Synchrotron X-ray and neutron small-angle scattering of lyotropic lipid mesophases, model biomembranes and proteins in solution at high pressure

A pressure-jump EPR system to monitor millisecond conformational exchange rates of spin-labeled proteins

Site-directed spin labeling electron paramagnetic resonance (SDSL-EPR) using nitroxide spin labels is a well-established technology for mapping site-specific secondary and tertiary structure and for monitoring conformational changes in proteins of any degree of complexity, including membrane proteins, with high sensitivity. SDSL-EPR also provides information on protein dynamics in the timescale of ps-μs using continuous wave lineshape analysis and spin lattice relaxation time methods. However, the functionally important time domain of μs-ms, corresponding to large-scale protein motions, is inaccessible to those methods. To extend SDSL-EPR to the longer time domain, the perturbation method of pressure-jump relaxation is implemented. Here, we describe a complete high-pressure EPR system at Q-band for both static pressure and ms-timescale pressure-jump measurements on spin-labeled proteins. The instrument enables pressure jumps both up and down from any holding pressure, ranging from atmospheric pressure to the maximum pressure capacity of the system components (~3500 bar). To demonstrate the utility of the system, we characterize a local folding-unfolding equilibrium of T4 lysozyme. The results illustrate the ability of the system to measure thermodynamic and kinetic parameters of protein conformational exchange on the ms timescale.

Mtc6/Ehg2 is a novel endoplasmic reticulum-resident glycoprotein essential for high-pressure tolerance

Hydrostatic pressure is a common mechanical stressor that modulates metabolism and reduces cell viability. Eukaryotic cells have genetic programs to cope with hydrostatic pressure stress and maintain intracellular homeostasis. However, the mechanism underlying hydrostatic pressure tolerance remains largely unknown. We have recently demonstrated that maintenance of telomere capping protein 6 (Mtc6) plays a protective role in the survival of the budding yeast Saccharomyces cerevisiae under hydrostatic pressure stress by supporting the integrity of nutrient permeases. The current study demonstrates that Mtc6 acts as an endoplasmic reticulum (ER) membrane protein. Mtc6 comprises two transmembrane domains, a C-terminal cytoplasmic domain and a luminal region with 12 Asn (N)-linked glycans attached to it. Serial mutational analyses showed that the cytoplasmic C-terminal amino acid residues GVPS Mtc6 activity. Multiple N-linked glycans in the luminal region are involved in the structural conformation of Mtc6. Moreover, deletion of MTC6 led to increased degradation of the leucine permease Bap2 under hydrostatic pressure, suggesting that Mtc6 facilitates the proper folding of nutrient permeases in the ER under stress conditions. We propose a novel model of molecular function in which the glycosylated luminal domain and cytoplasmic GVPS sequences of Mtc6 cooperatively support the nutrient permease activity.

Activation of CWI pathway through high hydrostatic pressure, enhancing glycerol efflux via the aquaglyceroporin Fps1 in Saccharomyces cerevisiae

The fungal cell wall is the initial barrier for the fungi against diverse external stresses, such as osmolarity changes, harmful drugs, and mechanical injuries. This study explores the roles of osmoregulation and the cell-wall integrity (CWI) pathway in response to high hydrostatic pressure in the yeast Saccharomyces cerevisiae. We demonstrate the roles of the transmembrane mechanosensor Wsc1 and aquaglyceroporin Fps1 in a general mechanism to maintain cell growth under high-pressure regimes. The promotion of water influx into cells at 25 MPa, as evident by an increase in cell volume and a loss of the plasma membrane eisosome structure, activates the CWI pathway through the function of Wsc1. Phosphorylation of Slt2, the downstream mitogen-activated protein kinase, was increased at 25 MPa. Glycerol efflux increases via Fps1 phosphorylation, which is initiated by downstream components of the CWI pathway, and contributes to the reduction in intracellular osmolarity under high pressure. The elucidation of the mechanisms underlying adaptation to high pressure through the well-established CWI pathway could potentially translate to mammalian cells and provide novel insights into cellular mechanosensation.

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.

Innovative pressure environment combining hydrostatic pressure gradient and mechanical compression for structural investigations of nanoporous soft films

The development of a new sample environment enabling X-ray scattering measurements at small and large angles under mechanical compression and hydraulic flow is presented. The cell, which is adapted for moderate pressures, includes beryllium windows, and allows applying simultaneously a compressive pressure up to 2.5 kbar in the perpendicular direction to the flow and either a hydrostatic pressure up to 300 bar or a pressure gradient of the same amplitude. The development of high-pressure devices for synchrotron experiments is relevant for many scientific fields in order to unveil details of a material's structure under relevant conditions of stresses. In particular, mechanical constraints coupled to hydrostatic pressure or flow, leading to complex stress tensor and mechanical response, and therefore unexpected deformations (swelling and pore deformation), are poorly addressed. Here, first the design of the environment is described, and then its performance with measurements carried out on a regenerated cellulose membrane is demonstrated.

