High pressure static fluorescence to study macromolecular structure-function

Enhancing Solubility and Reducing Thermal Aggregation in Pea Proteins through Protein Glutaminase-Mediated Deamidation

The limited solubility and stability of pea proteins hinder their utilization in liquid formulations. In this study, protein glutaminase (PG) was employed to modify pea protein isolates (PPIs) and obtain deamidated PPI with varying degrees of deamidation (DD, 10-25%). The solubility and thermal stability of these deamidated PPI samples were assessed, and a comprehensive analysis, including SDS-PAGE, zeta potential, FTIR, surface hydrophobicity, and intrinsic fluorescence, was conducted to elucidate the mechanism behind the improvement in their functional properties. The results reveal that PG modification greatly enhances the solubility and heat stability of PPI, with the most notable improvements observed at higher DD (>20%). PG modification increases the net charge of PPI, leading to the unfolding and extension of the protein structures, thus exposing more hydrophobic groups. These structural changes are particularly pronounced when DD exceeds 20%. This increased electrostatic repulsion between carboxyl groups would promote protein unfolding, enhancing interactions with water and hindering the aggregation of unfolded protein in the presence of salts at elevated temperatures (supported by high-performance size exclusion chromatography and transmission electron microscopy). Accordingly, PG-mediated deamidation shows promise in enhancing the functional properties of PPI.

Foaming properties are improved by interactions between brewer's spent grain proteins and carrageenans in aqueous solution

BACKGROUND

Foaming properties and macromolecular interactions in solution among brewer's spent grain proteins (CP) and iota and lambda carrageenans (i-CG and l-CG, respectively) as a function of aqueous medium pH (2-6) and protein-polysaccharide ratio, R_CP:CG (1:1, 2:1 and 4:1), were studied. At these conditions, the CP colloidal stability was favored by the formation of soluble electrostatic complexes with CG. Fluorescence (intrinsic and extrinsic) spectroscopy and dynamic light scattering techniques, including particle size and ζ-potential analysis, were applied to know the phase behavior of the biopolymer systems. The bubbling method was used to produce foams, and the foam expansion (%) and half-life time (t_1/2 ) were determined.

RESULTS

Both CG promoted an increased Trp fluorescence emission depending on the pH, suggesting conformational changes in CP. The CG in mixed systems produced a significant decrease in the extrinsic fluorescence intensity, mainly at low pH values, highlighting a reduction in CP surface hydrophobicity. At the examined pH range, the ζ-potential values for mixed-systems were negative, and their magnitudes were intermediate between CP and CG, revealing the associative electrostatic nature of biopolymer interactions, which were dependent on the R_CP:CG . The particle size analysis confirmed the formation of soluble electrostatic complexes in solution. Finally, using i-CG at pH 2 or 3 and 2:1 R_CP:CG , the best foaming properties for mixed systems were observed.

CONCLUSION

The formation of electrostatic complexes with a compact assembly among biopolymers, high negative net charge, and colloidal stability convert the CP-CG mixed solutions into promising biopolymer systems for food foams production. © 2022 Society of Chemical Industry.

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.

Unsupervised classification of PSII with and without water-oxidizing complex samples by PARAFAC resolution of excitation-emission fluorescence images

The potential of excitation-emission fluorescence spectroscopy combined with three-way analysis was investigated for discriminating the photosystem II (PSII) (with the water-oxidizing complex) and without the water-oxidizing complex (wPSII) using unsupervised classification methods. The water-oxidizing complex within PSII carry out the reaction of water splitting which is as a vital process on the earth. Therefore, discriminating the presence of the water-oxidizing complex in protein samples is crucial. Low cost and accurate spectroscopic determination of the amount of clusters inside PSII or any other protein containing species are important when investigating the inclusion and exclusion of such clusters into and from species. Fluorescence data of samples were similar, and we showed the potential usefulness of multivariate methods, such as parallel factor analysis (PARAFAC) and principal component analysis (PCA) for recognition of the two types of samples. Both techniques were applied to the excitation-emission fluorescence matrices (EEM) of solutions at two of different pH values (2.0 and 12.0). Three fluorescent components were found for all samples that are related to tyrosine (Tyr), tryptophan (Trp) and phenylalanine (Phe) amino acids. These three amino acids are representative of all datasets and indicate their similarities and differences. We then found the effectual wavelengths for separation of samples in a specific acidity, including the excitation wavelengths of 220 and 230 nm and the emission wavelengths of 300 and 305 nm. The acidity of the solutions has various influences on the conformation of proteins. In PSII and PSII the without water-oxidizing complex samples conformational changes can change their spectra which was applied for discrimination purpose. This separation was better in pH = 12.0. We also showed the effect of time on small conformational changes within datasets were higher in pH = 2.0. In the end, for indicating the high distribution of spectral data from proteins which is the result of conformational changes, we compared the distribution of measured spectral data with that from a simple organic molecule, fluorescein. Altogether, we could distinguish between the two groups of protein samples properly at pH = 12.0 using low-cost EEM spectral images and PARAFAC.

