Preparing Better Samples for Cryo-Electron Microscopy: Biochemical Challenges Do Not End with Isolation and Purification.

The preparation of extremely thin samples, which are required for high-resolution electron microscopy, poses extreme risk of damaging biological macromolecules due to interactions with the air-water interface. Although the rapid increase in the number of published structures initially gave little indication that this was a problem, the search for methods that substantially mitigate this hazard is now intensifying. The two main approaches under investigation are (a) immobilizing particles onto structure-friendly support films and (b) reducing the length of time during which such interactions may occur. While there is little possibility of outrunning diffusion to the interface, intentional passivation of the interface may slow the process of adsorption and denaturation. In addition, growing attention is being given to gaining more effective control of the thickness of the sample prior to vitrification.

A suicidal mechanism for the exquisite temperature sensitivity of TRPV1.

The vanilloid receptor TRPV1 is an exquisite nociceptive sensor of noxious heat, but its temperature-sensing mechanism is yet to define. Thermodynamics dictate that this channel must undergo an unusually energetic allosteric transition. Thus, it is of fundamental importance to measure directly the energetics of this transition in order to properly decipher its temperature-sensing mechanism. Previously, using submillisecond temperature jumps and patch-clamp recording, we estimated that the heat activation for TRPV1 opening incurs an enthalpy change on the order of 100 kcal/mol. Although this energy is on a scale unparalleled by other known biological receptors, the generally imperfect allosteric coupling in proteins implies that the actual amount of heat uptake driving the TRPV1 transition could be much larger. In this paper, we apply differential scanning calorimetry to directly monitor the heat flow in TRPV1 that accompanies its temperature-induced conformational transition. Our measurements show that heat invokes robust, complex thermal transitions in TRPV1 that include both channel opening and a partial protein unfolding transition and that these two processes are inherently coupled. Our findings support that irreversible protein unfolding, which is generally thought to be destructive to physiological function, is essential to TRPV1 thermal transduction and, possibly, to other strongly temperature-dependent processes in biology.

Contribution of the yeast bi-chaperone system in the restoration of the RNA helicase Ded1 and translational activity under severe ethanol stress.

Preexposure to mild stress often improves cellular tolerance to subsequent severe stress. Severe ethanol stress (10% v/v) causes persistent and pronounced translation repression in Saccharomyces cerevisiae. However, it remains unclear whether preexposure to mild stress can mitigate translation repression in yeast cells under severe ethanol stress. We found that the translational activity of yeast cells pretreated with 6% (v/v) ethanol was initially significantly repressed under subsequent 10% ethanol but was then gradually restored even under severe ethanol stress. We also found that 10% ethanol caused the aggregation of Ded1, which plays a key role in translation initiation as a DEAD-box RNA helicase. Pretreatment with 6% ethanol led to the gradual disaggregation of Ded1 under subsequent 10% ethanol treatment in wild-type cells but not in fes1Δhsp104Δ cells, which are deficient in Hsp104 with significantly reduced capacity for Hsp70. Hsp104 and Hsp70 are key components of the bi-chaperone system that play a role in yeast protein quality control. fes1Δhsp104Δ cells did not restore translational activity under 10% ethanol, even after pretreatment with 6% ethanol. These results indicate that the regeneration of Ded1 through the bi-chaperone system leads to the gradual restoration of translational activity under continuous severe stress. This study provides new insights into the acquired tolerance of yeast cells to severe ethanol stress and the resilience of their translational activity.

The interaction of thiocyanate with peptides-A computational study.

According to the Hofmeister series, thiocyanate is the strongest "salting in" anion. In fact, it has a strong denaturant activity against the native state of globular proteins. A molecular level rationalization of the Hofmeister series is still missing, and therefore the denaturant activity of thiocyanate also awaits a robust explanation. In the last years, different types of experimental studies have shown that thiocyanate is capable to directly interact with both polar and nonpolar groups of polypeptide chains. This finding has been scrutinized via a careful computational procedure based on density functional theory approaches. The results indicate that thiocyanate is able to make H-bonds via both the nitrogen and sulfur atom, and to make strong van der Waals interactions with almost all the groups of polypeptide chains, regardless of their polarity.

Clinical and Preclinical Methods of Heat-Stabilization of Human Vaccines.