Absorption of the [bmim][Cl] Ionic Liquid in DMPC Lipid Bilayers across Their Gel, Ripple, and Fluid Phases

Lipid bilayers are a key component of cell membranes and play a crucial role in life and in bio-nanotechnology. As a result, controlling their physicochemical properties holds the promise of effective therapeutic strategies. Ionic liquids (ILs)─a vast class of complex organic electrolytes─have shown a high degree of affinity with lipid bilayers and can be exploited in this context. However, the chemical physics of IL absorption and partitioning into lipid bilayers is yet to be fully understood. This work focuses on the absorption of the model IL [bmim][Cl] into 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) lipid bilayers across their gel, ripple, and fluid phases. Here, by small-angle neutron scattering, we show that (i) the IL cations are absorbed in the lipid bilayer in all its thermodynamic phases and (ii) the amount of IL inserted into the lipid phase increased with increasing temperature, changing from three to four IL cations per 10 lipids with increasing temperature from 10 °C in the gel phase to 40 °C in the liquid phase, respectively. An explicative hypothesis, based on the entropy gain coming from the IL hydration water, is presented to explain the observed temperature trend. The ability to control IL absorption with temperature can be used as a handle to tune the effect of ILs on biomembranes and can be exploited in bio-nanotechnological applications.

Alkanes as Membrane Regulators of the Response of Early Membranes to Extreme Temperatures

One of the first steps in the origin of life was the formation of a membrane, a physical boundary that allowed the retention of molecules in concentrated solutions. The proto-membrane was likely formed by self-assembly of simple readily available amphiphiles, such as short-chain fatty acids and alcohols. In the commonly accepted scenario that life originated near hydrothermal systems, how these very simple membrane bilayers could be stable enough in time remains a debated issue. We used various complementary techniques such as dynamic light scattering, small angle neutron scattering, neutron spin-echo spectroscopy, and Fourier-transform infrared spectroscopy to explore the stability of a novel protomembrane system in which the insertion of alkanes in the midplane is proposed to shift membrane stability to higher temperatures, pH, and hydrostatic pressures. We show that, in absence of alkanes, protomembranes transition into lipid droplets when temperature increases; while in presence of alkanes, membranes persist for longer times in a concentration-dependent manner. Proto-membranes containing alkanes are stable at higher temperatures and for longer times, have a higher bending rigidity, and can revert more easily to their initial state upon temperature variations. Hence, the presence of membrane intercalating alkanes could explain how the first membranes could resist the harsh and changing environment of the hydrothermal systems. Furthermore, modulating the quantity of alkanes in the first membranes appears as a possible strategy to adapt the proto-membrane behavior according to temperature fluctuations, and it offers a first glimpse into the evolution of the first membranes.

Molecular Responses to High Hydrostatic Pressure in Eukaryotes: Genetic Insights from Studies on Saccharomyces cerevisiae

Simple Summary

High hydrostatic pressure generally has an adverse effect on the biological systems of organisms inhabiting lands or shallow sea regions. Deep-sea piezophiles that prefer high hydrostatic pressure for growth have garnered considerable scientific attention. However, the underlying molecular mechanisms of their adaptation to high pressure remains unclear owing to the challenges of culturing and manipulating the genome of piezophiles. Humans also experience high hydrostatic pressure during exercise. A long-term stay in space can cause muscle weakness in astronauts. Thus, the human body indubitably senses mechanical stresses such as hydrostatic pressure and gravity. Nonetheless, the mechanisms underlying biological responses to high pressures are not clearly understood. This review summarizes the occurrence and significance of high-pressure effects in eukaryotic cells and how the cell responds to increasing pressure by particularly focusing on the physiology of S. cerevisiae at the molecular level.

Abstract

High hydrostatic pressure is common mechanical stress in nature and is also experienced by the human body. Organisms in the Challenger Deep of the Mariana Trench are habitually exposed to pressures up to 110 MPa. Human joints are intermittently exposed to hydrostatic pressures of 3–10 MPa. Pressures less than 50 MPa do not deform or kill the cells. However, high pressure can have various effects on the cell’s biological processes. Although Saccharomyces cerevisiae is not a deep-sea piezophile, it can be used to elucidate the molecular mechanism underlying the cell’s responses to high pressures by applying basic knowledge of the effects of pressure on industrial processes involving microorganisms. We have explored the genes associated with the growth of S. cerevisiae under high pressure by employing functional genomic strategies and transcriptomics analysis and indicated a strong association between high-pressure signaling and the cell’s response to nutrient availability. This review summarizes the occurrence and significance of high-pressure effects on complex metabolic and genetic networks in eukaryotic cells and how the cell responds to increasing pressure by particularly focusing on the physiology of S. cerevisiae at the molecular level. Mechanosensation in humans has also been discussed.

