Selective Immobilization of His-Tagged Enzyme on Ni-Chelated Ion Exchange Resin and Its Application in Protein Purification

Ion exchange resins are suitable as carriers for immobilized enzymes because of their stable physicochemical properties, appropriate particle size and pore structure, and lower loss in continuous operation. In this paper, we report the application of the Ni-chelated ion exchange resin in the immobilization of His-tagged enzyme and protein purification. Acrylic weak acid cation exchange resin (D113H) was selected from four cationic macroporous resins that could chelate the transition metal ion Ni. The maximum adsorption capacity of Ni was ~198 mg/g. Phosphomannose isomerase (PMI) can be successfully immobilized on Ni-chelated D113H from crude enzyme solution through chelation of transition metal ions with the His-tag on the enzyme. The maximum amount of immobilized PMI on the resin was ~143 mg/g. Notably, the immobilized enzyme showed excellent reusability and maintained 92% of its initial activity with 10 cycles of catalytic reaction. In addition, PMI was successfully purified using an affinity chromatography column prepared by Ni-chelated D113H, which showed the potential for the immobilization and purification process to be realized in one step.

Purification and characterization of a novel thermostable anticoagulant protein from medicinal leech Whitmania pigra Whitman

ETHNOPHARMACOLOGICAL RELEVANCE

The prevalence of cardiovascular disease (CVD) is increasing worldwide. Despite significant improvements in novel targeted treatment agents, natural products purified from medicinal animals with minimal side effects have attracted much attention. Several native proteins explored from suck-blood leeches, such as non-thermostable hirudin and its variants, revealed potent anticoagulant activity. Traditional Chinese medicine clinics have proved that non-suck-blood leech Whitmania pigra Whitman (W. pigra) also played notable roles in CVD treatments even after decoction. However, only a few natural proteins and peptides have been identified from the fresh material of this medicinal species.

AIM OF THE STUDY

We aimed to purify and characterize thermostable anticoagulant proteins from W. pigra for further development of a therapeutic agent for thrombosis.

MATERIALS AND METHODS

W. pigra crude extract was prepared by decoction in water. Anticoagulant proteins were purified by DEAE cellulose DE-52, Sephadex G-75, and reversed-phase liquid chromatography sequentially and analyzed by SDS-PAGE and LC-MS/MS for structural information. In addition, we conducted in vitro anticoagulant experiments, including plasma recalcification time (PRT) assay, fibrinolytic assay, activated partial thromboplastin time (APTT), prothrombin time (PT), thrombin time (TT), fibrinogen (Fib) assay, and cell viability assays. Furthermore, a carrageenan-induced chronic thromboembolism model was employed in ICR mice, and four coagulation factors (APTT, PT, TT, and Fib) activities were determined after intragastric administration.

RESULTS

The anticoagulant protein WP-77 has a relative molecular weight of ca. 20.8 kDa. It was effective over a broad temperature range from 20 °C to 100 °C and a pH 2-8 condition. The anticoagulant activity of WP-77 was retained after incubation with pepsin but was greatly inhibited by trypsin (P < 0.01). It significantly prolonged APTT and TT (P < 0.05) but had little effect on PT and Fib in vitro. Furthermore, WP-77 of a low concentration resulted in the recovery of injured EA.hy926 by thrombin. The protein also significantly prolonged APTT and TT (P < 0.01) and inhibited thrombus formation in carrageenan-induced thrombosis mice, demonstrating its antithrombotic effect in vivo.

CONCLUSION

Our results suggest that WP-77 from W. pigra plays a distinct role in treating thrombotic diseases, and it is an essential substance of anticoagulant activity of non-suck-blood medicinal leeches. This thermostable anticoagulant protein could be a promising candidate for the development of clinical antithrombosis medicines.

The antifibrotic effect of pheretima protein is mediated by the TGF-β1/Smad2/3 pathway and attenuates inflammation in bleomycin-induced idiopathic pulmonary fibrosis

ETHNOPHARMACOLOGICAL RELEVANCE

Pheretima is a traditional Chinese medicine that could treat various lung diseases such as asthma, pneumonia, and lung cancer effectively; however, limited studies on the use of Pheretima protein in the treatment of lung diseases have been conducted to date.

AIM OF THE STUDY

The aim of this study was to explain the antipulmonary fibrosis mechanism of the Pheretima protein and elucidate its possible cell signaling pathways.

MATERIAL AND METHODS

Fresh pheretima was freeze-dried to obtain the Pheretima protein. Divide C57BL/6 mice into control and bleomycin (BLM)-induced models, pirfenidone, and Pheretima protein-treatment groups. Three weeks later, they were treated with H&E and Masson's trichrome staining to assess lung injury and fibrosis. Pulmonary fibrosis was assessed using immunohistochemistry (IHC), realtime-PCR (RT-PCR), and western blotting. Inflammation was assessed using the alveolar lavage fluid.

RESULTS

Pheretima protein inhibited epithelial-mesenchymal transition (EMT) and extracellular matrix (ECM) deposition and reduced inflammation. It also reduced the levels of Smad2/3, pSmad2/3, and transforming growth factor-beta 1 (TGF-β1). Thus, our results indicate that Pheretima protein can alleviate BLM-induced pulmonary fibrosis in a mouse model.

CONCLUSION

Pheretima protein inhibits ECM, EMT, and antiinflammatory markers, which in turn ameliorates BLM-induced pulmonary fibrosis. Preliminary mechanistic studies indicated that Pheretima protein can exert its biological activity by downregulating the TGF-β1/Smad2/3 pathway.

Comparative Venomics of the Cryptic Cone Snail Species Virroconus ebraeus and Virroconus judaeus

The venom duct transcriptomes and proteomes of the cryptic cone snail species Virroconus ebraeus and Virroconus judaeus were obtained and compared. The most abundant and shared conotoxin precursor superfamilies in both species were M, O1, and O2. Additionally, three new putative conotoxin precursor superfamilies (Virro01-03) with cysteine pattern types VI/VII and XVI were identified. The most expressed conotoxin precursor superfamilies were SF-mi2 and M in V. ebraeus, and Cerm03 and M in V. judaeus. Up to 16 conotoxin precursor superfamilies and hormones were differentially expressed between both species, and clustered into two distinct sets, which could represent adaptations of each species to different diets. Finally, we predicted, with machine learning algorithms, the 3D structure model of selected venom proteins including the differentially expressed Cerm03 and SF-mi2, an insulin type 3, a Gastridium geographus GVIA-like conotoxin, and an ortholog to the Pionoconus magus ω-conotoxin MVIIA (Ziconotide).

Chemical characteristics and significant antitussive effect of the Erigeron canadensis polyphenolic polysaccharide-protein complex

ETHNOPHARMACOLOGICAL RELEVANCE

Erigeron canadensis has been used in traditional medicine to treat a variety of respiratory diseases, including acute upper and lower respiratory tract infections and cough-related asthma. There is as yet no relevant experimental or clinical study in the scientific literature evaluating the efficacy of plants in these disorders.

AIM OF THE STUDY

To investigate the active ingredients in Erigeron canadensis, a complex isolated from flowering parts of a plant was tested for airway defense reflexes, in particular for cough reflexes and airway reactivity. Both were experimentally induced by a chemical irritant that simulated the inflammatory conditions of their formation.