Thermodynamic, kinetic and conformational analysis of proteins diffusion-sorption on a solid surface

In this paper we examine particularly some of the more fundamental properties of protein conformational changes at a solid surface coupled with diffusion from the bulk of an aqueous solution and with the adsorption-desorption processes. We focus our attention on adsorbed protein monolayers upon a solid surface using a thermodynamic and kinetic analytical development. Account is also taken of the effects on the overall rate of the conformational change on a solid surface of deviation from ideality, of protein flexibility, of surface free energy and of interaction with reactive solid sites. Our theory applied to steady states is illustrated by examples such as folding-misfolding-unfolding of RNase and SNase on a solid surface after diffusion and adsorption from an aqueous solution. For this purpose, we put forward the determining steps which shall lead to the steady state. The existence of three situations is highlighted according to the values of the typical constants relevant for the protein considered: reaction rate determining step, diffusion and sorption determining steps, mixed adsorption diffusion and reaction rate. Finally, we have tried to link the developments of our theories to a large literature based on experimental results encountered during proteins diffusion-sorption-reaction processes, fundamental topics that has been since long investigated by Miller's team in MPKG.

High-pressure fluorescence applications

Fluorescence is the most widely used technique to study the effect of pressure on biochemical systems. The use of pressure as a physical variable sheds light into volumetric characteristics of reactions. Here we focus on the effect of pressure on protein solutions using a simple unfolding example in order to illustrate the applications of the methodology. Topics covered in this review include the relationships between practical aspects and technical limitations; the effect of pressure and the study of protein cavities; the interpretation of thermodynamic and relaxation kinetics; and the study of relaxation amplitudes. Finally, we discuss the insights available from the combination of fluorescence and other methods adapted to high pressure, such as SAXS or NMR. Because of the simplicity and accessibility of high-pressure fluorescence, the technique is a starting point that complements appropriately multi-methodological approaches related to understanding protein function, disfunction, and folding from the volumetric point of view.

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.

Interaction of curcumin with phosphocasein micelles processed or not by dynamic high-pressure

The binding of curcumin to native-like phosphocaseins (PC) dispersed in simulated milk ultrafiltrate at pH 6.6 was assessed by fluorescence spectrophotometry. Curcumin binds to native-like PC micelles with ∼1 binding site per casein molecule, and a binding constant of 0.6-5.6 × 10(4)M(-1). Dynamic high pressure (or ultra-high pressure homogenisation, UHPH) at 200 MPa did not affect the binding parameters of curcumin to processed PC. UHPH-processing of PC dispersions at 300 MPa was followed by a slight but significant (p=0.05) increase in the binding constant of curcumin to processed PC, which may result from the significant UHPH-induced dissociation of initial PC micelles into neo-micelles of smaller sizes, and from the corresponding 1.5-2-fold increase in micelle surface area. PC-curcumin complexes were resistant to pepsin but were degraded by pancreatin, providing the possibility of a spatiotemporally controlled release and protection of bound biomolecules. UHPH-processed PC did not induce TC7-cell damage or major inflammation as assessed by LDH release or IL-8 secretion, respectively, compared with native-like PC. PC micelles could provide a valuable submicron system to vectorise drugs and nutrients.