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

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

Alkanes increase the stability of early life membrane models under extreme pressure and temperature conditions

Terrestrial life appeared on our planet within a time window of [4.4-3.5] billion years ago. During that time, it is suggested that the first proto-cellular forms developed in the surrounding of deep-sea hydrothermal vents, oceanic crust fractures that are still present nowadays. However, these environments are characterized by extreme temperature and pressure conditions that question the early membrane compartment's capability to endure a stable structural state. Recent studies proposed an adaptive strategy employed by present-day extremophiles: the use of apolar molecules as structural membrane components in order to tune the bilayer dynamic response when needed. Here we extend this hypothesis on early life protomembrane models, using linear and branched alkanes as apolar stabilizing molecules of prebiotic relevance. The structural ordering and chain dynamics of these systems have been investigated as a function of temperature and pressure. We found that both types of alkanes studied, even the simplest linear ones, impact highly the multilamellar vesicle ordering and chain dynamics. Our data show that alkane-enriched membranes have a lower multilamellar vesicle swelling induced by the temperature increase and are significantly less affected by pressure variation as compared to alkane-free samples, suggesting a possible survival strategy for the first living forms.

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.

Structural Characterization of Biomaterials by Means of Small Angle X-rays and Neutron Scattering (SAXS and SANS), and Light Scattering Experiments

Scattering techniques represent non-invasive experimental approaches and powerful tools for the investigation of structure and conformation of biomaterial systems in a wide range of distances, ranging from the nanometric to micrometric scale. More specifically, small-angle X-rays and neutron scattering and light scattering techniques represent well-established experimental techniques for the investigation of the structural properties of biomaterials and, through the use of suitable models, they allow to study and mimic various biological systems under physiologically relevant conditions. They provide the ensemble averaged (and then statistically relevant) information under in situ and operando conditions, and represent useful tools complementary to the various traditional imaging techniques that, on the contrary, reveal more local structural information. Together with the classical structure characterization approaches, we introduce the basic concepts that make it possible to examine inter-particles interactions, and to study the growth processes and conformational changes in nanostructures, which have become increasingly relevant for an accurate understanding and prediction of various mechanisms in the fields of biotechnology and nanotechnology. The upgrade of the various scattering techniques, such as the contrast variation or time resolved experiments, offers unique opportunities to study the nano- and mesoscopic structure and their evolution with time in a way not accessible by other techniques. For this reason, highly performant instruments are installed at most of the facility research centers worldwide. These new insights allow to largely ameliorate the control of (chemico-physical and biologic) processes of complex (bio-)materials at the molecular length scales, and open a full potential for the development and engineering of a variety of nano-scale biomaterials for advanced applications.

Refining internal bilayer structure of bicelles resolved by extended-q small angle X-ray scattering

The internal profile across the bilayer reveals important structural information regarding the crystallinity of acyl chains or the positions of encapsulated species. Here, we demonstrate that a simple five-layer-core-shell discoidal model can be employed to best fit the extended-q small angle X-ray scattering (SAXS) data and resolve the bilayer internal structure (with sub-nanometer resolution) of a nanoscale discoidal system comprised of a mixture of long- and short- chain lipids (known as "bicelles"). In contrast to the traditional core-shell discoidal model, the detailed structure in the hydrophobic core such as the methylene and methyl groups can be distinguished via this model. The refined model is validated by the SAXS data of bicelles whose electron scattering length density of the hydrophobic core is adjusted by the addition of a long-chain lipid with a fluorine-end group. The higher resolution of the bilayer internal structure can be employed to advance our understanding of the interaction and conformation of the membrane and associated molecules, such as membrane-associated proteins and locations of entrapped species in the lipid nanoparticles.

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.

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

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

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.

Cholesterol modulates the pressure response of DMPC membranes

In this work, the effect of cholesterol on the pressure response of solid-supported phospholipid multilayers is analyzed. It is shown that DMPC multilayers become highly pressure-responsive by the incorporation of low amounts of cholesterol, resulting in a strong pressure-induced expansion of the bilayer spacing. This is accompanied by a high tendency of the multilayer system to detach from the substrate. Increasing the cholesterol concentration reduces the pressure-induced expansion and the membrane structure remains largely unchanged upon pressurization, consequently the stability of the multilayers improves. For a determination of the influence of the substrate, the pressure-dependent behavior of multilayers is compared to that of solid-supported bilayers and multi-lamellar vesicles in bulk solution. While single-supported bilayers remain largely unaffected by external pressure independent of their cholesterol content, multi-lamellar vesicles and multilayers behave similarly.

Interrogating the Structural Dynamics and Energetics of Biomolecular Systems with Pressure Modulation

High hydrostatic pressure affects the structure, dynamics, and stability of biomolecular systems and is a key parameter in the context of the exploration of the origin and the physical limits of life. This review lays out the conceptual framework for exploring the conformational fluctuations, dynamical properties, and activity of biomolecular systems using pressure perturbation. Complementary pressure-jump relaxation studies are useful tools to study the kinetics and mechanisms of biomolecular phase transitions and structural transformations, such as membrane fusion or protein and nucleic acid folding. Finally, the advantages of using pressure to explore biomolecular assemblies and modulate enzymatic reactions are discussed.