MATERIAL AND METHODS

The polyphenolic polysaccharide-protein (PPP) complex was isolated from the flowering parts of Erigeron canadensis by hot alkaline extraction and a multi-stage purification process. The antitussive activity was confirmed as a decrease in the number of citric acid-induced coughs and the bronchodilator effect was verified as a decrease in specific airway resistance (sRaw) in conscious guinea pigs.

RESULTS

The dark brown Erigeron complex with a molecular weight of 38,000 g/mol contained phenolics (13.2% wt%), proteins (16.3% wt%), and uronic acids (6.3% wt%). The neutral carbohydrate part of Erigeron consisted mainly of xylose (12.1 wt%), glucose (13.3 wt%), arabinose (24.1 wt%), and galactose (41.0 wt%) residues. Arabinogalactan and 4-OMe-glucuronoxylan have been found to be the major polysaccharides in the Erigeron complex. Using a method of chemically-induced cough reflex and guinea pigs test system the Erigeron complex exhibited statistically significant, the dose-dependent antitussive activity, which was similar to that of the centrally-acting opioid agonist codeine.

CONCLUSION

Pharmacological tests have revealed a new pharmacodynamic effect of the Erigeron complex, namely an antitussive effect. Its activity was most pronounced in comparison with all previously tested compounds from other medicinal plants and approached the effect of codeine, the most potent antitussive used in clinical practice. The results provide the scientific basis for the application of this herb in traditional medicine.

Combination of strong anion exchange liquid chromatography with microchip capillary electrophoresis sodium dodecyl sulfate for rapid two-dimensional separations of complex protein mixtures

Two-dimensional separations provide a simple way to increase the resolution and peak capacity of complex protein separations. The feasibility of a recently developed instrumental approach for two-dimensional separations of proteins was evaluated. The approach is based on the general principle of two-dimensional gel electrophoresis. In the first dimension, semi-preparative strong anion exchange high-performance liquid chromatography is utilized and fractions are collected by means of a fraction collector. They are subsequently analyzed in the second dimension with microchip capillary electrophoresis sodium dodecyl sulfate. Microchip capillary electrophoresis provides the necessary speed (approximately 1 min/fraction) for short analysis. In this study, three different samples were investigated. Different constructs of soluble guanylyl cyclase were expressed in Sf9-cells using the baculovirus expression system. Cell lysates were analyzed and the resulting separations were compared. In our experimental setup, the soluble guanylyl cyclase was identified among hundreds of other proteins in these cell lysates, indicating its potential for screening, process control, or analysis. The results were validated by immunoblotting. Samples from Chinese hamster ovary cell culture before and after a purification step were investigated and approximately 9% less impurities could be observed. The separation patterns obtained for human plasma are closely similar to patterns obtained with two-dimensional gel electrophoresis and a total of 218 peaks could be observed. Overall, the approach was well applicable to all samples and, based on these results, further directions for improvements were identified. .

A novel approach for the purification of aggregation prone proteins

The protein aggregation is one of the major challenges of the biotechnological industry, especially in the areas of development and commercialization of successful protein-based drug products. The inherent high aggregation tendency of proteins during various manufacturing processes, storage, and administration has significant impact upon the product quality, safety and efficacy. We have developed an interesting protein purification approach that separates the functionally active protein from inactive aggregates using a detergent concentration gradient. The C-terminally His tagged nucleocapsid protein of Crimean Congo Hemorrhagic fever virus (CCHFV) has high aggregation tendency and rapidly precipitates upon purification by NiNTA chromatography. Using the new purification approach reported here, the freshly purified protein by NiNTA chromatography was further processed using a detergent gradient. In this new purification approach the active protein is retained in the low detergent concentration zone while the inactive aggregates are promptly removed by their rapid migration to the high detergent concentration zone. The method prevented further aggregation and retained the RNA binding activity in the native protein despite numerous freeze thaw cycles. This simple approach prevents protein aggregation by rapidly separating the preformed early aggregates and creating the appropriate microenvironment for correctly folded proteins to retain their biological activity. It will be of potential importance to the biotechnological industry and other fields of protein biochemistry that routinely face the challenges of protein aggregation.

Optimization of ultrasound assisted extraction of abalone viscera protein and its effect on the iron-chelating activity

This study aims to investigate effects of ultrasound assisted extraction on the abalone viscera protein extraction rate and iron-chelating activity of peptides. The optimal conditions for ultrasound assisted extraction by response surface methodology was at sodium hydroxide concentration 14 g/kg, ultrasonic power 428 W and extraction time 52 min. Under the optimal conditions, protein extraction rate was 64.89%, compared with alkaline extraction of 55.67%. The iron-chelating activity of peptides affected by ultrasound technology was further evaluated by iron-chelating rate, FTIR spectroscopy and LC-HRMS/MS. Alcalase was the suitable enzyme for the preparation of iron-chelating peptides from two abalone viscera proteins, showing no significant difference between their iron-chelating rate of 16.24% (ultrasound assisted extraction) and 16.60% (alkaline extraction). Iron binding sites from the two hydrolysates include amino and carboxylate terminal groups and peptide bond of the peptide backbone as well as amino, imine and carboxylate from side chain groups. Moreover, 24 iron-chelating peptides were identified from hydrolysate (alcalase, ultrasound assisted extraction), which were different from the 27 iron-chelating peptides from hydrolysate (alcalase, alkaline extraction). This study suggests the application of ultrasound technology in the generation of abalone viscera-derived iron-chelating peptides which have the ability to combat iron deficiency.

Isolation of HDL by sequential flotation ultracentrifugation followed by size exclusion chromatography reveals size-based enrichment of HDL-associated proteins

High-density lipoprotein (HDL) particles have multiple beneficial and cardioprotective roles, yet our understanding of their full structural and functional repertoire is limited due to challenges in separating HDL particles from contaminating plasma proteins and other lipid-carrying particles that overlap HDL in size and/or density. Here we describe a method for isolating HDL particles using a combination of sequential flotation density ultracentrifugation and fast protein liquid chromatography with a size exclusion column. Purity was visualized by polyacrylamide gel electrophoresis and verified by proteomics, while size and structural integrity were confirmed by transmission electron microscopy. This HDL isolation method can be used to isolate a high yield of purified HDL from a low starting plasma volume for functional analyses. This method also enables investigators to select their specific HDL fraction of interest: from the least inclusive but highest purity HDL fraction eluting in the middle of the HDL peak, to pooling all of the fractions to capture the breadth of HDL particles in the original plasma sample. We show that certain proteins such as lecithin cholesterol acyltransferase (LCAT), phospholipid transfer protein (PLTP), and clusterin (CLUS) are enriched in large HDL particles whereas proteins such as alpha-2HS-glycoprotein (A2HSG), alpha-1 antitrypsin (A1AT), and vitamin D binding protein (VDBP) are enriched or found exclusively in small HDL particles.

