Fourier transform infrared spectroscopy in high-pressure studies on proteins

A study of OH···O hydrogen bonds along various isolines in 2-ethyl-1-hexanol. Temperature or pressure - which parameter controls their behavior?

The nature of H-bonding interactions is still far from being understood despite intense experimental and theoretical studies on this subject carried out by the leading research centers. In this paper, by a combination of unique high-pressure infrared, dielectric and volumetric data, the intramolecular dynamics of hydroxyl moieties (which provides direct information about H-bonds) was studied along various isolines, i.e., isotherms, isobars, isochrones, and isochores, in a simple monohydroxy alcohol (2-ethyl-1-hexanol). This allowed us to discover that the temperature controls the intermolecular hydrogen bonds, which then affect the intramolecular dynamics of OH units. Although the role of density fluctuations gets stronger as temperature rises. We also demonstrated a clear connection between the intra- and intermolecular dynamics of the associating liquid at high pressure. The data reported herein open a new perspective to explore this important aspect of the glass transition phenomenon and understand H-bonding interactions at varying thermodynamic conditions.

Effects of Different Zn2+ Concentrations and High Hydrostatic Pressures (HHP) on Chlorophyll Stability

This study provides a new idea for improving chlorophyll stability and color quality of green leafy vegetables by Zn2+ synergistic HHP. Zn-chlorophyll was prepared with zinc acetate and chlorophyll under HHP treatment. The effects of different zinc acetate concentrations and pressures on chlorophyll color, antioxidant activity, Zn2+ replacement rate, structure, and thermal stability were analyzed. Results showed with increased zinc acetate concentration and pressure, −a* value, antioxidant activity, and Zn2+ replacement rate of samples gradually increased. However, FTIR indicated the structure did not change. HHP fluorescence online analysis showed fluorescence intensity of samples decreased with zinc acetate concentration and pressure increasing. With zinc acetate 10 mg/100 mL and HHP 500 MPa, the highest −a* value (5.19), antioxidant activity (ABTS, DPPH, and FRAP were 37.03 g ACE/100 g, 25.95 g ACE/100 g, 65.43 g TE/100 g DW, respectively), and Zn2+ replacement rate (42.34%) were obtained. Thermal stability of Zn-chlorophyll obtained by synergistic effect was improved significantly.

Effects of High Hydrostatic Pressure Pretreatment on the Functional and Structural Properties of Rice Bran Protein Hydrolysates

Rice bran protein (RBP) hydrolysis was conducted after high hydrostatic pressure (HHP) pretreatment. The structural and functional properties of HHP-pretreated rice bran protein hydrolysates (RBPH) were investigated. HHP pretreatments were conducted at 100, 200, and 300 MPa; then, enzymatic hydrolysis at atmospheric pressure was performed using trypsin. An RBPH sample that had not been pretreated by HHP was used as a control. Free sulfhydryl (SH) content, SDS-PAGE profiles, high-performance size exclusion chromatography (HPSEC), Fourier transform infrared (FTIR) spectrum, scanning electron microscopy (SEM), intrinsic fluorescence spectrum, solubility, and emulsifying and foaming properties were evaluated. Changes in particle size and ζ-potential were monitored. Compared with the control, the results of solubility, the emulsifying activity index (EAI) and the emulsifying stability index (ESI) increased significantly (p < 0.05) at 200 MPa. The content of free SH increased significantly (p < 0.05) at 100 MPa. FTIR spectrum and fluorescence analysis confirmed the changes in the secondary and tertiary structures. The experimental results indicated that the structural and functional properties of HHP-pretreated RBPH improved.

Aggregation induced by the synergy of sodium chloride and high-pressure improves chlorophyll stability

The development of green vegetable processing is still limited by the imperfect green protection now. Chlorophyll (Chl), the main pigment presented in green vegetables, was studied that the effects of NaCl on the stability of it, and the synergy of NaCl and high-pressure on Chl protection. Compared to the control, the retention of Chl was increased by 80.14% and the activation energy was 62.7% higher in 7.8% NaCl solution. When the pressure was 600 MPa with 7.8% NaCl, the synergy of NaCl and high-pressure increased the Chl retention by 100%. The restriction of NaCl to H₂O provided Chl with a lower polarity environment and increased the contact between Chl molecules. And the fluorescence quenching confirmed the aggregation of Chls induced by high-pressure. This study explains the mechanism of green protection by NaCl and high-pressure, broadening the horizon for the development of color protection in vegetable processing.