Aescin-Cholesterol Complexes in DMPC Model Membranes: A DSC and Temperature-Dependent Scattering Study

The saponin aescin, a mixture of triterpenoid saponins, is obtained from the seeds of the horse chestnut tree Aesculus hippocastanum. The β-form employed in this study is haemolytically active. The haemolytic activity results from the ability of aescin to form strong complexes with cholesterol in the red blood cell membrane. In this study, we provide a structural analysis on the complex formation of aescin and cholesterol when embedded in a phospholipid model membrane formed by 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC). In this work, the temperatures investigated extend from DMPC’s L_β′ to its L_α phase in dependence of different amounts of the saponin (0–6 mol% for calorimetric and 0–1 mol% for structural analyses) and the steroid (1–10 mol%). At these aescin contents model membranes are conserved in the form of small unilamellar vesicles (SUVs) and major overall structural modifications are avoided. Additionally, interactions between aescin and cholesterol can be studied for both phase states of the lipid, the gel and the fluid state. From calorimetric experiments by differential scanning calorimetry (DSC), it could be shown that both, the steroid and the saponin content, have a significant impact on the cooperative phase transition behaviour of the DMPC molecules. In addition, it becomes clearly visible that the entire phase behaviour is dominated by phase separation which indeed also depends on the complexes formed between aescin and cholesterol. We show by various methods that the addition of cholesterol alters the impact of aescin on structural parameters ranging from the acyl chain correlation to vesicle-vesicle interactions. While the specific saponin-phospholipid interaction is reduced, addition of cholesterol leads to deformation of SUVs. The analyses of the structures formed were performed by wide-angle X-ray scattering (WAXS), small-angle X-ray scattering (SAXS), and small-angle neutron scattering (SANS).

Picosecond Dynamical Response to a Pressure-Induced Break of the Tertiary Structure Hydrogen Bonds in a Membrane Chromoprotein

We used elastic incoherent neutron scattering (EINS) to find out if structural changes accompanying local hydrogen bond rupture are also reflected in global dynamical response of the protein complex. Chromatophore membranes from LH2-only strains of the photosynthetic bacterium Rhodobacter sphaeroides, with spheroidenone or neurosporene as the major carotenoids, were subjected to high hydrostatic pressure at ambient temperature. Optical spectroscopy conducted at high pressure confirmed rupture of tertiary structure hydrogen bonds. In parallel, we used EINS to follow average motions of the hydrogen atoms in LH2, which reflect the flexibility of this complex. A decrease of the average atomic mean square displacements of hydrogen atoms was observed up to a pressure of 5 kbar in both carotenoid samples due to general stiffening of protein structures, while at higher pressures a slight increase of the displacements was detected in the neurosporene mutant LH2 sample only. These data show a correlation between the local pressure-induced breakage of H-bonds, observed in optical spectra, with the altered protein dynamics monitored by EINS. The slightly higher compressibility of the neurosporene mutant sample shows that even subtle alterations of carotenoids are manifested on a larger scale and emphasize a close connection between the local structure and global dynamics of this membrane protein complex.

Effects of the deep-sea osmolyte TMAO on the temperature and pressure dependent structure and phase behavior of lipid membranes

The deep-sea osmolyte TMAO does not only stabilize proteins against high pressure, it affects also the fluidity and lateral organization of membranes.

Combined effects of osmotic and hydrostatic pressure on multilamellar lipid membranes in the presence of PEG and trehalose

We studied the interaction of lipid membranes with the disaccharide trehalose (TRH), which is known to stabilize biomembranes against various environmental stress factors. Generally, stress factors include low/high temperature, shear, osmotic and hydrostatic pressure. Small-angle X-ray-scattering was applied in combination with fluorescence spectroscopy and calorimetric measurements to get insights into the influence of trehalose on the supramolecular structure, hydration level, and elastic and thermodynamic properties as well as phase behavior of the model biomembrane DMPC, covering a large region of the temperature, osmotic and hydrostatic pressure phase space. We observed distinct effects of trehalose on the topology of the lipid's supramolecular structure. Trehalose, unlike osmotic pressure induced by polyethylene glycol, leads to a decrease of lamellar order and a swelling of multilamellar vesicles, which is attributable to direct interactions between the membrane and trehalose. Our results revealed a distinct biphasic concentration dependence of the observed effects of trehalose. While trehalose intercalates between the polar head groups at low concentrations, the effects after saturation are dominated by the exclusion of trehalose from the membrane surface.

Irreversible aggregation of alternating tetra-block-like amphiphile in water

As a frontier topic of soft condensed matter physics, irreversible aggregation has drawn attention for a better understanding of the complex behavior of biomaterials. In this study, we have described the synthesis of an artificial amphiphilic molecule, an alternating tetra-block-like amphiphile, which was able to diversify its aggregate structure in water. The aggregated state of its aqueous dispersion was obtained by slow evaporation of the organic solvent at room temperature, and it collapsed irreversibly at ~ 50°C. By using a cryo-transmission electron microscope and a differential scanning calorimeter, it was revealed that two types of molecular nanostructures were formed and developed into submicro- and micrometer-sized fibrils in the aggregated material.

