesting for the efficient selection of the anion type in developing sodium-reduced industrial meat products.

High pressure inhibits signaling protein binding to the flagellar motor and bacterial chemotaxis through enhanced hydration

High pressure below 100 MPa interferes inter-molecular interactions without causing pressure denaturation of proteins. In Escherichia coli, the binding of the chemotaxis signaling protein CheY to the flagellar motor protein FliM induces reversal of the motor rotation. Using molecular dynamics (MD) simulations and parallel cascade selection MD (PaCS-MD), we show that high pressure increases the water density in the first hydration shell of CheY and considerably induces water penetration into the CheY-FliM interface. PaCS-MD enabled us to observe pressure-induced dissociation of the CheY-FliM complex at atomic resolution. Pressure dependence of binding free energy indicates that the increase of pressure from 0.1 to 100 MPa significantly weakens the binding. Using high-pressure microscopy, we observed that high hydrostatic pressure fixes the motor rotation to the counter-clockwise direction. In conclusion, the application of pressure enhances hydration of the proteins and weakens the binding of CheY to FliM, preventing reversal of the flagellar motor.

High hydrostatic pressure induces vigorous flagellar beating in Chlamydomonas non-motile mutants lacking the central apparatus

The beating of eukaryotic flagella (also called cilia) depends on the sliding movements between microtubules powered by dynein. In cilia/flagella of most organisms, microtubule sliding is regulated by the internal structure of cilia comprising the central pair of microtubules (CP) and radial spokes (RS). Chlamydomonas paralyzed-flagella (pf) mutants lacking CP or RS are non-motile under physiological conditions. Here, we show that high hydrostatic pressure induces vigorous flagellar beating in pf mutants. The beating pattern at 40 MPa was similar to that of wild type at atmospheric pressure. In addition, at 80 MPa, flagella underwent an asymmetric-to-symmetric waveform conversion, similar to the one triggered by an increase in intra-flagella Ca2+ concentration during cell's response to strong light. Thus, our study establishes that neither beating nor waveform conversion of cilia/flagella requires the presence of CP/RS in the axoneme.

Pressure Induced Structural Changes of Proteins Affecting the Ice Nucleation Temperature of Pork Loins

This study investigated the effects of pressure-mediated protein changes on the ice nucleation temperature of pork loins. To variate chemical state of meat proteins, pork loin was pressurized at varying pressure levels (100–500 MPa) for 3 min, and moisture content, expressible moisture (EM) and differential scanning calorimetry (DSC) were analyzed. Although, all treatments showed similar moisture content, EM and degree of protein unfolding of pork loin showed different features as of 300 MPa. At moderate pressure treatments (100–200 MPa), all protein fractions were detected in DSC experiments, and pork loin had lower EM than control (p<0.05). Meanwhile, myosin and actin of pork loin treated at greater than 300 MPa were completely unfolded, and the treatments showed high EM compared to control (p<0.05). Unfolding of meat proteins was a factor suppressing ice nucleation, and the ice nucleation temperature tended to decrease with increasing applied pressure level. The ice nucleation characteristics of pressurized pork loin exhibited a potential application in freezing storage of pressurized meat with less tissue damage comparing to freeze fresh meat, and further exploration regarding the quality change after freezing of fresh and pressurized meat was warranted.

Molecular dynamics simulation of proteins under high pressure: Structure, function and thermodynamics

BACKGROUND

Molecular dynamics (MD) simulation is well-recognized as a powerful tool to investigate protein structure, function, and thermodynamics. MD simulation is also used to investigate high pressure effects on proteins. For conducting better MD simulation under high pressure, the main issues to be addressed are: (i) protein force fields and water models were originally developed to reproduce experimental properties obtained at ambient pressure; and (ii) the timescale to observe the pressure effect is often much longer than that of conventional MD simulations.