Vaccines have historically faced challenges regarding stability, especially in regions lacking a robust cold chain infrastructure. This review delves into established and emergent techniques to improve the thermostability of vaccines. We discuss the widely practiced lyophilization method, effectively transforming liquid vaccine formulations into a solid powdered state, enhancing storage and transportation ability. However, potential protein denaturation during lyophilization necessitates alternative stabilization methods. Cryoprotectants, namely, starch and sugar molecules, have shown promise in protecting vaccine antigens and adjuvants from denaturation and augmenting the stability of biologics during freeze-drying. Biomineralization, a less studied yet innovative approach, utilizes inorganic or organic-inorganic hybrids to encapsulate biological components of vaccines with a particular emphasis on metal-organic coordination polymers. Encapsulation in organic matrices to form particles or microneedles have also been studied in the context of vaccine thermostability, showing some ability to store outside the cold-chain. Unfortunately, few of these techniques have advanced to clinical trials that evaluate differences in storage conditions. Nonetheless, early trials suggest that alternative storage techniques are viable and emphasize the need for more comprehensive studies. This review underscores the pressing need for heat-stable vaccines, especially in light of the increasing global distribution challenges. Combining traditional methods with novel approaches holds promise for the future adaptability of vaccine distribution and use.

NMR Dynamic View of the Destabilization of WW4 Domain by Chaotropic GdmCl and NaSCN.

GdmCl and NaSCN are two strong chaotropic salts commonly used in protein folding and stability studies, but their microscopic mechanisms remain enigmatic. Here, by CD and NMR, we investigated their effects on conformations, stability, binding and backbone dynamics on ps-ns and µs-ms time scales of a 39-residue but well-folded WW4 domain at salt concentrations ≤200 mM. Up to 200 mM, both denaturants did not alter the tertiary packing of WW4, but GdmCl exerted more severe destabilization than NaSCN. Intriguingly, GdmCl had only weak binding to amide protons, while NaSCN showed extensive binding to both hydrophobic side chains and amide protons. Neither denaturant significantly affected the overall ps-ns backbone dynamics, but they distinctively altered µs-ms backbone dynamics. This study unveils that GdmCl and NaSCN destabilize a protein before the global unfolding occurs with differential binding properties and µs-ms backbone dynamics, implying the absence of a simple correlation between thermodynamic stability and backbone dynamics of WW4 at both ps-ns and µs-ms time scales.

Evaluating the effects of graphene nanoparticles combined radio-frequency thawing on the physicochemical quality and protein conformation in hairtail (Trichiurus lepturus) dorsal muscle.

BACKGROUND: The thawing process is an essential step for a frozen marine fish. The present study aimed to investigate the effects of graphene magnetic nanoparticles combined radio-frequency thawing methods on frozen hairtail (Trichiurus lepturus) dorsal muscle. Seven thawing methods were used: air thawing, 4 °C cold storage thawing, water thawing, radio-frequency thawing (RT), radio frequency thawing combined with graphene nanoparticles (G-RT), radio frequency thawing combined with graphene oxide nanoparticles (GO-RT) and radio-frequency thawing combined with graphene magnetic nanoparticles (GM-RT). The thawing loss and centrifugal loss, electric conductivity, total volatile basic nitrogen, thiobarbituric acid reactive substances and color of thawed hairtail dorsal muscle were determined. The carbonyl content, total sulfhydryl groups, Ca2+ -ATPase activity, raman spectroscopy measurements and Fourier-transform infrared spectrometry measurements were determined using myofibrillar extracted from the dorsal muscle of hairtail. The water distribution was determined using low-field NMR techniques. RESULTS: The results demonstrated that the RT, G-RT, GO-RT and GM-RT could significantly shorten the thawing time. Moreover, GO-RT and GM-RT efficiently preserved the color of fish dorsal muscle and reduced the impact of thawing on fish quality by reducing lipid and protein oxidation. Meanwhile, the myofibrillar protein structure thawed by GO-RT and GM-RT were more stable and had a more stable secondary structure, which maintained strong systemic stability at the same time as slowing down protein oxidation. CONCLUSION: The results showed that GO-RT and GM-RT can significantly improve the thawing efficiency at the same time as effectively maintaining and improving the color and texture of thawed fish, slowing down the oxidation of proteins and lipids, and maintaining a good quality of thawed fish meat. © 2023 Society of Chemical Industry.

Progress in the application of novel cryoprotectants for the stabilization of myofibrillar proteins.