Functionality of Food Components and Emerging Technologies

This review article introduces nutrition and functional food ingredients, explaining the widely cited terms of bioactivity, bioaccessibility, and bioavailability. The factors affecting these critical properties of food components are analyzed together with their interaction and preservation during processing. Ultimately, the effect of emerging (non-thermal) technologies on different food components (proteins, carbohydrates, lipids, minerals, vitamins, polyphenols, glucosinolates, polyphenols, aroma compounds, and enzymes) is discussed in spite of preserving their functional properties. Non-thermal technologies can maintain the bioavailability of food components, improve their functional and technological properties, and increase the recovery yields from agricultural products. However, the optimization of operational parameters is vital to avoid degradation of macromolecules and the oxidation of labile compounds.

Effects of heat treatment on the antigenicity, antigen epitopes, and structural properties of β-conglycinin

In this study, the effects of heat treatment on antigenicity, antigen epitopes, and structural changes in β-conglycinin were investigated. Results showed that the IgG (Immunoglobulin G) binding capacity of heated protein was inhibited with increased temperature, although IgE (Immunoglobulin E) binding capacity increased. Linear antigen epitopes generally remained intact during heat treatment. After heat treatment, β-conglycinin was more easily hydrolyzed by digestive enzymes, and a large number of linear epitopes was destroyed. In addition, heat denaturation of β-conglycinin led to the formation of protein aggregates and reduction of disulfide bonds. The contents of random coils and β-sheet of heated β-conglycinin decreased, but the contents of β-turn and α-helix increased. Moreover, the protein structure of heated β-conglycinin unfolded, more hydrophobic regions were exposed, and the tertiary structure of β-conglycinin was destroyed. Heat treatment affected the antigenicity and potential sensitization of β-conglycinin by changing its structure.

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

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

Enzymatic hydrolysis increases ginsenoside content in Korean red ginseng (Panax ginseng CA Meyer) and its biotransformation under hydrostatic pressure

BACKGROUND

Enzymatic hydrolysis and high hydrostatic pressure (HHP) are common processing techniques in the extraction of active compounds from food materials. The aim of this study was to investigate the effects of enzymatic hydrolysis combined with HHP treatments on ginsenoside metabolites in red ginseng.

RESULTS

The yield and changes in the levels of polyphenol and ginsenoside were measured in red ginseng treated with commercial enzymes such as Ultraflo L, Viscozyme, Cytolase PCL5, Rapidase and Econase E at atmospheric pressure (0.1 MPa), 50 MPa, and 100 MPa. β-Glucosidase activity of Cytolase was the highest at 4258.2 mg^-1 , whereas Viscozyme showed the lowest activity at 10.6 mg^-1 . Pressure of 100 MPa did not affect the stability or the activity of the β-glucosidase. Treatment of red ginseng with Cytolase and Econase at 100 MPa significantly increased the dry weight and polyphenol content of red ginseng, compared with treatments at 0.1 MPa and 50 MPa (P < 0.05). The amounts of ginsenoside and ginsenoside metabolites derived from red ginseng processed using Cytolase were higher than those derived from red ginseng treated with the other enzymes. Treatment with Cytolase also significantly increased the skin and intestinal permeability of red ginseng-derived polyphenols.

CONCLUSION

Cytolase could be useful as an enzymatic treatment to enhance the yield of bioactive compounds from ginseng under HHP. In addition, ginsenoside metabolites obtained by Cytolase hydrolysis combined with HHP are functional substances with increased intestinal and skin permeability. © 2019 Society of Chemical Industry.

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.

Infrared and Raman spectroscopy of non-conventional hydrogen bonding between N,N'-disubstituted urea and thiourea groups: a combined experimental and theoretical investigation

The variety of H bond (HB) interactions is a source of inspiration for bottom-up molecular engineering through self-aggregation. Non-conventional intermolecular HBs between N,N'-disubstituted urea and thiourea are studied in detail by vibrational spectroscopies and ab initio calculations. Raman and IR mode assignments are given. We show that it is possible to study selectively the different intermolecular bifurcated intra- and inter-dimer HBs with the two types of HB acceptors. Through the ab initio calculation, the thioamide I mode, a specific marker of N-HS[double bond, length as m-dash]C HB interactions, is unambiguously identified.