Intact Protein Mass Spectrometry for Therapeutic Protein Quantitation, Pharmacokinetics, and Biotransformation in Preclinical and Clinical Studies: An Industry Perspective

Recent advancements in immunocapture methods and mass spectrometer technology have enabled intact protein mass spectrometry to be applied for the characterization of antibodies and other large biotherapeutics from in-life studies. Protein molecules have not been traditionally studied by intact mass or screened for catabolites in the same manner as small molecules, but the landscape has changed. Researchers have presented methods that can be applied to the drug discovery and development stages, and others are exploring the possibilities of the new approaches. However, a wide variety of options for assay development exists without clear recommendation on best practice, and data processing workflows may have limitations depending on the vendor. In this perspective, we share experiences and recommendations for current and future application of mass spectrometry for biotherapeutic molecule monitoring from preclinical and clinical studies.

Utilizing RAFT Polymerization for the Preparation of Well-Defined Bicontinuous Porous Polymeric Supports: Application to Liquid Chromatography Separation of Biomolecules

Polymer-based monolithic high-performance liquid chromatography (HPLC) columns are normally obtained by conventional free-radical polymerization. Despite being straightforward, this approach has serious limitations with respect to controlling the structural homogeneity of the monolith. Herein, we explore a reversible addition-fragmentation chain transfer (RAFT) polymerization method for the fabrication of porous polymers with well-defined porous morphology and surface chemistry in a confined 200 μm internal diameter (ID) capillary format. This is achieved via the controlled polymerization-induced phase separation (controlled PIPS) synthesis of poly(styrene-co-divinylbenzene) in the presence of a RAFT agent dissolved in an organic solvent. The effects of the radical initiator/RAFT molar ratio as well as the nature and amount of the organic solvent were studied to target cross-linked porous polymers that were chemically bonded to the inner wall of a modified silica-fused capillary. The morphological and surface properties of the obtained polymers were thoroughly characterized by in situ nuclear magnetic resonance (NMR) experiments, nitrogen adsorption-desorption experiments, elemental analyses, field-emission scanning electron microscopy (FESEM), scanning electron microscopy-energy-dispersive X-ray (SEM-EDX) spectroscopy, and X-ray photoelectron spectroscopy (XPS) as well as time-of-flight secondary ion mass spectrometry (ToF-SIMS) revealing the physicochemical properties of these styrene-based materials. When compared with conventional synthetic methods, the controlled-PIPS approach affects the kinetics of polymerization by delaying the onset of phase separation, enabling the construction of materials with a smaller pore size. The results demonstrated the potential of the controlled-PIPS approach for the design of porous monolithic columns suitable for liquid separation of biomolecules such as peptides and proteins.

Protein adsorption on ion exchange adsorbers: A comparison of a stoichiometric and non-stoichiometric modeling approach

For mechanistic modeling of ion exchange (IEX) processes, a profound understanding of the adsorption mechanism is important. While the description of protein adsorption in IEX processes has been dominated by stoichiometric models like the steric mass action (SMA) model, discrepancies between experimental data and model results suggest that the conceptually simple stoichiometric description of protein adsorption provides not always an accurate representation of nonlinear adsorption behavior. In this work an alternative colloidal particle adsorption (CPA) model is introduced. Based on the colloidal nature of proteins, the CPA model provides a non-stoichiometric description of electrostatic interactions within IEX columns. Steric hindrance at the adsorber surface is considered by hard-body interactions between proteins using the scaled-particle theory. The model's capability of describing nonlinear protein adsorption is demonstrated by simulating adsorption isotherms of a monoclonal antibody (mAb) over a wide range of ionic strength and pH. A comparison of the CPA model with the SMA model shows comparable model results in the linear adsorption range, but significant differences in the nonlinear adsorption range due to the different mechanistic interpretation of steric hindrance in both models. The results suggest that nonlinear adsorption effects can be overestimated by the stoichiometric formalism of the SMA model and are generally better reproduced by the CPA model.

Applications of western blot technique: From bench to bedside

Western blot (WB) or immunoblot is a workhorse method. It is commonly used by biologists for study of different aspects of protein biomolecules. In addition, it has been widely used in disease diagnosis. Despite some limitations such as long time, different applications of WB have not been limited. In the present review, we have summarized scientific and clinical applications of WB. In addition, we described some new generation of WB techniques.

Comparison of Pollen Grain Treatments Without Mechanical Fracturation Prior to Protein Quantification

Protein and amino acids in pollen are important nutritional components for larval development in several insect species, especially in Apoidea. The Bradford assay is a widely used method to measure relative protein content of pollen, which can shed light on pollen quality and consequences to fitness. Prior to using the Bradford assay, protein must be released from pollen grains, often using a mixture of chemical and mechanical fracturation methods. In this study, we tested the efficacy of protein extraction without using mechanical fracturation. We used pollen collected by the solitary bee Osmia lignaria Say to compare two known buffers associated with pollen protein analysis: phosphate-buffered saline and sodium hydroxide, and deionized water, and with different pollen weights from which we quantified protein using the Bradford assay. While all buffers and deionized water were useful in releasing protein from pollen grains collected by O. lignaria, the use of sodium hydroxide resulted in significantly higher protein quantification across all pollen weights. This methodological study can inform future studies of pollen nutrition in pollen-foraging species.

Protocol for in vitro BCR-mediated plasma cell differentiation and purification of chromatin-associated proteins

Molecular-level understanding of plasma cell (PC) differentiation has been modeled using lipopolysaccharide (LPS) stimulation in vitro. However, this system does not involve the B-cell receptor (BCR)-a critical component of B cell biology. Here, we present a protocol for in vitro PC differentiation system dependent on BCR signaling that easily scales up for cell number-demanding applications, including protein complex purification. We describe how to set up this system and detail applications for endogenous complex purification of chromatin-associated proteins. For further details on the use and execution of this protocol, please refer to Sciammas et al. (2011) and Ochiai et al. (2018, 2020).

Proposal of a laboratory course dedicated to the generation of protein molecular weight standards for sodium dodecyl sulfate-polyacrylamide gel electrophoresis

Protein molecular weight standards are routinely employed in sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) to estimate the apparent sizes of unknown proteins within a sample. For training students, a laboratory course based on the production of marker proteins is proposed. Following fractionation by column chromatography, a series of purified proteins and mixtures of proteins were combined to generate various sets of unstained, prestained and fluorescently labeled molecular weight ladders for SDS-PAGE. The produced material can be used in successive laboratory practices as an alternative to commercial protein markers.

Ultrasound in the deproteinization process for chitin and chitosan production

Recently, chitin and chitosan are widely investigated for food preservation and active packaging applications. Chemical, as well as biological methods, are usually adopted for the production of these biopolymers. In this study, modification to a chemical method of chitin synthesis from shrimp shells has been proposed through the application of high-frequency ultrasound. The impact of sonication time on the deproteinization step of chitin and chitosan preparation was examined. The chemical identities of chitin and chitosan were verified using infrared spectroscopy. The influence of ultrasound on the deacetylation degree, molecular weight and particle size of the biopolymer products was analysed. The microscopic characteristics, crystallinity and the colour characteristics of the as-obtained biopolymers were investigated. Application of ultrasound for the production of biopolymers reduced the protein content as well as the particle size of chitin. Chitosan of high deacetylation degree and medium molecular weight was produced through ultrasound assistance. Finally, the as-derived chitosan was applied for beef preservation. High values of luminosity, chromatid and chrome were noted for the beef samples preserved using chitosan films, which were obtained by employing biopolymer subjected to sonication for 15, 25 and 40 min. Notably; these characteristics were maintained even after ten days of packaging. The molecular weight of these samples are 73.61 KDa, 86.82 KDa and 55.66 KDa, while the deacetylation degree are 80.60%, 92.86% and 94.03%, respectively; in the same order, the particle size of chitosan are 35.70 μm, 25.51 μm and 20.10 μm.