In this review, the physicochemical and conformational changes of myofibrillar proteins (MPs) of freeze-induced mince-based aquatic foods were comprehensively summarized in depth. Studies have demonstrated that temperature fluctuation and long-time freezing negatively affect food quality, resulting in texture alteration, drip fluid, flavor degradation, and nutrition loss due to MPs denaturation, aggregation, and oxidation. Attempts have been made in ice-recrystallization inhibition, freezing point depression, and ice shape and growth control for better cryopreservation. Moreover, to further minimize the quality deterioration, cryoprotectants were acknowledged to reduce the denaturation and aggregation of the MPs effectively. Recently, interest in novel functional ingredients, including oligosaccharides, protein hydrolysates, and natural polyphenols demonstrated excellent cryoprotective effects while avoiding health concerns and undesirable flavor caused by traditional sugar-based or phosphates-based cryoprotectants. Therefore, the present review provides a systematic overview of these low molecular weight multifunctional substances with a particular sequence and highlights their underlying mechanism in the inhibition of ice recrystallization the stabilization of MPs.

Tulsi (Ocimum sanctum) mediated Co nanoparticles with their anti-inflammatory, anti-cancer, and methyl orange dye adsorption properties.

Nanotechnology is an emerging technology that uses medicinal plants to extract nanoparticles for conventional applications. In the present investigation, the medical plant Tulsi (Ocimum sanctum) has used in the synthesis of cobalt (Co) nanoparticles in a cost-effective, feasible process. The efficiency of nanoparticles in removing methyl orange dye was evaluated by analyzing their applications in wastewater treatment. An analysis of the anti-inflammatory and anti-cancer properties of Tulsi-mediated Co nanoparticles was conducted to examine their medical application. Morphological analysis of Co nanoparticles showed that the synthesized nanoparticles were in crystal shape with a mean particle size of 110 nm. A batch adsorption study has shown that incubation periods of 5 h, pH 2, temperatures of 70 °C, and adsorbent dosage of 125 µg/mL are optimal for removing methyl orange dye from wastewater. To examine the anti-inflammatory properties of Tulsi-mediated Co nanoparticles, protein denaturation and nitric oxide scavenging assays were performed. The maximum anti-inflammatory response was recorded at a concentration of 250 µg/mL of Co nanoparticles. MTT assays against MDA-MB-231 human breast cancer cells were used to evaluate the anti-cancer properties of Co nanoparticles. This study investigates the economical extraction of Co nanoparticles from tulsi and its potential use in wastewater purification and biomedical applications.

Blue light stimulates light stress and phototactic behavior when received in the brain of Diaphorina citri.

Blue light with a wavelength of 400-470 nm is the composition of the visible light. However, in recent years, blue light contributed the most significance to light pollution due to the artificial light at night. Previously, we have demonstrated that the Asian citrus psyllid (ACP), Diaphorina citri, an important pest in citrus production, has significant positive phototaxis with a light-emitting diode light of 400 nm. In this study, ACP with positive phototactic behavior to 400 nm light (PH) and non-phototactic behavior to 400 nm light (NP) were collected, individually. Transcriptome dynamics of head tissues of PH and NP groups were captured by using RNA-sequencing technology, respectively. Forty-three to 46 million clean reads with high-quality values were obtained, and 1773 differential expressed genes (DEGs) were detected. Compared with the NP group, there were 841 up-regulated DEGs and 932 down-regulated DEGs in the PH group. Eight pathways were significantly enriched in the PH group in the KEGG database, while 43 up-regulated pathways and 25 down-regulated pathways were significantly enriched in the PH group in the GO database. The DGE approach was reliable validated by real time quantitative PCR. Results indicated that the blue light acted as an abiotic stress causing physiological and biochemical responses such as oxidative stress, protein denaturation, inflammation and tumor development in ACPs. Additionally, the light was absorbed by photoreceptors of ACPs, and converted into electrical signal to regulate neuromodulation. This study provides basic information for understanding the molecular mechanisms of ACP in response to blue light and provides a reference for further studies to elucidate phototactic behavior.

Change in the Kinetic Regime of Aggregation of Yeast Alcohol Dehydrogenase in the Presence of 2-Hydroxypropyl-ß-cyclodextrin.