Advancements of two dimensional correlation spectroscopy in protein researches

The developments of two-dimensional correlation spectroscopy (2DCOS) applications in protein studies are discussed, especially for the past two decades. The powerful utilities of 2DCOS combined with various analytical techniques in protein studies are summarized. The emphasis is on the vibration spectroscopic techniques including IR, NIR, Raman and optical activity (ROA), as well as vibration circular dichroism (VCD) and fluorescence spectroscopy. In addition, some new developments, such as hetero-spectral 2DCOS, moving-window correlation, and model based correlation, are also reviewed for their utility in the investigation of the secondary structure, denaturation, folding and unfolding changes of protein. Finally, the new possibility and challenges of 2DCOS in protein research are highlighted as well.

Highly water pressurized brown rice improves cognitive dysfunction in senescence-accelerated mouse prone 8 and reduces amyloid beta in the brain

Background

Alzheimer’s disease (AD) is the most common form of dementia and the number of AD patients continues to increase worldwide. Components of the germ layer and bran of Brown rice (BR) help maintain good health and prevent AD. Because the germ layer and bran absorb little water and are very hard and difficult to cook, they are often removed during processing. To solve these problems, in this study, we tried to use a high-pressure (HP) technique.

Methods

We produced the highly water pressurized brown rice (HPBR) by pressurizing BR at 600 MPa, and then we fed it to an AD mouse model, senescence-accelerated mouse prone 8, to investigate the therapeutic effects of HPBR on cognitive dysfunction by Y-maze spatial memory test.

Results

HP treatment increased the water absorbency of BR without nutrient loss. HPBR ameliorated cognitive dysfunction and reduced the levels of amyloid-β, which is a major protein responsible for AD, in the brain.

Conclusions

These results suggest that HPBR is effective for preventing AD.

Two-dimensional correlation spectroscopy in protein science, a summary for past 20years

Two-dimensional correlation spectroscopy (2DCOS) has been widely used to Infrared, Raman, Near IR, Optical Activity (ROA), Vibrational Circular Dichroism (VCD) and Fluorescence spectroscopy. In addition, several new developments, such as 2D hetero-correlation analysis, moving-window two-dimensional (MW2D) correlation, model based correlation (βν and kν correlation analyses) have also well incorporated into protein research. They have been used to investigate secondary structure, denaturation, folding and unfolding changes of protein, and have contributed greatly to the field of protein science. This review provides an overview of the applications of 2DCOS in the field of protein science for the past 20 year, especially to memory our old friend, Dr. Boguslawa Czarnik-Matusewicz, for her great contribution in this research field. The powerful utility of 2DCOS combined with various analytical techniques in protein studies is summarized. The noteworthy developments and perspective of 2DCOS in this field are highlighted finally.

Miniature diamond-anvil cells for FTIR-microspectroscopy of small quantities of biosamples

A small amount of biosample is mounted on a diamond anvil cell and spectra registered using simple 15× infrared objective instead of being grown on a diamond and measured by FTIR-ATR.

The effects of osmolytes and crowding on the pressure-induced dissociation and inactivation of dimeric LADH

Compatible osmolytes are able to efficiently modulate the oligomeric state, stability and activity of enzymes at high pressures.

Probing conformational and functional substates of calmodulin by high pressure FTIR spectroscopy: influence of Ca2+ binding and the hypervariable region of K-Ras4B

Using pressure perturbation, conformational substates of CaM could be uncovered that conceivably facilitate target recognition by exposing the required binding surfaces.

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.