Preparation of co-crystals of human PPAR-LBD and ligand for high-resolution X-ray crystallography

Peroxisome proliferator-activated receptors (PPARs) are nuclear receptor-type transcription factors with three subtypes (α, δ, and γ) that regulate cell differentiation and metabolism. Co-crystals of human PPARα-ligand-binding domain (LBD)-PPARα ligand for X-ray crystallography have been difficult to obtain. Recombinant human PPARα-LBD proteins contain intrinsic fatty acids (iFAs of Escherichia coli origin) and may be unstable without ligands during crystallization. To circumvent these limitations, we have successfully applied various crystallization techniques, including co-crystallization, cross-seeding, soaking, delipidation, and coactivator peptide supplementation.

For complete details on the use and execution of this protocol, please refer to Kamata et al. (2020).

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Protocols for recombinant PPARα ligand-binding domain protein purification

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Techniques to prepare PPARα-ligand co-crystals for high-resolution X-ray crystallography

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Strategy to obtain PPARα co-crystals with low-affinity PPARα ligands

Photonic resonator interferometric scattering microscopy

Interferometric scattering microscopy is increasingly employed in biomedical research owing to its extraordinary capability of detecting nano-objects individually through their intrinsic elastic scattering. To significantly improve the signal-to-noise ratio without increasing illumination intensity, we developed photonic resonator interferometric scattering microscopy (PRISM) in which a dielectric photonic crystal (PC) resonator is utilized as the sample substrate. The scattered light is amplified by the PC through resonant near-field enhancement, which then interferes with the <1% transmitted light to create a large intensity contrast. Importantly, the scattered photons assume the wavevectors delineated by PC's photonic band structure, resulting in the ability to utilize a non-immersion objective without significant loss at illumination density as low as 25 W cm-2. An analytical model of the scattering process is discussed, followed by demonstration of virus and protein detection. The results showcase the promise of nanophotonic surfaces in the development of resonance-enhanced interferometric microscopies.

Preparation of Fe3O4@PMAA@Ni Microspheres towards the Efficient and Selective Enrichment of Histidine-Rich Proteins

Magnetic material is considered to as a major concern material for the enrichment of histidine-rich proteins (His-proteins) via metal-ion affinity. In this work, magnetic polymer microspheres with core-shell structure (Fe₃O₄@PMAA@Ni) were successfully prepared via reflux-precipitation polymerization followed by in situ reduction and growth of Ni²⁺. The obtained Ni nanofoams with flower-like structure and uniform pore size (3.34 nm) provided numerous binding sites for His-proteins. The adsorption performance of Fe₃O₄@PMAA@Ni microspheres for His-proteins was estimated via selectively separating bovine hemoglobin (BHb) and bovine serum albumin (BSA) from a matrix composed of BHb, BSA, and lysozyme (LYZ). The results indicated that Fe₃O₄@PMAA@Ni microspheres could efficiently and selectively separate His-proteins from the matrix, with a maximum adsorption capacity of ∼2660 mg/g for BHb. Moreover, Fe₃O₄@PMAA@Ni microspheres exhibited good stability and recyclability for BHb separation over seven cycles. Therefore, this work reported a novel and facile strategy to prepare core-shell Fe₃O₄@PMAA@Ni microspheres, which was promising for practical applications of His-protein separation and purification in proteomics.

Valency and Binding Affinity Variations Can Regulate the Multilayered Organization of Protein Condensates with Many Components

Biomolecular condensates, which assemble via the process of liquid-liquid phase separation (LLPS), are multicomponent compartments found ubiquitously inside cells. Experiments and simulations have shown that biomolecular condensates with many components can exhibit multilayered organizations. Using a minimal coarse-grained model for interacting multivalent proteins, we investigate the thermodynamic parameters governing the formation of multilayered condensates through changes in protein valency and binding affinity. We focus on multicomponent condensates formed by scaffold proteins (high-valency proteins that can phase separate on their own via homotypic interactions) and clients (proteins recruited to condensates via heterotypic scaffold-client interactions). We demonstrate that higher valency species are sequestered to the center of the multicomponent condensates, while lower valency proteins cluster towards the condensate interface. Such multilayered condensate architecture maximizes the density of LLPS-stabilizing molecular interactions, while simultaneously reducing the surface tension of the condensates. In addition, multilayered condensates exhibit rapid exchanges of low valency proteins in and out, while keeping higher valency proteins-the key biomolecules involved in condensate nucleation-mostly within. We also demonstrate how modulating the binding affinities among the different proteins in a multicomponent condensate can significantly transform its multilayered structure, and even trigger fission of a condensate into multiple droplets with different compositions.

Light-Regulated Liquid-Liquid Phase Separation for Spatiotemporal Protein Recruitment and Cell Aggregation

We have previously shown that the upper critical solution temperature-type thermoresponsive ureido polymers such as polyallylurea and poly(2-ureidoethylmethacrylate) derivatives show liquid-liquid phase separation (LLPS), also known as simple coacervation, under physiological conditions below their phase-separation temperatures (T_p). The addition of the polymer-rich coacervate droplets that result from LLPS to a monolayer cell culture induced aggregation of cells into multicellular spheroids. In this study, we prepared a ureido copolymer, poly(vinylamine-co-vinylurea), with azobenzene substituents (Azo-PVU) and demonstrated light-guided assembly and disassembly of LLPS coacervates. Azo-PVUs with T_p values ranging from 10 to 52 °C were prepared by changing the azobenzene content. Ultraviolet light caused a decrease in the T_p of Azo-PVU because of trans-to-cis photoisomerization of the azobenzene and irradiation with visible light increased the T_p. Thus, LLPS of Azo-PVU was reversibly controlled. The coacervate droplets deposited on a dish surface were immediately dissolved by targeted UV irradiation (owing to a decrease in the T_p). Spatially controlled recruitment of proteins on the dish surface was achieved when protein solution was added to the light-patterned surface. Furthermore, the light-guided deposition of coacervates resulted in the spatiotemporal transformation of monolayer cells to aggregates. This light-controlled LLPS will allow the preparation of novel liquid-based materials for biomolecular and cellular engineering.

Proteomics for the study of new biomarkers in Fabry disease: State of the art

Nephropathy represents a major complication of Fabry Disease and its accurate characterization is of paramount importance in predicting the disease progression and assessing the therapeutic responses. The diagnostic process still relies on performing renal biopsy, nevertheless many efforts have been made to discover early reliable biomarkers allowing us to avoid invasive procedures. In this field, proteomics offers a sensitive and fast method leading to an accurate detection of specific pathological proteins and the discovery of diagnostic and prognostic biomarkers that reflect disease progression and facilitate the evaluation of therapeutic responses. Here, we report a review of selected literature focusing on the investigation of several proteomic techniques highlighting their advantages, limitations and future perspectives in their application in the routine study of Fabry Nephropathy.