Coupling between GABA(A)-R ligand-binding activity and membrane organization in β-cyclodextrin-treated synaptosomal membranes from bovine brain cortex: new insights from EPR experiments

Correlations between GABA(A) receptor (GABA(A)-R) activity and molecular organization of synaptosomal membranes (SM) were studied along the protocol for cholesterol (Cho) extraction with β-cyclodextrin (β-CD). The mere pre-incubation (PI) at 37°C accompanying the β-CD treatment was an underlying source of perturbations increasing [(3)H]-FNZ maximal binding (70%) and K (d) (38%), plus a stiffening of SMs' hydrocarbon core region. The latter was inferred from an increased compressibility modulus (K) of SM-derived Langmuir films, a blue-shifted DPH fluorescence emission spectrum and the hysteresis in DPH fluorescence anisotropy (A (DPH)) in SMs submitted to a heating-cooling cycle (4-37-4°C) with A (DPH,heating) < A (DPH,cooling). Compared with PI samples, the β-CD treatment reduced B (max) by 5% which correlated with a 45%-decrement in the relative Cho content of SM, a decrease in K and in the order parameter in the EPR spectrum of a lipid spin probe labeled at C5 (5-SASL), and significantly increased A (TMA-DPH). PI, but not β-CD treatment, could affect the binding affinity. EPR spectra of 5-SASL complexes with β-CD-, SM-partitioned, and free in solution showed that, contrary to what is usually assumed, β-CD is not completely eliminated from the system through centrifugation washings. It was concluded that β-CD treatment involves effects of at least three different types of events affecting membrane organization: (a) effect of PI on membrane annealing, (b) effect of residual β-CD on SM organization, and (c) Cho depletion. Consequently, molecular stiffness increases within the membrane core and decreases near the polar head groups, leading to a net increase in GABA(A)-R density, relative to untreated samples.

Untangling the folding mechanism of the 5(2)-knotted protein UCH-L3

Proteins possessing deeply embedded topological knots in their structure add a stimulating new challenge to the already complex protein-folding problem. The most complicated knotted topology observed to date belongs to the human enzyme ubiquitin C-terminal hydrolase UCH-L3, which is an integral part of the ubiquitin-proteasome system. The structure of UCH-L3 contains five distinct crossings of its polypeptide chain, and it adopts a 5(2)-knotted topology, making it a fascinating target for folding studies. Here, we provide the first in depth characterization of the stability and folding of UCH-L3. We show that the protein can unfold and refold reversibly in vitro without the assistance of molecular chaperones, demonstrating that all the information necessary for the protein to find its knotted native structure is encoded in the amino acid sequence, just as with any other globular protein, and that the protein does not enter into any deep kinetic traps. Under equilibrium conditions, the unfolding of UCH-L3 appears to be two-state, however, multiphasic folding and unfolding kinetics are observed and the data are consistent with a folding pathway in which two hyperfluorescent intermediates are formed. In addition, a very slow phase in the folding kinetics is shown to be limited by proline-isomerization events. Overall, the data suggest that a knotted topology, even in its most complex form, does not necessarily limit folding in vitro, however, it does seem to require a complex folding mechanism which includes the formation of several distinct intermediate species.

Determination of liposome permeability of ionizable carbamates of zidovudine by steady state fluorescence spectroscopy

In the present paper the relative permeabilities of AZT-Pyp and AZT-Ethy across a phospholipid bilayer were estimated by the means of fluorescence spectroscopy. The center of spectral mass of both non-encapsulated AZT-derivatives (AZT-der) emission spectra increased as a function of the illumination time inside the spectrofluorimeter cell. This phenomenon was even more evident when drugs were incubated under an UV mercury lamp, suggesting its photolytic origin. AZT-der were protected from photolysis inside liposomes and decomposed upon irradiation when they were free in the aqueous phase. The time-dependent decrease in the fluorescence intensity at a constant wavelength was fitted to a two-exponential equation and the values of rate constants for permeability and photolysis were calculated. It was concluded that AZT-Pyp but not AZT-Ethy diffused across the bilayer. This behavior correlated with the molecular volumes of AZT-Pyp (379.6A(3)) and AZT-Ethy (450.5A(3)), determined from the minimum energy conformations but not with previously reported logP values. These results reinforce the concept that not only lipophilicity but also membrane structure and AZT-der molecular size had a critical influence in passive diffusion across bilayers and may help in future refinements of other AZT-der molecular design.

