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1.
Methods Mol Biol ; 2564: 299-315, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36107350

RESUMO

Green fluorescent proteins (GFPs) have lightened up almost every aspect of biological research including protein sciences. In the field of membrane protein structural biology, GFPs have been used widely to monitor membrane protein localization, expression level, the purification process and yield, and the stability inside the cells and in the test tube. Of particular interest is the fluorescence-detector size-exclusion chromatography-based thermostability assay (FSEC-TS). By simple heating and FSEC, the generally applicable method allows rapid assessment of the thermostability of GFP-fused membrane proteins without purification. Here we describe the experimental details and some typical results for the FSEC-TS method.


Assuntos
Proteínas de Membrana , Cromatografia em Gel , Proteínas de Fluorescência Verde/metabolismo , Proteínas de Membrana/metabolismo
2.
Methods Mol Biol ; 2554: 141-153, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36178625

RESUMO

The roles of small molecules in every aspect of life have been gaining increased recognition. Many are known to exert their effect by binding proteins-but a comprehensive overview of protein-metabolite interactions (PMIs) is missing. Recently we devised a non-targeted method for detecting PMIs using size-exclusion chromatography followed by proteomic and metabolomic analysis: PROMIS. Under test this method was able to identify known PMIs such as enzyme-cofactor complexes as well as novel ones.


Assuntos
Proteínas , Proteômica , Cromatografia em Gel , Espectrometria de Massas/métodos , Metabolômica , Proteômica/métodos
3.
Rapid Commun Mass Spectrom ; 36(21): e9395, 2022 Nov 15.
Artigo em Inglês | MEDLINE | ID: mdl-36068720

RESUMO

RATIONALE: Native mass spectrometry (MS) is an analytical technique used to determine the molecular mass of protein complexes without cross-linking. Size exclusion chromatography (SEC) coupled with native MS using conventional electrospray ionization (ESI) has been reported to allow online buffer exchange. To detect a wide variety of protein complexes without a collapse in the ionization process, it is important to build an online system that enables robust analysis with a low flow rate. METHODS: We created an online native MS system equipped with nanoESI connected to the SEC component (online SEC/nanoESI system) and optimized several parameters for SEC separation and ionization. The constructed system was used to measure a solution consisting of a protein mixture of various molecular masses (10-300 kDa) to verify characteristics such as the measurable molecular mass range, reproducibility, and online buffer exchange. RESULTS: The optimal flow rates for SEC separation and nanoESI analysis using this system were 200 and 1 µL/min, respectively. This system was able to analyze proteins in the ranges of 10-300 and 20-300 kDa for protein samples in ammonium acetate and nonvolatile buffer, respectively. Furthermore, the results of consecutive measurements showed that the relative standard deviations of the retention times and observed masses for each protein were sufficiently small. CONCLUSIONS: We created an online SEC/nanoESI system and evaluated its utility for the analysis of various proteins in conventional measurement solvent and nonvolatile buffer. As a result, the structural stability and resolution of the proteins were found to be sufficient when using online buffer exchange. Therefore, this online SEC/nanoESI system would be a useful technique for obtaining mass spectra of various proteins automatically with good resolution, simply by loading samples into an autosampler.


Assuntos
Proteínas , Espectrometria de Massas por Ionização por Electrospray , Cromatografia em Gel , Proteínas/química , Reprodutibilidade dos Testes , Solventes , Espectrometria de Massas por Ionização por Electrospray/métodos
4.
J Synchrotron Radiat ; 29(Pt 5): 1318-1328, 2022 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-36073892

RESUMO

The second phase of the ESRF upgrade program did not only provide a new storage ring (Extremely Brilliant Source, EBS) but also allowed several beamlines to be refurbished. The BioSAXS beamline (located on port BM29) was upgraded with a new wiggler source and a larger detector. All analysis software has been rewritten to cope with the increased data flux and continues to provide beamline users with reduced and pre-processed data in real time. This article describes FreeSAS, an open-source collection of various small-angle scattering analysis algorithms needed to reduce and analyze BioSAXS data, and Dahu, the tool used to interface data analysis with beamline control. It further presents the data-processing pipelines for the different data acquisitions modes of the beamline, using either a sample changer for individual homogeneous samples or an inline size-exclusion chromatography setup.