Expressing Cloned Genes for Protein Production, Purification, and Analysis

Obtaining high quantities of a specific protein directly from native sources is often challenging, particularly when dealing with human proteins. To overcome this obstacle, many researchers take advantage of heterologous expression systems by cloning genes into artificial vectors designed to operate within easily cultured cells, such as Escherichia coli, Pichia pastoris (yeast), and several varieties of insect and mammalian cells. Heterologous expression systems also allow for easy modification of the protein to optimize expression, mutational analysis of specific sites within the protein and facilitate their purification with engineered affinity tags. Some degree of purification of the target protein is usually required for functional analysis. Purification to near homogeneity is essential for characterization of protein structure by X-ray crystallography or nuclear magnetic resonance (NMR) and characterization of the biochemical and biophysical properties of a protein, because contaminating proteins almost always adversely affect the results. Methods for producing and purifying proteins in several different expression platforms and using a variety of vectors are introduced here.

Advances and applications of in-tube solid-phase microextraction for analysis of proteins

In-tube solid-phase microextraction (IT-SPME) with capillary column as extraction device is a well-established green extraction technique with a lot of applications in the fields of biomedicine, food and environment. This article reviews the research contributions of IT-SPME for analysis of proteins. The paper first briefly describes the history of IT-SPME. Then, the development and principle of IT-SPME for analysis of proteins are introduced, in which capillary column configurations of IT-SPME and instruments for quantitative analysis of proteins are summarized. Subsequently, the synthesis strategy and recognition principle of different recognition units, including antibodies, aptamers, molecularly imprinted polymers, and boronate affinity materials, are discussed in detail. This part also introduces several rare recognition units, including lectins, restricted access materials, lysine modified with β-cyclodextrin and cell membrane. The development trend and possible future direction of IT-SPME for analysis of proteins are mentioned.

Mesenchymal Stem Cell-Derived Extracellular Vesicle Isolation and Their Protein Cargo Characterization

In the present protocol, extracellular vesicles (EVs) released from a primary culture of human umbilical cord mesenchymal stem cells (MSCs) were isolated by ultracentrifugation processes, characterized by transmission electron microscopy (TEM) and measured by nanoparticle tracking analysis (NTA). Protein was extracted from EVs using RIPA buffer and then was assessed for integrity. The proteomic content of the total EV protein samples was analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) after labeling by tandem mass tag (TMT). This combined approach allowed the development of an effective strategy to study the protein cargo from MSC-derived EVs.

Expression, purification and crystallization of the N-terminal Solanaceae domain of the Sw-5b NLR immune receptor

Plant nucleotide-binding domain and leucine-rich repeat receptors (NLRs) play crucial roles in recognizing pathogen effectors and activating plant immunity. The tomato NLR Sw-5b is a coiled-coil NLR (CC-NLR) immune receptor that confers resistance against tospoviruses, which cause serious economic losses in agronomic crops worldwide. Compared with other CC-NLRs, Sw-5b possesses an extended N-terminal Solanaceae domain (SD). The SD of Sw-5b is critical for recognition of the tospovirus viral movement protein NSm. An SD is also frequently detected in many NLRs from Solanaceae plants. However, no sequences homologous to the SD have been detected in animals or in plants other than Solanaceae. The properties of the SD protein are largely unknown, and thus 3D structural information is vital in order to better understand its role in pathogen perception and the activation of immune receptors. Here, the expression, purification and crystallization of Sw-5b SD (amino acids 1-245) are reported. Native and selenomethionine-substituted crystals of the SD protein belonged to space group P3112, with unit-cell parameters a = 81.53, b = 81.53, c = 98.44 Å and a = 81.63, b = 81.63, c = 98.80 Å, respectively. This is the first report of a structural study of the noncanonical SD domain of the NLR proteins from Solanaceae plants.

Media Selection in Ion Exchange Chromatography in a Single Microplate

High-throughput process development is more and more used in chromatography. Limitations are the tools provided by the manufacturers. Here, we describe a method to select ion exchange chromatographic media using a 96-well filter microplate.

A Protocol for Isolation, Purification, Characterization, and Functional Dissection of Exosomes

Extracellular vesicles (EVs) are membrane-enclosed vesicles released by cells. They carry proteins, nucleic acids, and metabolites which can be transferred to a recipient cell, locally or at a distance, to elicit a functional response. Since their discovery over 30 years ago, the functional repertoire of EVs in both physiological (e.g., organ morphogenesis, embryo implantation) and pathological (e.g., cancer, neurodegeneration) conditions has cemented their crucial role in intercellular communication. Moreover, because the cargo encapsulated within circulating EVs remains protected from degradation, their diagnostic as well as therapeutic (such as drug delivery tool) applications have garnered vested interest. Global efforts have been made to purify EV subtypes from biological fluids and in vitro cell culture media using a variety of strategies and techniques, with a major focus on EVs of endocytic origin called exosomes (30-150 nm in size). Given that the secretome comprises of soluble secreted proteins, protein aggregates, RNA granules, and EV subtypes (such as exosomes, shed microvesicles, apoptotic bodies), it is imperative to purify exosomes to homogeneity if we are to perform biochemical and biophysical characterization and, importantly, functional dissection. Besides understanding the composition of EV subtypes, defining molecular bias of how they reprogram target cells also remains of paramount importance in this area of active research. Here, we outline a systematic "how to" protocol (along with useful insights/tips) to obtain highly purified exosomes and perform their biophysical and biochemical characterization. This protocol employs a mass spectrometry-based proteomics approach to characterize the protein composition of exosomes. We also provide insights on different isolation strategies and their usefulness in various downstream applications. We outline protocols for lipophilic labeling of exosomes to study uptake by a recipient cell, investigating cellular reprogramming using proteomics and studying functional response to exosomes in the Transwell-Matrigel™ Invasion assay.

Protein fractional synthesis rates within tissues of high- and low-active mice

With the rise in physical inactivity and its related diseases, it is necessary to understand the mechanisms involved in physical activity regulation. Biological factors regulating physical activity are studied to establish a possible target for improving the physical activity level. However, little is known about the role metabolism plays in physical activity regulation. Therefore, we studied protein fractional synthesis rate (FSR) of multiple organ tissues of 12-week-old male mice that were previously established as inherently low-active (n = 15, C3H/HeJ strain) and high-active (n = 15, C57L/J strain). Total body water of each mouse was enriched to 5% deuterium oxide (D₂O) via intraperitoneal injection and maintained with D₂O enriched drinking water for about 24 h. Blood samples from the jugular vein and tissues (kidney, heart, lung, muscle, fat, jejunum, ileum, liver, brain, skin, and bone) were collected for enrichment analysis of alanine by LC-MS/MS. Protein FSR was calculated as -ln(1-enrichment). Data are mean±SE as fraction/day (unpaired t-test). Kidney protein FSR in the low-active mice was 7.82% higher than in high-active mice (low-active: 0.1863±0.0018, high-active: 0.1754±0.0028, p = 0.0030). No differences were found in any of the other measured organ tissues. However, all tissues resulted in a generally higher protein FSR in the low-activity mice compared to the high-activity mice (e.g. lung LA: 0.0711±0.0015, HA: 0.0643±0.0020, heart LA: 0.0649± 0.0013 HA: 0.0712±0.0073). Our observations suggest that high-active mice in most organ tissues are no more inherently equipped for metabolic adaptation than low-active mice, but there may be a connection between protein metabolism of kidney tissue and physical activity level. In addition, low-active mice have higher organ-specific baseline protein FSR possibly contributing to the inability to achieve higher physical activity levels.