Simulated pressure denaturation thermodynamics of ubiquitin

Simulations of protein thermodynamics are generally difficult to perform and provide limited information. It is desirable to increase the degree of detail provided by simulation and thereby the potential insight into the thermodynamic properties of proteins. In this study, we outline how to analyze simulation trajectories to decompose conformation-specific, parameter free, thermodynamically defined protein volumes into residue-based contributions. The total volumes are obtained using established methods from Fluctuation Solution Theory, while the volume decomposition is new and is performed using a simple proximity method. Native and fully extended ubiquitin are used as the test conformations. Changes in the protein volumes are then followed as a function of pressure, allowing for conformation-specific protein compressibility values to also be obtained. Residue volume and compressibility values indicate significant contributions to protein denaturation thermodynamics from nonpolar and coil residues, together with a general negative compressibility exhibited by acidic residues.

Hydrophilic nanoparticles stabilising mesophase curvature at low concentration but disrupting mesophase order at higher concentrations

Using high pressure small angle X-ray scattering (HP-SAXS), we have studied monoolein (MO) mesophases at 18 wt% hydration in the presence of 10 nm silica nanoparticles (NPs) at NP-lipid number ratios (ν) of 1 × 10(-6), 1 × 10(-5) and 1 × 10(-4) over the pressure range 1-2700 bar and temperature range 20-60 °C. In the absence of the silica NPs, the pressure-temperature (p-T) phase diagram of monoolein exhibited inverse bicontinuous cubic gyroid (Q), lamellar alpha (Lα), and lamellar crystalline (Lc) phases. The addition of the NPs significantly altered the p-T phase diagram, changing the pressure (p) and the temperature (T) at which the transitions between these mesophases occurred. In particular, a strong NP concentration effect on the mesophase behaviour was observed. At low NP concentration, the p-T region pervaded by the Q phase and the Lα-Q mixture increased, and we attribute this behaviour to the NPs forming clusters at the mesophase domain boundaries, encouraging transition to the mesophase with a higher curvature. At high NP concentrations, the Q phase was no longer observed in the p-T phase diagram. Instead, it was dominated by the lamellar (L) phases until the transition to a fluid isotropic (FI) phase at 60 °C at low pressure. We speculate that NPs formed aggregates with a "chain of pearls" structure at the mesophase domain boundaries, hindering transitions to the mesophases with higher curvatures. These observations were supported by small angle neutron scattering (SANS) and scanning electron microscopy (SEM). Our results have implications to nanocomposite materials and nanoparticle cellular entry where the interactions between NPs and organised lipid structures are an important consideration.

Effect of the food matrix on pressure resistance of Shiga-toxin producing Escherichia coli

The pressure resistance of Shiga-toxin producing Escherichia coli (STEC) depends on food matrix. This study compared the resistance of two five-strain E. coli cocktails, as well as the pressure resistant strain E. coli AW1.7, to hydrostatic pressure application in bruschetta, tzatziki, yoghurt and ground beef at 600 MPa, 20 °C for 3 min and during post-pressure survival at 4 °C. Pressure reduced STEC in plant and dairy products by more than 5 logs (cfu/ml) but not in ground beef. The pH affected the resistance of STEC to pressure as well as the post-pressure survival. E. coli with food constituents including calcium, magnesium, glutamate, caffeic acid and acetic acid were treated at 600 MPa, 20 °C. All compounds exhibited a protective effect on E. coli. The antimicrobial compounds ethanol and phenylethanol enhanced the inactivation by pressure. Calcium and magnesium also performed protective effects on E. coli during storage. Glutamate, glutamine or glutathione did not significantly influence the post-pressure survival over 12 days. Preliminary investigation on cell membrane was further performed through the use of fluorescence probe 1-N-phenylnaphthylamine. Pressure effectively permeabilised cell membrane, whereas calcium showed no effects on membrane permeabilisation.

Hydrophobic nanoparticles promote lamellar to inverted hexagonal transition in phospholipid mesophases

This study focuses on how the mesophase transition behaviour of the phospholipid dioleoyl phosphatidylethanolamine (DOPE) is altered by the presence of 10 nm hydrophobic and 14 nm hydrophilic silica nanoparticles (NPs) at different concentrations. The lamellar to inverted hexagonal phase transition (Lα-HII) of phospholipids is energetically analogous to the membrane fusion process, therefore understanding the Lα-HII transition with nanoparticulate additives is relevant to how membrane fusion may be affected by these additives, in this case the silica NPs. The overriding observation is that the HII/Lα boundaries in the DOPE p-T phase diagram were shifted by the presence of NPs: the hydrophobic NPs enlarged the HII phase region and thus encouraged the inverted hexagonal (HII) phase to occur at lower temperatures, whilst hydrophilic NPs appeared to stabilise the Lα phase region. This effect was also NP-concentration dependent, with a more pronounced effect for higher concentration of the hydrophobic NPs, but the trend was less clear cut for the hydrophilic NPs. There was no evidence that the NPs were intercalated into the mesophases, and as such it was likely that they might have undergone microphase separation and resided at the mesophase domain boundaries. Whilst the loci and exact roles of the NPs invite further investigation, we tentatively discuss these results in terms of both the surface chemistry of the NPs and the effect of their curvature on the elastic bending energy considerations during the mesophase transition.