Chemical chaperones are low-molecular-weight compounds that suppress protein aggregation. They can influence different stages of the aggregation process-the stage of protein denaturation, the nucleation stage and the stage of aggregate growth-and this may lead to a change in the aggregation kinetic regime. Here, the possibility of changing the kinetic regime in the presence of a chemical chaperone 2-hydroxypropyl-ß-cyclodextrin (2-HP-ß-CD) was investigated for a test system based on the thermally induced aggregation of yeast alcohol dehydrogenase (yADH) at 56 °C. According to differential scanning calorimetry data, 2-HP-ß-CD did not affect the stage of the protein molecule unfolding. Dynamic light scattering data indicated changes in the aggregation kinetics of yADH during the nucleation and aggregate growth stages in the presence of the chaperone. The analysis of kinetic curves showed that the order of aggregation with respect to protein (nc), calculated for the stage of aggregate growth, changed from nc = 1 to nc = 2 with the addition of 100 mM 2-HP-ß-CD. The mechanism of 2-HP-ß-CD action on the yADH thermal aggregation leading to a change in its kinetic regime of aggregation is discussed.

Chrysin, a 5,7-dihydroxyflavone restrains inflammatory arthritis in rats via subsiding oxidative stress biomarkers and inflammatory cytokines.

This study was intended to appraise the anti-inflammatory and anti-arthritic potential of Chrysin (CR), a natural dietary flavone found in several plant genera, including Passiflora and Propalis, and honey. The in vitro anti-arthritic potential was assessed by protein denaturation and membrane stabilization assays. The acute anti-inflammatory action was assessed by Carrageenan and Xylene induced oedema models in Wistar rats. For determining anti-arthritic potential, 0.1 ml Complete Freund's adjuvant was injected into the left hind paw of rats to induce adjuvant-induced arthritis, followed by initiation of treatment with individual CR at 25, 50, 100 mg/kg and in combination with methotrexate (MTX) by oral gavage for 21 days. The standard treatment group was given MTX (1 mg/kg). Treatment with MTX, chrysin and their combination exhibited a notable inhibition of paw oedema and pain, restoration of body weight and immune organ weight as evident by the histology of ankle joints. Treatment with chrysin alone and in combination significantly (p < 0.0001) restored altered blood parameters (CRP, RF, Hb, WBC, and platelets) with notable (p < 0.0001) down-regulation of interleukin (IL)-6,-1ß, tumor necrosis factor-α, NF-κß, and cyclooxygenase-2 and up-regulation (p < 0.0001) of IL-4, 10, and I-κß in contrast to disease control rats. The treatment with the combination noticeably improved the superoxide dismutase, and catalase activities while reduced the peroxidation level in liver homogenate. It can be concluded from the findings that chrysin especially in combination with MTX ameliorated CFA-induced arthritis owing to its profound anti-oxidant, analgesic and anti-inflammatory actions.

Diosgenin, a steroidal sapogenin, arrests arthritis through modulation of inflammatory cytokines and oxidative stress biomarkers in Wistar rats.

Diosgenin (DGN) is a well-known steroidal sapogenin that is obtained from the hydrolysis of dioscin. The current research aimed to explore the anti-inflammatory and anti-arthritic potential of DGN alone and in combination with methotrexate (MTX). The in-vitro antioxidant, and anti-arthritic potential was assessed by protein denaturation and Human red blood cell membrane stabilization assays. The in-vivo anti-inflammatory effect was examined by carrageenan-induced paw edema and xylene-induced ear edema methods. The arthritis was induced in Wistar rats by inoculation of 0.1 ml Complete Freund's adjuvant in the left hind paw at day 1. The arthritic animals received MTX 1 mg/kg as standard, DGN at 5, 10, 20 mg/kg, and a combination treatment (DGN 20 mg/kg + MTX) was administered orally from 8 to 28th day while normal and disease control received normal saline. DGN at 1600 µg/ml exhibited the highest in-vitro activities in contrast to other tested concentrations. DGN at 20 mg/kg exhibited the maximum (p < 0.05-0.0001) inhibition of inflammation in carrageenan and xyleneinduced edema models. Treatment with DGN and MTX alone and in combination significantly reduced the paw diameter, body weight, arthritic index, and pain. It restored altered blood parameters and oxidative stress biomarkers in contrast to the diseased control rats. DGN profoundly (P < 0.0001) downregulated mRNA expression of TNF-α, IL-1ß, NF-ĸß, and COX-2 while upregulated IL-4 and -10 in treated rats. The combination of DGN with MTX showed the highest therapeutic efficacy than individual therapy, so it can be used as an adjunct for rheumatoid arthritis treatment.