Progress in Modern Marine Biomaterials Research

The growing demand for new, sophisticated, multifunctional materials has brought natural structural composites into focus, since they underwent a substantial optimization during long evolutionary selection pressure and adaptation processes. Marine biological materials are the most important sources of both inspiration for biomimetics and of raw materials for practical applications in technology and biomedicine. The use of marine natural products as multifunctional biomaterials is currently undergoing a renaissance in the modern materials science. The diversity of marine biomaterials, their forms and fields of application are highlighted in this review. We will discuss the challenges, solutions, and future directions of modern marine biomaterialogy using a thorough analysis of scientific sources over the past ten years.

NMR in target driven drug discovery: why not?

No matter the source of compounds, drug discovery campaigns focused directly on the target are entirely dependent on a consistent stream of reliable data that reports on how a putative ligand interacts with the protein of interest. The data will derive from many sources including enzyme assays and many types of biophysical binding assays such as TR-FRET, SPR, thermophoresis and many others. Each method has its strengths and weaknesses, but none is as information rich and broadly applicable as NMR. Here we provide a number of examples of the utility of NMR for enabling and providing ongoing support for the early pre-clinical phase of small molecule drug discovery efforts. The examples have been selected for their usefulness in a commercial setting, with full understanding of the need for speed, cost-effectiveness and ease of implementation.

Current Research Landscape of Marine-Derived Anti-Atherosclerotic Substances

Atherosclerosis is a chronic disease characterized by lipid accumulation and chronic inflammation of the arterial wall, which is the pathological basis for coronary heart disease, cerebrovascular disease and thromboembolic disease. Currently, there is a lack of low-cost therapeutic agents that effectively slow the progression of atherosclerosis. Therefore, the development of new drugs is urgently needed. The research and development of marine-derived drugs have gained increasing interest from researchers across the world. Many marine organisms provide a rich material basis for the development of atherosclerotic drugs. This review focuses on the latest technological advances in the structures and mechanisms of action of marine-derived anti-atherosclerotic substances and the challenges of the application of these substances including marine polysaccharides, proteins and peptides, polyunsaturated fatty acids and small molecule compounds. Here, we describe the theoretical basis of marine biological resources in the treatment of atherosclerosis.

Identification, Purification and Molecular Characterization of Chondrosin, a New Protein with Anti-tumoral Activity from the Marine Sponge Chondrosia Reniformis Nardo 1847

: Chondrosia reniformis is a common marine demosponge showing many peculiarities, lacking silica spicules and with a body entirely formed by a dense collagenous matrix. In this paper, we have described the identification of a new cytotoxic protein (chondrosin) with selective activity against specific tumor cell lines, from C. reniformis, collected from the Liguria Sea. Chondrosin was extracted and purified using a salting out approach and molecular weight size exclusion chromatography. The cytotoxic fractions were then characterized by two-dimensional gel electrophoresis and mass spectrometry analysis and matched the results with C. reniformis transcriptome database. The procedure allowed for identifying a full-length cDNA encoding for a 199-amino acids (aa) polypeptide, with a signal peptide of 21 amino acids. The mature protein has a theoretical molecular weight of 19611.12 and an IP of 5.11. Cell toxicity assays showed a selective action against some tumor cell lines (RAW 264.7 murine leukemia cells in particular). Cell death was determined by extracellular calcium intake, followed by cytoplasmic reactive oxygen species overproduction. The in silico modelling of chondrosin showed a high structural homology with the N-terminal region of the ryanodine receptor/channel and a short identity with defensin. The results are discussed suggesting a possible specific interaction of chondrosin with the Cav 1.3 ion voltage calcium channel expressed on the target cell membranes.

Protein Recovery from Underutilised Marine Bioresources for Product Development with Nutraceutical and Pharmaceutical Bioactivities

The global demand for dietary proteins and protein-derived products are projected to dramatically increase which cannot be met using traditional protein sources. Seafood processing by-products (SPBs) and microalgae are promising resources that can fill the demand gap for proteins and protein derivatives. Globally, 32 million tonnes of SPBs are estimated to be produced annually which represents an inexpensive resource for protein recovery while technical advantages in microalgal biomass production would yield secure protein supplies with minimal competition for arable land and freshwater resources. Moreover, these biomaterials are a rich source of proteins with high nutritional quality while protein hydrolysates and biopeptides derived from these marine proteins possess several useful bioactivities for commercial applications in multiple industries. Efficient utilisation of these marine biomaterials for protein recovery would not only supplement global demand and save natural bioresources but would also successfully address the financial and environmental burdens of biowaste, paving the way for greener production and a circular economy. This comprehensive review analyses the potential of using SPBs and microalgae for protein recovery and production critically assessing the feasibility of current and emerging technologies used for the process development. Nutritional quality, functionalities, and bioactivities of the extracted proteins and derived products together with their potential applications for commercial product development are also systematically summarised and discussed.

Applications of Converged Various Forces for Detection of Biomolecules and Novelty of Dielectrophoretic Force in the Applications

Since separation of target biomolecules is a crucial step for highly sensitive and selective detection of biomolecules, hence, various technologies have been applied to separate biomolecules, such as deoxyribonucleic acid (DNA), protein, exosome, virus, etc. Among the various technologies, dielectrophoresis (DEP) has the significant advantage that the force can provide two different types of forces, attractive and repulsive DEP force, through simple adjustment in frequency or structure of microfluidic chips. Therefore, in this review, we focused on separation technologies based on DEP force and classified various separation technologies. First, the importance of biomolecules, general separation methods and various forces including DEP, electrophoresis (EP), electrothermal flow (ETF), electroosmosis (EO), magnetophoresis, acoustophoresis (ACP), hydrodynamic, etc., was described. Then, separating technologies applying only a single DEP force and dual force, moreover, applying other forces simultaneously with DEP force were categorized. In addition, advanced technologies applying more than two different kinds of forces, namely complex force, were introduced. Overall, we critically reviewed the state-of-the-art of converged various forces for detection of biomolecules with novelty of DEP.

Effects of negative and positive cooperative adsorption of proteins on hydrophobic interaction chromatography media

The adsorption behavior of the model proteins: alpha-Lactalbumin, Bovine Serum Albumin, Lysozyme, and a monoclonal antibody, in single component and in binary mixtures, was investigated on two different hydrophobic interaction chromatography resins using both static and dynamic methods. A kinetic model of the adsorption process was developed, which accounted for protein unfolding and intermolecular interactions in the adsorbed phase. The latter incorporated positive cooperative interactions, resulting from preferred and multilayer adsorption on the adsorbent surface, as well as negative cooperative interactions attributed to exclusion effects due to size exclusion and repulsion. Cooperative adsorption resulted in negative or positive deviations from the Langmuir model for both single and multicomponent isotherms. The model was used to assess possible contributions of different adsorption mechanisms of proteins and their structurally different forms to the overall adsorption pattern, as well as to simulate chromatographic band profiles under different loading conditions. For proteins with unstable structure, the overall adsorption isotherm was dominated by binding of unfolded species at low surface coverage and by positive cooperative adsorption at high surface coverage. Furthermore, regardless of structural stability, exclusion effects influenced strongly adsorption equilibrium, particularly at low surface coverages. In case of chromatographic elution, i.e. under dynamic conditions, unfolding, negative cooperative adsorption, and kinetic effects governed the retention behavior and determined peak shapes, whereas the effect of positive cooperative adsorption was negligible.