SCOPE OF REVIEW

First, we describe recent developments in MD simulation methodologies for studying the high-pressure structure and dynamics of protein molecules. These developments include force fields for proteins and water molecules, and enhanced simulation techniques. Then, we summarize recent studies of MD simulations of proteins in water under high pressure.

MAJOR CONCLUSIONS

Recent MD simulations of proteins in solution under pressure have reproduced various phenomena identified by experiments using high pressure, such as hydration, water penetration, conformational change, helix stabilization, and molecular stiffening.

GENERAL SIGNIFICANCE

MD simulations demonstrate differences in the properties of proteins and water molecules between ambient and high-pressure conditions. Comparing the results obtained by MD calculations with those obtained experimentally could reveal the mechanism by which biological molecular machines work well in collaboration with water molecules.

High-pressure study of magnetic nanoparticles with a polyelectrolyte brush as carrier particles for enzymes

The recovery of enzymes from a reaction medium can be achieved in a convenient way by using magnetic nanoparticles (MNP) as carriers. Here, we present MNP with a polyelectrolyte brush composed of poly(ethylene imine) (PEI) to provide a benign environment for the immobilized enzyme molecules. Yeast alcohol dehydrogenase (ADH) has been tested for enzymatic activity when it is free in solution or adsorbed on the PEI brush-MNP. Furthermore, the effect of pressure on the enzymatic activity has been studied to reveal activation volumes, which are a sensitive probe of the transition state geometry. The results of this study indicate that the secondary structure of ADH is pressure-stable up to 9 kbar. The enzymatic activity of ADH can be analyzed using Michaelis-Menten kinetics free in solution and adsorbed on the PEI brush-MNP. Remarkably, no significant changes of the Michaelis constant and the activation volume are observed upon adsorption. Thus, it can be assumed that the turnover number of ADH is also the same in the free and adsorbed state. However, the maximum enzymatic rate is reduced when ADH is adsorbed, which must be explained by a lower effective enzyme concentration due to steric hindrance of the enzyme inside the PEI brush of the MNP. In this way, the pressure experiments carried out in this study enable a distinction between steric and kinetic effects on the enzymatic rate of adsorbed ADH.

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.

Osmolytes modify protein dynamics and function of tetrameric lactate dehydrogenase upon pressurization

We present a study of the combined effects of natural cosolvents (TMAO, glycine, urea) and pressure on the activity of the tetrameric enzyme lactate dehydrogenase (LDH). To this end, high-pressure stopped-flow methodology in concert with fast UV/Vis spectroscopic detection of product formation was applied. To reveal possible pressure effects on the stability and dynamics of the enzyme, FTIR spectroscopic and neutron scattering measurements were carried out. In neat buffer solution, the catalytic turnover number of the enzyme, k_cat, increases up to 1000 bar, the pressure range where dissociation of the tetrameric species to dimers sets in. Accordingly, we obtain a negative activation volume, ΔV^# = -45.3 mL mol^-1. Further, the enzyme substrate complex has a larger volume compared to the enzyme and substrate in the unbound state. The neutron scattering data show that changes in the fast internal dynamics of the enzyme are not responsible for the increase of k_cat upon compression. Whereas the magnitude of k_cat is similar in the presence of the osmolytes, the pressure of deactivation is modulated by the addition of cosolvents. TMAO and glycine increase the pressure of deactivation, and in accordance with the observed stabilizing effect both cosolvents exhibit against denaturation and/or dissociation of proteins. While urea does not markedly affect the magnitude of the Michaelis constant, K_M, both 1 M TMAO and 1 M glycine exhibit smaller K_M values of about 0.07 mM and 0.05 mM below about 1 kbar. Such positive effect on the substrate affinity could be rationalized by the effect the two cosolutes impose on the thermodynamic activities of the reactants, which reflect changes in water-mediated intermolecular interactions. Our data show that the intracellular milieu, i.e., the solution conditions that have evolved, may be sufficient to maintain enzymatic activity under extreme environmental conditions, including the whole pressure range encountered on Earth.