Membrane homeoviscous adaptation in the piezo-hyperthermophilic archaeon Thermococcus barophilus

The archaeon Thermococcus barophilus, one of the most extreme members of hyperthermophilic piezophiles known thus far, is able to grow at temperatures up to 103°C and pressures up to 80 MPa. We analyzed the membrane lipids of T. barophilus by high performance liquid chromatography–mass spectrometry as a function of pressure and temperature. In contrast to previous reports, we show that under optimal growth conditions (40 MPa, 85°C) the membrane spanning tetraether lipid GDGT-0 (sometimes called caldarchaeol) is a major membrane lipid of T. barophilus together with archaeol. Increasing pressure and decreasing temperature lead to an increase of the proportion of archaeol. Reversely, a higher proportion of GDGT-0 is observed under low pressure and high temperature conditions. Noticeably, pressure and temperature fluctuations also impact the level of unsaturation of apolar lipids having an irregular polyisoprenoid carbon skeleton (unsaturated lycopane derivatives), suggesting a structural role for these neutral lipids in the membrane of T. barophilus. Whether these apolar lipids insert in the membrane or not remains to be addressed. However, our results raise questions about the structure of the membrane in this archaeon and other Archaea harboring a mixture of di- and tetraether lipids.

Mechanisms of pressure-mediated cell death and injury in Escherichia coli: from fundamentals to food applications

High hydrostatic pressure is commercially applied to extend the shelf life of foods, and to improve food safety. Current applications operate at ambient temperature and 600 MPa or less. However, bacteria that may resist this pressure level include the pathogens Staphylococcus aureus and strains of Escherichia coli, including shiga-toxin producing E. coli. The resistance of E. coli to pressure is variable between strains and highly dependent on the food matrix. The targeted design of processes for the safe elimination of E. coli thus necessitates deeper insights into mechanisms of interaction and matrix-strain interactions. Cellular targets of high pressure treatment in E. coli include the barrier properties of the outer membrane, the integrity of the cytoplasmic membrane as well as the activity of membrane-bound enzymes, and the integrity of ribosomes. The pressure-induced denaturation of membrane bound enzymes results in generation of reactive oxygen species and subsequent cell death caused by oxidative stress. Remarkably, pressure resistance at the single cell level relates to the disposition of misfolded proteins in inclusion bodies. While the pressure resistance E. coli can be manipulated by over-expression or deletion of (stress) proteins, the mechanisms of pressure resistance in wild type strains is multi-factorial and not fully understood. This review aims to provide an overview on mechanisms of pressure-mediated cell death in E. coli, and the use of this information for optimization of high pressure processing of foods.

A hypothesis to reconcile the physical and chemical unfolding of proteins

High pressure (HP) or urea is commonly used to disturb folding species. Pressure favors the reversible unfolding of proteins by causing changes in the volumetric properties of the protein-solvent system. However, no mechanistic model has fully elucidated the effects of urea on structure unfolding, even though protein-urea interactions are considered to be crucial. Here, we provide NMR spectroscopy and 3D reconstructions from X-ray scattering to develop the "push-and-pull" hypothesis, which helps to explain the initial mechanism of chemical unfolding in light of the physical events triggered by HP. In studying MpNep2 from Moniliophthora perniciosa, we tracked two cooperative units using HP-NMR as MpNep2 moved uphill in the energy landscape; this process contrasts with the overall structural unfolding that occurs upon reaching a threshold concentration of urea. At subdenaturing concentrations of urea, we were able to trap a state in which urea is preferentially bound to the protein (as determined by NMR intensities and chemical shifts); this state is still folded and not additionally exposed to solvent [fluorescence and small-angle X-ray scattering (SAXS)]. This state has a higher susceptibility to pressure denaturation (lower p1/2 and larger ΔVu); thus, urea and HP share concomitant effects of urea binding and pulling and water-inducing pushing, respectively. These observations explain the differences between the molecular mechanisms that control the physical and chemical unfolding of proteins, thus opening up new possibilities for the study of protein folding and providing an interpretation of the nature of cooperativity in the folding and unfolding processes.