Exploring Echinops polyceras Boiss. from Jordan: Essential Oil Composition, COX, Protein Denaturation Inhibitory Power and Antimicrobial Activity of the Alcoholic Extract.

In this article, we present the first detailed analysis of the hydro-distilled essential oil (HDEO) of the inflorescence heads of Echinops polyceras Boiss. (Asteraceae) from the flora of Jordan, offering observations at different growth (pre-flowering, full-flowering and post-flowering) stages. Additionally, we investigated the methanolic extract obtained from the aerial parts of the plant material at the full flowering stage in order to determine its inhibitory activity in terms of COX and protein denaturation and evaluate its antimicrobial effects against S. aureus (Gram-positive) and E. coli (Gram-negative) bacteria. Performing GC/MS analysis of HDEO, obtained from the fresh inflorescence heads at the different growth stages, resulted in the identification of 192 constituents. The main class of compounds detected in these three stages comprised aliphatic hydrocarbons and their derivatives, which amounted to 50.04% (pre-flower), 40.28% (full-flower) and 41.34% (post-flower) of the total composition. The oils also contained appreciable amounts of oxygenated terpenoids, primarily sesquiterpenoids and diterpenoids. The pre-flowering stage was dominated by (2E)-hexenal (8.03%) in addition to the oxygenated diterpene (6E,10E)-pseudo phytol (7.54%). The full-flowering stage primarily contained (6E,10E)-pseudo phytol (7.84%), ß-bisabolene (7.53%, SH) and the diterpene hydrocarbon dolabradiene (5.50%). The major constituents detected in the HDEO obtained at the post-flowering stage included the oxygenated sesquiterpenoid intermedeol (5.53%), the sesquiterpene hydrocarbon (E)-caryophyllene (5.01%) and (6E,10E)-pseudo phytol (4.47%). The methanolic extract obtained from air-dried aerial parts of E. polyceras displayed more COX-2 inhibition than COX-1 inhibition at a concentration level of 200 µg/mL. The extract exhibited a capacity to inhibit protein denaturation that was comparable with respect to the activity of diclofenac sodium and displayed moderate levels of antimicrobial activity against both bacterial species. The current results demonstrate the need to perform further detailed phytochemical investigations to isolate and characterize active constituents.

Exploring the Chemical Constituents, Antioxidant, Xanthine Oxidase and COX Inhibitory Activity of Commiphora gileadensis Commonly Grown Wild in Saudi Arabia.

The use of the synthetic drugs has increased in the last few decades; however, these drugs exhibit various side effects. Scientists are therefore seeking alternatives from natural sources. Commiphora gileadensis has long been used to treat various disorders. It is commonly known as bisham or balm of Makkah. This plant contains various phytochemicals, including polyphenols and flavonoids, with biological potential. We found that steam-distilled essential oil of C. gileadensis exhibited higher antioxidant activity (IC50, 22.2 µg/mL) than ascorbic acid (IC50, 1.25 µg/mL). The major constituents (>2%) in the essential oil were ß-myrcene, nonane, verticiol, ß-phellandrene, ß-cadinene, terpinen-4-ol, ß-eudesmol, α-pinene, cis-ß-copaene and verticillol, which might be responsible for the antioxidant and antimicrobial activity against Gram-positive bacteria. The extract of C. gileadensis exhibited inhibitory activity against cyclooxygenase (IC50, 450.1 µg/mL), xanthine oxidase (251.2 µg/mL) and protein denaturation (110.5 µg/mL) compared to standard treatments, making it a viable treatment from a natural plant source. LC-MS analysis revealed the presence of phenolic compounds such as caffeic acid phenyl ester, hesperetin, hesperidin, chrysin and transient amounts of catechin, gallic acid, rutin and caffeic acid. The chemical constituents of this plant can be explored further to investigate its wide variety of therapeutic potential.

Aggregation of Lactoferrin Caused by Droplet Atomization Process via a Two-Fluid Nozzle: The Detrimental Effect of Air-Water Interfaces.