Dielectrophoresis of proteins: experimental data and evolving theory

The ability to selectively move and trap proteins is core to their effective use as building blocks and for their characterization. Analytical and preparative strategies for proteins have been pursued and modeled for nearly a hundred years, with great advances and success. Core to all of these studies is the separation, isolation, purification, and concentration of pure homogeneous fractions of a specific protein in solution. Processes to accomplish this useful solution include biphasic equilibrium (chromatographies, extractions), mechanical, bulk property, chemical equilibria, and molecular recognition. Ultimately, the goal of all of these is to physically remove all non-like protein molecules-to the finest detail: all atoms in the full three-dimensional structure being identical down the chemical bond and bulk structure chirality. One strategy which has not been effectively pursued is exploiting the higher order subtle electrical properties of the protein-solvent system. The advent of microfluidic systems has enabled the use of very high electric fields and well-defined gradients such that extremely high resolution separations of protein mixtures are possible. These advances and recognition of these capabilities have caused a re-evaluation of the underlying theoretical models and they were found to be inadequate. New theoretical descriptions are being considered which align more closely to the total forces present and the subtlety of differences between similar proteins. These are focused on the interfacial area between the protein and hydrating solvent molecules, as opposed to the macroscale assumptions of homogeneous solutions and particles. This critical review examines all data which has been published that place proteins in electric field gradients which induce collection of those proteins, demonstrating a force greater than dispersive effects or countering forces. Evolving theoretical constructs are presented and discussed, and a general estimate of future capabilities using the higher order effects and the high fields and precise gradients of microfluidic systems is discussed. Graphical abstract.

Protein Phase Separation during Stress Adaptation and Cellular Memory

Cells need to organise and regulate their biochemical processes both in space and time in order to adapt to their surrounding environment. Spatial organisation of cellular components is facilitated by a complex network of membrane bound organelles. Both the membrane composition and the intra-organellar content of these organelles can be specifically and temporally controlled by imposing gates, much like bouncers controlling entry into night-clubs. In addition, a new level of compartmentalisation has recently emerged as a fundamental principle of cellular organisation, the formation of membrane-less organelles. Many of these structures are dynamic, rapidly condensing or dissolving and are therefore ideally suited to be involved in emergency cellular adaptation to stresses. Remarkably, the same proteins have also the propensity to adopt self-perpetuating assemblies which properties fit the needs to encode cellular memory. Here, we review some of the principles of phase separation and the function of membrane-less organelles focusing particularly on their roles during stress response and cellular memory.

Electro-Osmotic Vortices Promote the Capture of Folded Proteins by PlyAB Nanopores

Biological nanopores are emerging as powerful tools for single-molecule analysis and sequencing. Here, we engineered the two-component pleurotolysin (PlyAB) toxin to assemble into 7.2 × 10.5 nm cylindrical nanopores with a low level of electrical noise in lipid bilayers, and we addressed the nanofluidic properties of the nanopore by continuum simulations. Surprisingly, proteins such as human albumin (66.5 kDa) and human transferrin (76-81 kDa) did not enter the nanopore. We found that the precise engineering of the inner surface charge of the PlyAB induced electro-osmotic vortices that allowed the electrophoretic capture of the proteins. Once inside the nanopore, two human plasma proteins could be distinguished by the characteristics of their current blockades. This fundamental understanding of the nanofluidic properties of nanopores provides a practical method to promote the capture and analysis of folded proteins by nanopores.

Extraction of Protein from Four Different Seaweeds Using Three Different Physical Pre-Treatment Strategies

Seaweeds are a rich source of protein and can contain up to 47% on the dry weight basis. It is challenging to extract proteins from the raw biomass of seaweed due to resilient cell-wall complexes. Four species of macroalgae were used in this study-two brown, Fucus vesiculosus and Alaria esculenta, and two red, Palmaria palmata and Chondrus crispus. Three treatments were applied individually to the macroalgal species: (I) high-pressure processing (HPP); (II) laboratory autoclave processing and (III) a classical sonication and salting out method. The protein, ash and lipid contents of the resulting extracts were estimated. Yields of protein recovered ranged from 3.2% for Fucus vesiculosus pre-treated with high pressure processing to 28.9% protein recovered for Chondrus crispus treated with the classical method. The yields of protein recovered using the classical, HPP and autoclave pre-treatments applied to Fucus vesiculosus were 35.1, 23.7% and 24.3%, respectively; yields from Alaria esculenta were 18.2%, 15.0% and 17.1% respectively; yields from Palmaria palmata were 12.5%, 14.9% and 21.5% respectively, and finally, yields from Chondrus crispus were 35.2%, 16.1% and 21.9%, respectively. These results demonstrate that while macroalgal proteins may be extracted using either physical or enzymatic methods, the specific extraction procedure should be tailored to individual species.

Recent advances in robotic protein sample preparation for clinical analysis and other biomedical applications

Discovery of new protein biomarker candidates has become a major research goal in the areas of clinical chemistry, analytical chemistry, and biomedicine. These important species constitute the molecular target when it comes to diagnosis, prognosis, and further monitoring of disease. However, their analysis requires powerful, selective and high-throughput sample preparation and product (analyte) characterisation approaches. In general, manual sample processing is tedious, complex and time-consuming, especially when large numbers of samples have to be processed (e.g., in clinical studies). Automation via microtiter-plate platforms involving robotics has brought improvements in high-throughput performance while comparable or even better precisions and repeatability (intra-day, inter-day) were achieved. At the same time, waste production and exposure of laboratory personnel to hazards were reduced. In comprehensive protein analysis workflows (e.g., liquid chromatography-tandem mass spectrometry analysis), sample preparation is an unavoidable step. This review surveys the recent achievements in automation of bottom-up and top-down protein and/or proteomics approaches. Emphasis is put on high-end multi-well plate robotic platforms developed for clinical analysis and other biomedical applications. The literature from 2013 to date has been covered.

Native LESA TWIMS-MSI: Spatial, Conformational, and Mass Analysis of Proteins and Protein Complexes

We have previously demonstrated native liquid extraction surface analysis (LESA) mass spectrometry imaging of small intact proteins in thin tissue sections. We also showed calculation of collision cross sections for specific proteins extracted from discrete locations in tissue by LESA traveling wave ion mobility spectrometry (TWIMS). Here, we demonstrate an integrated native LESA TWIMS mass spectrometry imaging (MSI) workflow, in which ion mobility separation is central to the imaging experiment and which provides spatial, conformational, and mass information on endogenous proteins in a single experiment. The approach was applied to MSI of a thin tissue section of mouse kidney. The results show that the benefits of integration of TWIMS include improved specificity of the ion images and the capacity to calculate collision cross sections for any protein or protein complex detected in any pixel (without a priori knowledge of the presence of the protein).