Misfolding, Aggregation, and Disordered Segments in c-Abl and p53 in Human Cancer

The current understanding of the molecular mechanisms that lead to cancer is not sufficient to explain the loss or gain of function in proteins related to tumorigenic processes. Among them, more than 100 oncogenes, 20-30 tumor-suppressor genes, and hundreds of genes participating in DNA repair and replication have been found to play a role in the origins of cancer over the last 25 years. The phosphorylation of serine, threonine, or tyrosine residues is a critical step in cellular growth and development and is achieved through the tight regulation of protein kinases. Phosphorylation plays a major role in eukaryotic signaling as kinase domains are found in 2% of our genes. The deregulation of kinase control mechanisms has disastrous consequences, often leading to gains of function, cell transformation, and cancer. The c-Abl kinase protein is one of the most studied targets in the fight against cancer and is a hotspot for drug development because it participates in several solid tumors and is the hallmark of chronic myelogenous leukemia. Tumor suppressors have the opposite effects. Their fundamental role in the maintenance of genomic integrity has awarded them a role as the guardians of DNA. Among the tumor suppressors, p53 is the most studied. The p53 protein has been shown to be a transcription factor that recognizes and binds to specific DNA response elements and activates gene transcription. Stress triggered by ionizing radiation or other mutagenic events leads to p53 phosphorylation and cell-cycle arrest, senescence, or programed cell death. The p53 gene is the most frequently mutated gene in cancer. Mutations in the DNA-binding domain are classified as class I or class II depending on whether substitutions occur in the DNA contact sites or in the protein core, respectively. Tumor-associated p53 mutations often lead to the loss of protein function, but recent investigations have also indicated gain-of-function mutations. The prion-like aggregation of mutant p53 is associated with loss-of-function, dominant-negative, and gain-of-function effects. In the current review, we focused on the most recent insights into the protein structure and function of the c-Abl and p53 proteins that will provide us guidance to understand the loss and gain of function of these misfolded tumor-associated proteins.

Understanding nanoparticle cellular entry: A physicochemical perspective

Understanding interactions between nanoparticles (NPs) with biological matter, particularly cells, is becoming increasingly important due to their growing application in medicine and materials, and consequent biological and environmental exposure. For NPs to be utilised to their full potential, it is important to correlate their functional characteristics with their physical properties, which may also be used to predict any adverse cellular responses. A key mechanism for NPs to impart toxicity is to gain cellular entry directly. Many parameters affect the behaviour of nanomaterials in a cellular environment particularly their interactions with cell membranes, including their size, shape and surface chemistry as well as factors such as the cell type, location and external environment (e.g. other surrounding materials, temperature, pH and pressure). Aside from in vitro and in vivo experiments, model cell membrane systems have been used in both computer simulations and physicochemical experiments to elucidate the mechanisms for NP cellular entry. Here we present a brief overview of the effects of NPs physical parameters on their cellular uptake, with focuses on 1) related research using model membrane systems and physicochemical methodologies; and 2) proposed physical mechanisms for NP cellular entrance, with implications to their nanotoxicity. We conclude with a suggestion that the energetic process of NP cellular entry can be evaluated by studying the effects of NPs on lipid mesophase transitions, as the molecular deformations and thus the elastic energy cost are analogous between such transitions and endocytosis. This presents an opportunity for contributions to understanding nanotoxicity from a physicochemical perspective.

Small angle scattering methods to study porous materials under high uniaxial strain

We developed a high pressure cell for the in situ study of the porosity of solids under high uniaxial strain using neutron small angle scattering. The cell comprises a hydraulically actioned piston and a main body equipped with two single-crystal sapphire windows allowing for the neutron scattering of the sample. The sample cavity is designed to allow for a large volume variation as expected when compressing highly porous materials. We also implemented a loading protocol to adapt an existing diamond anvil cell for the study of porous materials by X-ray small angle scattering under high pressure. The two techniques are complementary as the radiation beam and the applied pressure are in one case perpendicular to each other (neutron cell) and in the other case parallel (X-ray cell). We will illustrate the use of these two techniques in the study of lamellar porous systems up to a maximum pressure of 0.1 GPa and 0.3 GPa for the neutron and X-ray cells, respectively. These devices allow obtaining information on the evolution of porosity with pressure in the pore dimension subdomain defined by the wave-numbers explored in the scattering process. The evolution with the applied load of such parameters as the fractal dimension of the pore-matrix interface or the apparent specific surface in expanded graphite and in expanded vermiculite is used to illustrate the use of the high pressure cells.

Pressure Effects on Artificial and Cellular Membranes

We review the combined effect of temperature and pressure on the structure, dynamics and phase behavior of lipid bilayers, differing in chain length, headgroup structure and composition as revealed by thermodynamic, spectroscopic and scattering experiments. The effect of additives, such as ions, cholesterol, and anaesthetics is discussed as well. Our data include also reports on the effect of pressure on the lateral organization of heterogeneous lipid membranes and lipid extracts from cellular membranes, as well as the influence of peptide and protein incorporation on the pressure-dependent structure and phase behavior of lipid membranes. Moreover, the effects of pressure on membrane protein function are summarized. Finally, we introduce pressure as a kinetic variable for studying the kinetics of various lipid phase transformations.