Biological macromolecules, especially therapeutic proteins, are delicate and highly sensitive to denaturation from stresses encountered during the manufacture of dosage forms. Thin-film freeze-drying (TFFD) and spray freeze-drying (SFD) are two processes used to convert liquid forms of protein into dry powders. In the production of inhalable dry powders that contain proteins, these potential stressors fall into three categories based on their occurrence during the primary steps of the process: (1) droplet formation (e.g., the mechanism of droplet formation, including spray atomization), (2) freezing, and (3) frozen water removal (e.g., sublimation). This study compares the droplet formation mechanism used in TFFD and SFD by investigating the effects of spraying on the stability of proteins, using lactoferrin as a model. This study considers various perspectives on the denaturation (e.g., conformation) of lactoferrin after subjecting the protein solution to the atomization process using a pneumatic two-fluid nozzle (employed in SFD) or a low-shear drop application through the nozzle. The surface activity of lactoferrin was examined to explore the interfacial adsorption tendency, diffusion, and denaturation process. Subsequently, this study also investigates the secondary and tertiary structure of lactoferrin and the quantification of monomers, oligomers, and, ultimately, aggregates. The spraying process affected the tertiary structure more negatively than the tightly woven secondary structure, resulting in the peak position corresponding to the tryptophan (Trp) residues red-shifting by 1.5 nm. This conformational change can either (a) be reversed at low concentrations via relaxation or (b) proceed to form irreversible aggregates at higher concentrations. Interestingly, when the sample was allowed to progress into micrometer-sized aggregates, such a dramatic change was not detected using methods such as size-exclusion chromatography, polyacrylamide gel electrophoresis, and dynamic light scattering at 173°. A more complete understanding of the heterogeneous protein sample was achieved only through a combination of 173 and 13° backward and forward scattering, a combination of derived count rate measurements, and microflow imaging (MFI). After studying the impact of droplet formation mechanisms on aggregation tendency of lactoferrin, we further investigated two additional model proteins with different surface activity: bovine IgG (serving as a non surface-active negative reference), and ß-galactosidase (another surface-active protein). The results corroborated the lactoferrin findings that spray-atomization-related stress-induced protein aggregation was much more pronounced for proteins that are surface active (lactoferrin and ß-galactosidase), but it was minimal for non-surface-active protein (bovine IgG). Finally, compared to the low-shear dripping used in the TFFD process, lactoferrin underwent a relatively fast conformational change upon exposure to the high air-water interface of the two-fluid atomization nozzle used in the SFD process as compared to the low shear dripping used in the TFFD process. The interfacial-induced denaturation that occurred during spraying was governed primarily by the size of the atomized droplets, regardless of the duration of exposure to air. The percentage of denatured protein population and associated activity loss, in the case of ß-galactosidase, was determined to range from 2 to 10% depending on the air-flow rate of the spraying process.

Freezing-induced denaturation of myofibrillar proteins in frozen meat.

Freezing is commonly used to extend the shelf life of meat and meat products but may impact the overall quality of those products by inducing structural changes in myofibrillar proteins (MPs) through denaturation, chemical modification, and encouraging protein aggregation. This review covers the effect of freezing on the denaturation of MPs in terms of the effects of ice crystallization on solute concentrations, cold denaturation, and protein oxidation. Freezing-induced denaturation of MPs begins with ice crystallization in extracellular spaces and changes in solute concentrations in the unfrozen water fraction. At typical temperatures for freezing meat (lower than -18 °C), cold denaturation of proteins occurs, accompanied by an alteration in their secondary and tertiary structure. Moreover, the disruption of muscle cells triggers the release of cellular enzymes, accelerating protein degradation and oxidation. To minimize severe deterioration during the freezing and frozen storage of meat, there is a vital need to use an appropriate freezing temperature below the glass transition temperature and to avoid temperature fluctuations during storage to prevent recrystallization. Such an understanding of MP denaturation can be applied to determine the optimum freezing conditions for meat products with highly retained sensory, nutritional, and functional qualities.

Sample Preparation by Easy Extraction and Digestion (SPEED) - A Universal, Rapid, and Detergent-free Protocol for Proteomics Based on Acid Extraction.