In vitro evaluation of the tribological response of Mo-doped graphite-like carbon film in different biological media

Complicated tribochemical reactions with the surrounding media often occur at the prosthesis material, which is a dominant factor causing the premature failure in revision surgery. Graphite-like carbon (GLC) film has been proven to be an excellent tribological adaption to water-based media, and this work focused on the friction and wear behavior of Mo-doped GLC (Mo-GLC)-coated poly(aryl ether ether ketone) sliding against Al2O3 counterpart in physiological saline, simulated body fluid, and fetal bovine serum (FBS), which mainly emphasized the interface interactions of the prosthetic materials/lubricant. Results showed different tribological responses of Mo-GLC/Al2O3 pairs strongly correlated with the interfacial reactions of the contacting area. Particularly, a transfer layer was believed to be responsible for the excellent wear reduction of Mo-GLC/Al2O3 pair in FBS medium, in which graphitic carbon and protein species were contained. The wear mechanisms are tentatively discussed according to the morphologies and chemical compositions of the worn surfaces examined by scanning electron microscope as well as X-ray photoelectron spectroscopy.

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.

High Pressure Treatment in Foods

High hydrostatic pressure (HHP), a non-thermal technology, which typically uses water as a pressure transfer medium, is characterized by a minimal impact on food characteristics (sensory, nutritional, and functional). Today, this technology, present in many food companies, can effectively inactivate bacterial cells and many enzymes. All this makes HHP very attractive, with very good acceptance by consumers, who value the organoleptic characteristics of products processed by this non-thermal food preservation technology because they associate these products with fresh-like. On the other hand, this technology reduces the need for non-natural synthetic additives of low consumer acceptance.

Single-molecule analysis of the rotation of F₁-ATPase under high hydrostatic pressure

F1-ATPase is the water-soluble part of ATP synthase and is an ATP-driven rotary molecular motor that rotates the rotary shaft against the surrounding stator ring, hydrolyzing ATP. Although the mechanochemical coupling mechanism of F1-ATPase has been well studied, the molecular details of individual reaction steps remain unclear. In this study, we conducted a single-molecule rotation assay of F1 from thermophilic bacteria under various pressures from 0.1 to 140 MPa. Even at 140 MPa, F1 actively rotated with regular 120° steps in a counterclockwise direction, showing high conformational stability and retention of native properties. Rotational torque was also not affected. However, high hydrostatic pressure induced a distinct intervening pause at the ATP-binding angles during continuous rotation. The pause was observed under both ATP-limiting and ATP-saturating conditions, suggesting that F1 has two pressure-sensitive reactions, one of which is evidently ATP binding. The rotation assay using a mutant F1(βE190D) suggested that the other pressure-sensitive reaction occurs at the same angle at which ATP binding occurs. The activation volumes were determined from the pressure dependence of the rate constants to be +100 Å(3) and +88 Å(3) for ATP binding and the other pressure-sensitive reaction, respectively. These results are discussed in relation to recent single-molecule studies of F1 and pressure-induced protein unfolding.

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.

Effects of high hydrostatic pressure (HHP) on the protein structure and thermal stability of Sauvignon blanc wine

Protein haze development in bottled white wines is attributed to the slow denaturation of unstable proteins, which results in their aggregation and flocculation. These protein fractions can be removed by using bentonite; however, a disadvantage of this technique is its cost. The effects of high hydrostatic pressure (HHP) on wine stability were studied. Fourier transform infrared spectroscopy experiments were performed to analyse the secondary structure of protein, thermal stability was evaluated with differential scanning calorimetry, while a heat test was performed to determine wine protein thermal stability. The results confirmed that high pressure treatments modified the α-helical and β-sheet structures of wine proteins. Throughout the 60 days storage period the α-helix structure in HHP samples decreased. Structural changes by HHP (450 MPa for 3 and 5 min) improve thermal stability of wine proteins and thus delay haze formation in wine during storage.

Bacterial motility measured by a miniature chamber for high-pressure microscopy

Hydrostatic pressure is one of the physical stimuli that characterize the environment of living matter. Many microorganisms thrive under high pressure and may even physically or geochemically require this extreme environmental condition. In contrast, application of pressure is detrimental to most life on Earth; especially to living organisms under ambient pressure conditions. To study the mechanism of how living things adapt to high-pressure conditions, it is necessary to monitor directly the organism of interest under various pressure conditions. Here, we report a miniature chamber for high-pressure microscopy. The chamber was equipped with a built-in separator, in which water pressure was properly transduced to that of the sample solution. The apparatus developed could apply pressure up to 150 MPa, and enabled us to acquire bright-field and epifluorescence images at various pressures and temperatures. We demonstrated that the application of pressure acted directly and reversibly on the swimming motility of Escherichia coli cells. The present technique should be applicable to a wide range of dynamic biological processes that depend on applied pressures.