High Pressure Small-Angle X-Ray Scattering

Small-angle scattering, solution scattering from proteins in solution, reflects the shape of the scatter as a spread of electron density, which is common to protein crystallography. Although the obtained resolution of small-angle scattering is inferior to that of crystallography, it shows the global image of protein structure in solution without constraints of neighboring molecules in crystal lattice. At ambient pressure, data collection technology and analyses of small-angle scattering method developed so greatly in recent 10 years that it is recognized as one of the powerful method of structural biology. In parallel, many efforts have been made to apply this technique under high pressure. The instrumentation and interpretation of small-angle scattering under pressure, however, requires special considerations. The present chapter reviews the technological aspect of scattering from protein solution especially optimized for synchrotron X-ray sources.

High-Pressure Microscopy for Studying Molecular Motors

Movement is a fundamental characteristic of all living things. This biogenic function is carried out by various nanometer-sized molecular machines. Molecular motor is a typical molecular machinery in which the characteristic features of proteins are integrated; these include enzymatic activity, energy conversion, molecular recognition and self-assembly. These biologically important reactions occur with the association of water molecules that surround the motors. Applied pressures can alter the intermolecular interactions between the motors and water. In this chapter we describe the development of a high-pressure microscope and a new motility assay that enables the visualization of the motility of molecular motors under conditions of high-pressure. Our results demonstrate that applied pressure dynamically changes the motility of molecular motors such as kinesin, F1-ATPase and bacterial flagellar motors.

Exploring the structure and phase behavior of plasma membrane vesicles under extreme environmental conditions

A protocol was developed to generate GPMVs showing phase separation under ambient conditions and theirp,T-dependent phase behavior was studied.

Effects of High Hydrostatic Pressure on Microbial Cell Membranes: Structural and Functional Perspectives

Biological processes associated with dynamic structural features of membranes are highly sensitive to changes in hydrostatic pressure and temperature. Marine organisms potentially experience a broad range of pressure and temperature fluctuations. Hence, they have specialized cell membranes to perform membrane protein functions under various environmental conditions. Although the effects of high pressure on artificial lipid bilayers have been investigated in detail, little is known about how high pressure affects the structure of natural cell membranes and how organisms cope with pressure alterations. This review focused on the recent advances in research on the effects of high pressure on microbial membranes, particularly on the use of time-resolved fluorescence anisotropy measurement to determine membrane dynamics in deep-sea piezophiles.

Tip-induced deformation of a phospholipid bilayer: theoretical perspective of sum frequency generation imaging

The paper addresses theory of Sum Frequency Generation imaging of an atomic force microscopy tip-induced deformation of a bilayer phospholipid membrane deposited over a pore: known as a nano-drum system. Image modeling employed nonlinearities of the normal modes specific to hydrocarbon terminal methyls, which are distributed about the deformed surfaces of inner and outer leaflets. The deformed profiles are according to the solutions of shape equation for Canham-Helfrich Hamiltonian accounting properties of four membranes, which differ in elasticity and adhesion. The results indicate that in continuous deformed surfaces, the difference in the curvature of the outer and inner leaflets dominates in the imaged nonlinearity. This is different comparing to the results for a perfect bilayer spherical cap system (the subject of previous study), where nonlinear image response is dominated by the mismatch of the inner and outer leaflets' surface areas (as projected to the image plane) at the edge of perfectly spherical structure. The results of theoretical studies, here, demonstrate that Sum Frequency Generation imaging in continuous and deformed bilayer surfaces are helpful to address curvature locally and anticipate mechanical properties of membrane. The articles discuss applicability and practical limitations of the approach. Combination of Atomic Force Microscopy and Sum Frequency Generation imaging under controlled tip-induced deformation provides a good opportunity to probe and test membranes physical properties with rigor of adopted theory.

Thermodynamic and functional characteristics of deep-sea enzymes revealed by pressure effects

Hydrostatic pressure analysis is an ideal approach for studying protein dynamics and hydration. The development of full ocean depth submersibles and high pressure biological techniques allows us to investigate enzymes from deep-sea organisms at the molecular level. The aim of this review was to overview the thermodynamic and functional characteristics of deep-sea enzymes as revealed by pressure axis analysis after giving a brief introduction to the thermodynamic principles underlying the effects of pressure on the structural stability and function of enzymes.

X-ray reflectivity measurements of liquid/solid interfaces under high hydrostatic pressure conditions

A high-pressure cell for in situ X-ray reflectivity measurements of liquid/solid interfaces at hydrostatic pressures up to 500 MPa (5 kbar), a pressure regime that is particularly important for the study of protein unfolding, is presented. The original set-up of this hydrostatic high-pressure cell is discussed and its unique properties are demonstrated by the investigation of pressure-induced adsorption of the protein lysozyme onto hydrophobic silicon wafers. The presented results emphasize the enormous potential of X-ray reflectivity studies under high hydrostatic pressure conditions for the in situ investigation of adsorption phenomena in biological systems.