Folding studies of two hydrostatic pressure sensitive proteins

High hydrostatic pressure combined with various spectroscopies is a powerful technique to study protein folding. An ideal model system for protein folding studies should have the following characteristics. (1) The protein should be sensitive to pressure, so that the protein can be unfolded under mild pressure. (2) The folding process of the protein should be easily modulated by several chemical or physical factors. (3) The folding process should be easily monitored by some spectroscopic parameters. Here, we summarized the pressure induced folding studies of two proteins isolated from spinach photosystem II, namely the 23-kDa and the 33-kDa protein. They have all the characteristics mention above and might be an ideal model protein system for pressure studies.

High-pressure studies of aggregation of recombinant human interleukin-1 receptor antagonist: thermodynamics, kinetics, and application to accelerated formulation studies

Recombinant human interleukin-1 receptor antagonist (IL-1ra) in aqueous solutions unfolds and aggregates when subjected to hydrostatic pressures greater than about 180 MPa. This study examined the mechanism and thermodynamics of pressure-induced unfolding and aggregation of IL-1ra. The activation free energy for growth of aggregates (DeltaG-/+(aggregation)) was found to be 37 +/- 3 kJ/mol, whereas the activation volume (DeltaV-/+(aggregation)) was -120 +/- 20 mL/mol. These values compare closely with equilibrium values for denaturation: The free energy for denaturation, DeltaG(denaturation), was 20 +/- 5 kJ/mol, whereas the partial specific volume change for denaturation, DeltaV(denaturation), was -110 +/- 30 mL/mol. When IL-1ra begins to denature at pressures near 140 MPa, cysteines that are normally buried in the native state become exposed. Under oxidizing conditions, this results in the formation of covalently cross-linked aggregates containing nonnative, intermolecular disulfide bonds. The apparent activation free energy for nucleation of aggregates, DeltaG-/+(nuc), was 42 +/- 4 kJ/mol, and the activation volume for nucleation, DeltaV-/+(nuc),was -175 +/- 37 mL/mol, suggesting that a highly solvent-exposed conformation is needed for nucleation. We hypothesize that the large specific volume of IL-1ra, 0.752 +/- 0.004 mL/g, coupled with its relatively low conformational stability, leads to its susceptibility to denaturation at relatively low pressures. The positive partial specific adiabatic compressibility of IL-1ra, 4.5 +/- 0.7 +/- 10(-12) cm2/dyn, suggests that a significant component of the DeltaV(denaturation) is attributable to the elimination of solvent-free cavities. Lastly, we propose that hydrostatic pressure is a useful variable to conduct accelerated formulation studies of therapeutic proteins.

Dimethyl sulfoxide targets phage RNA polymerases to promote transcription

Dimethyl sulfoxide (DMSO) is a "universal" solvent in pharmaceutical sciences and cell biology. DMSO was previously reported to facilitate in vitro transcription of chromatin and supercoiled plasmid, with the underlying mechanism being attributed to the alteration of the template structure. Here, we demonstrated that low concentrations of DMSO significantly increase the phage polymerase-catalyzed RNA synthesis when the naked and short PCR products were used as templates, suggesting that DMSO promotes transcription through additional mechanism(s). Interestingly, SP6 RNA polymerase was more sensitive to the DMSO stimulation than T7 RNA polymerase, suggesting that the polymerase is an important target for DMSO stimulation of RNA synthesis. Consistent with this finding, we also showed that DMSO dramatically elevated the RNA polymerase activity. This elevated activity is explained by altered polymerase structure as reflected by a change in intrinsic fluorescence. Furthermore, DMSO was shown to simultaneously accumulate both the abortive and full-length transcripts, leading us to conclude that the DMSO-altered polymerase structure primarily encodes an enhanced activity at the stage of transcription initiation. DMSO-induced alteration of the polymerase structure and function highlights a potentially generalized mechanism in interpreting the molecular action of this popular solvent.

Pressure equilibrium and jump study on unfolding of 23-kDa protein from spinach photosystem II

Pressure-induced unfolding of 23-kDa protein from spinach photosystem II has been systematically investigated at various experimental conditions. Thermodynamic equilibrium studies indicate that the protein is very sensitive to pressure. At 20 degrees C and pH 5.5, 23-kDa protein shows a reversible two-state unfolding transition under pressure with a midpoint near 160 MPa, which is much lower than most natural proteins studied to date. The free energy (DeltaG(u)) and volume change (DeltaV(u)) for the unfolding are 5.9 kcal/mol and -160 ml/mol, respectively. It was found that NaCl and sucrose significantly stabilize the protein from unfolding and the stabilization is associated not only with an increase in DeltaG(u) but also with a decrease in DeltaV(u). The pressure-jump studies of 23-kDa protein reveal a negative activation volume for unfolding (-66.2 ml/mol) and a positive activation volume for refolding (84.1 ml/mol), indicating that, in terms of system volume, the protein transition state lies between the folded and unfolded states. Examination of the temperature effect on the unfolding kinetics indicates that the thermal expansibility of the transition state and the unfolded state of 23-kDa protein are closer to each other and they are larger than that of the native state. The diverse pressure-refolding pathways of 23-kDa protein in some conditions were revealed in pressure-jump kinetics.