Intensified recovery of lipids, proteins, and carbohydrates from wastewater-grown microalgae Desmodesmus sp. by using ultrasound or ozone

This study evaluates the effect of ultrasound and ozone pretreatments for the subsequent recovery of Desmodesmus sp. biocomponents-lipids, proteins, and carbohydrates-using a response surface methodology. Both pretreatments impact on the recovered lipids quality, solvent waste production and extraction time is analysed for process intensification purposes. For ultrasound pretreatment, independent parameters were energy applied (50-200 kWh/kg dry biomass), biomass concentration (25-75 g/L), and ultrasonic intensity (0.32 and 0.53 W/mL). While for ozone pretreatment, independent parameters were ozone concentration (3-9 mg O₃/L), biomass concentration (25-75 g/L), and contact time (5-15 min). In the case of ultrasound pretreatment, recovery yield reached 97 ± 0.4%, 89 ± 3%, and 73 ± 0.6% for proteins, carbohydrates and lipids respectively. Given process required: energy applied of 50 kWh/kg dry biomass, 75 g/L of biomass concentration, 0.32 W/mL of ultrasonic intensity, and 56 min of time process. Ultrasound caused high cell disruption releasing all proteins, thereby obviating downstream processing for its recovery. Ozone pretreatment recovery yield was 85 ± 2%, 48 ± 1.4%, and 25 ± 1.3%, for carbohydrates, lipids and proteins respectively, under the following conditions: 9 mg O₃/L of ozone concentration, 25 g/L of biomass concentration, and 5 min of contact time that depicts an energy consumption of 30.64 kWh/kg dry biomass. It was found that ultrasound and ozone pretreatments intensified the lysis and biocomponents recovery process by reducing solvent consumption by at least 92% and extraction time between 80% and 90% compared with extraction of untreated biomass biocomponents. Both pretreatments improve the composition of the recovered lipids. It was noted that the yield of neutral lipids increased from 28% to 67% for ultrasound pretreatment while for ozone pretreatment from 49% to 63%. The method used for lipid extraction may also have an effect but here it was kept constant.

Rapid diagnosis of periodontitis, a feasibility study using MALDI-TOF mass spectrometry

AIM

The aim of the present study was to assess the feasibility and diagnostic contribution of protein profiling using MALDI-TOF mass spectrometry applied to saliva, gingival crevicular fluid (GCF) and dental plaque from periodontitis and healthy subjects. We hypothesized that rapid routine and blinded MALDI-TOF analysis could accurately classify these three types of samples according to periodontal state.

MATERIALS AND METHODS

Unstimulated saliva, GCF and dental plaque, collected from periodontitis subjects and healthy controls, were analyzed by MALDI-TOF MS. Based on the differentially expressed peaks between the two groups, diagnostic decision trees were built for each sample.

RESULTS

Among 141 patients (67 periodontitis and 74 healthy controls), the decision trees diagnosed periodontitis with a sensitivity = 70.3% (± 0.211) and a specificity = 77.8% (± 0.165) for saliva, a sensitivity = 79.6% (± 0.188) and a specificity = 75.7% (± 0.195) for GCF, and a sensitivity = 72.1% (± 0.202) and a specificity = 72.2% (± 0.195) for dental plaque. The sensitivity and specificity of the tests were improved to 100% (CI 95% = [0.91;1]) and 100% (CI 95% = [0.92;1]), respectively, when two samples were tested.

CONCLUSION

We developed, for the first time, diagnostic tests based on protein profiles of saliva, GCF and dental plaque between periodontitis patients and healthy subjects. When at least 2 of these samples were tested, the best results were obtained.

Lysosomal protein thermal stability does not correlate with cellular half-life: global observations and a case study of tripeptidyl-peptidase 1

Late-infantile neuronal ceroid lipofuscinosis (LINCL) is a neurodegenerative lysosomal storage disorder caused by mutations in the gene encoding the protease tripeptidyl-peptidase 1 (TPP1). Progression of LINCL can be slowed or halted by enzyme replacement therapy, where recombinant human TPP1 is administered to patients. In this study, we utilized protein engineering techniques to increase the stability of recombinant TPP1 with the rationale that this may lengthen its lysosomal half-life, potentially increasing the potency of the therapeutic protein. Utilizing multiple structure-based methods that have been shown to increase the stability of other proteins, we have generated and evaluated over 70 TPP1 variants. The most effective mutation, R465G, increased the melting temperature of TPP1 from 55.6°C to 64.4°C and increased its enzymatic half-life at 60°C from 5.4 min to 21.9 min. However, the intracellular half-life of R465G and all other variants tested in cultured LINCL patient-derived lymphoblasts was similar to that of WT TPP1. These results provide structure/function insights into TPP1 and indicate that improving in vitro thermal stability alone is insufficient to generate TPP1 variants with improved physiological stability. This conclusion is supported by a proteome-wide analysis that indicates that lysosomal proteins have higher melting temperatures but also higher turnover rates than proteins of other organelles. These results have implications for similar efforts where protein engineering approaches, which are frequently evaluated in vitro, may be considered for improving the physiological properties of proteins, particularly those that function in the lysosomal environment.

Differential Detergent Lysis of Cellular Fractions for Immunoprecipitation

Differential detergent fractionation of cells is a rapid method for extraction of cytoplasmic and nuclear proteins in preparation of an immunoprecipitation. This method can be applied for use of adherent or suspension cells and can significantly reduce nonspecific background in an immunoprecipitation by separation of cellular compartments into individual fractions. The lysis of cells by differential detergents permits the rapid extraction of proteins from the cytoplasm (digitonin), the cytoplasmic membranes, and organelles (Triton X-100), and nucleoplasm (Tween/DOC), facilitated through the use of distinct extraction buffers. Cytoplasmic and nuclear matrix proteins as well as DNA are left behind during the detergent-based extraction.

An erosion-type hydrolysis behavior of insoluble protein fraction from Chlorella protothecoides

BACKGROUND

Acid-induced hydrolysis of proteins has been used to improve the solubility and functional properties of various proteins, and could be a promising tool to facilitate the use of currently underutilized insoluble microalgae protein-rich fractions in food applications. However, the results of a prior study showed an unusual resistance of an insoluble microalgae protein-rich fraction to acid hydrolysis at room temperature.

RESULTS

In the present study, the insoluble protein-rich fraction extracted from microalgae Chlorella prothothecoides was treated with 0.5 mol L^-1 hydrochloric acid at 25, 45, 65 or 85 °C for 0-4 h. The results showed that hydrolysis of the fraction at 85 °C for 4 h led to decreases in the amount of insoluble protein-rich aggregates and the formation of fragments with a lower molecular weight, as well as an increase in protein solubility by approximately 40%. Nevertheless, some aggregated insoluble protein-rich particles remained, even after hydrolysis at 85 °C for 4 h.

CONCLUSION

The higher temperature improved the efficiency of the acid hydrolysis of the insoluble protein fraction from microalgae Chlorella prothothecoides, which is highly acid-resistant. Overall, an erosion-based mechanism was suggested for the acid hydrolysis of insoluble microalgae protein fraction. © 2019 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.