The main challenge of bottom-up proteomic sample preparation is to extract proteomes in a manner that enables efficient protein digestion for subsequent mass spectrometric analysis. Today's sample preparation strategies are commonly conceptualized around the removal of detergents, which are essential for extraction but strongly interfere with digestion and LC-MS. These multi-step preparations contribute to a lack of reproducibility as they are prone to losses, biases and contaminations, while being time-consuming and labor-intensive. We report a detergent-free method, named Sample Preparation by Easy Extraction and Digestion (SPEED), which consists of three mandatory steps, acidification, neutralization and digestion. SPEED is a universal method for peptide generation from various sources and is easily applicable even for lysis-resistant sample types as pure trifluoroacetic acid (TFA) is used for highly efficient protein extraction by complete sample dissolution. The protocol is highly reproducible, virtually loss-less, enables very rapid sample processing and is superior to the detergent/chaotropic agent-based methods FASP, ISD-Urea and SP3 for quantitative proteomics. SPEED holds the potential to dramatically simplify and standardize sample preparation while improving the depth of proteome coverage especially for challenging samples.

In Vitro Anti-Inflammatory Activities of Fucoidans from Five Species of Brown Seaweeds.

This study aimed to compare the anti-inflammatory effects of fucoidans from brown seaweeds (Saccharina japonica (SJ), Fucus vesiculosus (FV), Fucus distichus (FD), Fucus serratus (FS), and Ascophyllum nodosum (AN)), and determine the relationship between composition and biological activity. The anti-inflammatory activity was tested in vitro. It is believed that inflammation could be triggered by free radicals. Fucoidans from F. vesiculosus (FV1 and FV3) showed the strongest 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging activity with an IC50 = 0.05 mg/mL. In the total antioxidant capacity (TAC) test, the activity was concentration-dependent. Notable, the TAC of fucoidans except samples of FV2 and SJ (which have a lower phenolic content) was higher than that of phloroglucinol. The TAC of fucoidans strongly and positively correlated with polyphenol content. A weak correlation was associated with xylose content. The synergistic effect for fucoidans was calculated for the first time using carbohydrates and polyphenols as model mixtures. The synergy in the DPPH test was found only for FV1 and FV3 (mixture effect ME = 2.68 and 2.04, respectively). The ME strongly positively correlated with polyphenols. The relationship of ME with fucose content was positive but moderate. It was first established that the anti-inflammatory effects of fucoidan could be mediated via the inhibition of protein denaturation. The inhibition was concentration-dependent and strongly correlated with the fucose content and moderate with sulfate content. The purified fucoidan FV2 showed the most promising activity (IC50 = 0.20 mg/mL vs. IC50 = 0.37 mg/mL for diclofenac sodium). Similar relations were also observed in the membrane protection model. Fucoidans were able to stabilize the cell membrane integrity of human red blood corpuscles (HRBC). The results of our study support the rationality of fucoidan use as a promising agent for the treatment of inflammatory-related diseases via mechanisms of radical scavenging, antioxidant activity, inhibition of protein denaturation, and HRBC membrane stabilization.

Conformational Stability and Denaturation Processes of Proteins Investigated by Electrophoresis under Extreme Conditions.

The functional structure of proteins results from marginally stable folded conformations. Reversible unfolding, irreversible denaturation, and deterioration can be caused by chemical and physical agents due to changes in the physicochemical conditions of pH, ionic strength, temperature, pressure, and electric field or due to the presence of a cosolvent that perturbs the delicate balance between stabilizing and destabilizing interactions and eventually induces chemical modifications. For most proteins, denaturation is a complex process involving transient intermediates in several reversible and eventually irreversible steps. Knowledge of protein stability and denaturation processes is mandatory for the development of enzymes as industrial catalysts, biopharmaceuticals, analytical and medical bioreagents, and safe industrial food. Electrophoresis techniques operating under extreme conditions are convenient tools for analyzing unfolding transitions, trapping transient intermediates, and gaining insight into the mechanisms of denaturation processes. Moreover, quantitative analysis of electrophoretic mobility transition curves allows the estimation of the conformational stability of proteins. These approaches include polyacrylamide gel electrophoresis and capillary zone electrophoresis under cold, heat, and hydrostatic pressure and in the presence of non-ionic denaturing agents or stabilizers such as polyols and heavy water. Lastly, after exposure to extremes of physical conditions, electrophoresis under standard conditions provides information on irreversible processes, slow conformational drifts, and slow renaturation processes. The impressive developments of enzyme technology with multiple applications in fine chemistry, biopharmaceutics, and nanomedicine prompted us to revisit the potentialities of these electrophoretic approaches. This feature review is illustrated with published and unpublished results obtained by the authors on cholinesterases and paraoxonase, two physiologically and toxicologically important enzymes.