An FT-IR study on packing defects in mixed β-aggregates of poly(L-glutamic acid) and poly(D-glutamic acid): a high-pressure rescue from a kinetic trap

Under favorable conditions of pH and temperature, poly(L-glutamic acid) (PLGA) adopts different types of secondary and quaternary structures, which include spiral assemblies of amyloid-like fibrils. Heating of acidified solutions of PLGA (or PDGA) triggers formation of β(2)-type aggregates with morphological and tinctorial properties typical for amyloid fibrils. In contrast to regular antiparallel β-sheet (β(1)), the amide I' vibrational band of β(2)-fibrils is unusually red-shifted below 1600 cm(-1), which has been attributed to bifurcated hydrogen bonds coupling C═O and N-D groups of the main chains to glutamic acid side chains. However, unlike for pure PLGA, the amide I' band of aggregates precipitating from racemic mixtures of PLGA and PDGA (β(1)) is dominated by components at 1613 and 1685 cm(-1)-typically associated with intermolecular antiparallel β-sheets. The coaggregation of PLGA and PDGA chains is slower and biphasic and leads to less-structured assemblies of fibrils, which is reflected in scanning electron microscopy images, sedimentation properties, and fluorescence intensity after staining with thioflavin T. The β(1)-type aggregates are metastable, and they slowly convert to fibrils with the infrared characteristics of β(2)-type fibrils. The process is dramatically accelerated under high pressure. This implies the presence of void volumes within structural defects in racemic aggregates, preventing the precise alignment of main and side chains necessary to zip up ladders of bifurcated hydrogen bonds. As thermodynamic costs associated with maintaining void volumes within the racemic aggregate increase under high pressure, a hyperbaric treatment of misaligned chains leads to rectifying the packing defects and formation of the more compact form of fibrils.

Revealing conformational substates of lipidated N-Ras protein by pressure modulation

Regulation of protein function is often linked to a conformational switch triggered by chemical or physical signals. To evaluate such conformational changes and to elucidate the underlying molecular mechanisms of subsequent protein function, experimental identification of conformational substates and characterization of conformational equilibria are mandatory. We apply pressure modulation in combination with FTIR spectroscopy to reveal equilibria between spectroscopically resolved substates of the lipidated signaling protein N-Ras. Pressure has the advantage that its thermodynamic conjugate is volume, a parameter that is directly related to structure. The conformational dynamics of N-Ras in its different nucleotide binding states in the absence and presence of a model biomembrane was probed by pressure perturbation. We show that not only nucleotide binding but also the presence of the membrane has a drastic effect on the conformational dynamics and selection of conformational substates of the protein, and a new substate appearing upon membrane binding could be uncovered. Population of this new substate is accompanied by structural reorientations of the G domain, as also indicated by complementary ATR-FTIR and IRRAS measurements. These findings thus illustrate that the membrane controls signaling conformations by acting as an effective interaction partner, which has consequences for the G-domain orientation of membrane-associated N-Ras, which in turn is known to be critical for its effector and modulator interactions. Finally, these results provide insights into the influence of pressure on Ras-controlled signaling events in organisms living under extreme environmental conditions as they are encountered in the deep sea where pressures reach the kbar range.

Protein dynamics and pressure: what can high pressure tell us about protein structural flexibility?

After a brief overview of NMR and X-ray crystallography studies on protein flexibility under pressure, we summarize the effects of hydrostatic pressure on the native fold of azurin from Pseudomonas aeruginosa as inferred from the variation of the intrinsic phosphorescence lifetime and the acrylamide bimolecular quenching rate constants of the buried Trp residue. The pressure/temperature response of the globular fold and modulation of its dynamical structure is analyzed both in terms of a reduction of internal cavities and of the hydration of the polypeptide. The study of the effect of two single point cavity forming mutations, F110S and I7S, on the unfolding volume change (ΔV(0)) of azurin and on the internal dynamics of the protein fold under pressure demonstrate that the creation of an internal cavity will enhance the plasticity and lower the stability of the globular structure. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.