High-pressure fluorescence correlation spectroscopy

We demonstrate that a novel high-pressure cell is suitable for fluorescence correlation spectroscopy (FCS). The pressure cell consists of a single fused silica microcapillary. The cylindrical shape of the capillary leads to refraction of the excitation light, which affects the point spread function of the system. We characterize the influence of these beam distortions by FCS and photon-counting histogram (PCH) analysis and identify the optimal position for fluorescence fluctuation experiments in the capillary. At this position within the capillary, FCS and photon-counting histogram experiments are described by the same equations as used in standard FCS experiments. We report the first experimental realization of fluorescence fluctuation spectroscopy under high pressure. A fluorescent dye was used as a model system for evaluating the properties of the capillary under pressure. The autocorrelation function and the photon count distribution were measured in the pressure range from 0 to 300 MPa. The fluctuation amplitude and the diffusion coefficient show a small pressure dependence. The changes of these parameters, which are on the order of 10%, are due to the pressure changes of the viscosity and the density of the aqueous medium.

Fluorescence and FTIR study of pressure-induced structural modifications of horse liver alcohol dehydrogenase (HLADH)

The process of pressure-induced modification of horse liver alcohol dehydrogenase (HLADH) was followed by measuring in situ catalytic activity (up to 250 MPa), intrinsic fluorescence (0.1-600 MPa) and modifications of FTIR spectra (up to 1000 MPa). The tryptophan fluorescence measurements and the kinetic data indicated that the pressure-induced denaturation of HLADH was a process involving several transitions and that the observed transient states have characteristic properties of molten globules. Low pressure (< 100 MPa) induced no important modification in the catalytic efficiency of the enzyme and slight conformational changes, characterized by a small decrease in the centre of spectral mass of the enzyme's intrinsic fluorescence: a native-like state was assumed. Higher pressures (100-400 MPa) induced a strong decrease of HLADH catalytic efficiency and further conformational changes. At 400 MPa, a dimeric molten globule-like state was proposed. Further increase of pressure (400-600 MPa) seemed to induce the dissociation of the dimer leading to a transition from the first dimeric molten globule state to a second monomeric molten globule. The existence of two independent structural domains in HLADH was assumed to explain this transition: these domains were supposed to have different stabilities against high pressure-induced denaturation. FTIR spectroscopy was used to follow the changes in HLADH secondary structures. This technique confirmed that the intermediate states have a low degree of unfolding and that no completely denatured form seemed to be reached, even up to 1000 MPa.

A rare protein fluorescence behavior where the emission is dominated by tyrosine: case of the 33-kDa protein from spinach photosystem II

An abnormal fluorescence emission of protein was observed in the 33-kDa protein which is one component of the three extrinsic proteins in spinach photosystem II particle (PS II). This protein contains one tryptophan and eight tyrosine residues, belonging to a "B type protein". It was found that the 33-kDa protein fluorescence is very different from most B type proteins containing both tryptophan and tyrosine residues. For most B type proteins studied so far, the fluorescence emission is dominated by the tryptophan emission, with the tyrosine emission hardly being detected when excited at 280 nm. However, for the present 33-kDa protein, both tyrosine and tryptophan fluorescence emissions were observed, the fluorescence emission being dominated by the tyrosine residue emission upon a 280 nm excitation. The maximum emission wavelength of the 33-kDa protein tryptophan fluorescence was at 317 nm, indicating that the single tryptophan residue is buried in a very strong hydrophobic region. Such a strong hydrophobic environment is rarely observed in proteins when using tryptophan fluorescence experiments. All parameters of the protein tryptophan fluorescence such as quantum yield, fluorescence decay, and absorption spectrum including the fourth derivative spectrum were explored both in the native and pressure-denatured forms.