Assuntos
Análise de Dados , Síncrotrons , Cromatografia em Gel , Espalhamento a Baixo Ângulo , Software
5.
J Chromatogr A ; 1681: 463461, 2022 Oct 11.
Artigo em Inglês | MEDLINE | ID: mdl-36108352

RESUMO

How to improve the performance of chromatographic media is very important in chromatography. Uniform agarose microspheres were successfully prepared using membrane emulsification method with a controllable particle size, followed by multi-step crosslinking and dextran-grafting, respectively. To obtain both fine pore structure and good pressure-resistant property, the effects of both dextran-grafting and crosslinking process were studied carefully and also, the preparation conditions were delicately adjusted. Inverse size-exclusion chromatography was used for determining the pore structure of these agarose microspheres. Uniform agarose microspheres with an average particle size of about 8 µm were obtained with regularly spherical, transparent and smooth appearance. By introducing a certain molecular weight of dextran or pentaerythritol glycidyl ether at different crosslinking steps, both the pressure-resistant and the chromatographic properties of microspheres were improved. Both the maximum flow velocity and the corresponding pressure drop increased with the decrease of the molecular weight of dextran, i.e., 99 cm/h and 3.22 MPa, respectively, using dextran T3 (3 kDa). The average pore size of agarose microspheres decreased from 6.04±0.56 nm to 2.50±0.12 nm with the increase of the molecular weight of dextran from dextran T3 (3 kDa) to dextran T100 (100 kDa), with a high resolution obtained for a certain molecular range of model proteins. Also, the pressure-resistant property was highly improved in multi-step crosslinking process, with a maximum flow velocity of 107 cm/h and a corresponding pressure drop of 3.62 MPa obtained after the whole crosslinking steps. The average pore size of agarose microspheres was 3.72±0.32, 3.90±0.21 and 3.60±0.27 nm for the introduction of pentaerythritol glycidyl ether as the crosslinking agent at different steps, respectively. These uniform dextran-grafted agarose microspheres have a finely controllable molecular range with a high resolution compared with traditional ones, which are beneficial for chromatographic selectivity. Therefore, they are very useful for high-resolution chromatography and have wide applications in downstream process.


Assuntos
Dextranos , Cromatografia em Gel , Dextranos/química , Compostos de Epóxi , Microesferas , Tamanho da Partícula , Porosidade , Propilenoglicóis , Sefarose/química
6.
J Extracell Vesicles ; 11(9): e12266, 2022 09.
Artigo em Inglês | MEDLINE | ID: mdl-36124834

RESUMO

Small extracellular vesicles (sEVs) provide major promise for advances in cancer diagnostics, prognostics, and therapeutics, ascribed to their distinctive cargo reflective of pathophysiological status, active involvement in intercellular communication, as well as their ubiquity and stability in bodily fluids. As a result, the field of sEV research has expanded exponentially. Nevertheless, there is a lack of standardisation in methods for sEV isolation from cells grown in serum-containing media. The majority of researchers use serum-containing media for sEV harvest and employ ultracentrifugation as the primary isolation method. Ultracentrifugation is inefficient as it is devoid of the capacity to isolate high sEV yields without contamination of non-sEV materials or disruption of sEV integrity. We comprehensively evaluated a protocol using tangential flow filtration and size exclusion chromatography to isolate sEVs from a variety of human and murine cancer cell lines, including HeLa, MDA-MB-231, EO771 and B16F10. We directly compared the performance of traditional ultracentrifugation and tangential flow filtration methods, that had undergone further purification by size exclusion chromatography, in their capacity to separate sEVs, and rigorously characterised sEV properties using multiple quantification devices, protein analyses and both image and nano-flow cytometry. Ultracentrifugation and tangential flow filtration both enrich consistent sEV populations, with similar size distributions of particles ranging up to 200 nm. However, tangential flow filtration exceeds ultracentrifugation in isolating significantly higher yields of sEVs, making it more suitable for large-scale research applications. Our results demonstrate that tangential flow filtration is a reliable and robust sEV isolation approach that surpasses ultracentrifugation in yield, reproducibility, time, costs and scalability. These advantages allow for implementation in comprehensive research applications and downstream investigations.


Assuntos
Vesículas Extracelulares , Animais , Cromatografia em Gel , Vesículas Extracelulares/química , Filtração/métodos , Humanos , Camundongos , Reprodutibilidade dos Testes , Ultracentrifugação/métodos
7.
Sheng Wu Gong Cheng Xue Bao ; 38(8): 2948-2958, 2022 Aug 25.
Artigo em Chinês | MEDLINE | ID: mdl-36002423

RESUMO

This paper aims to detect the antigens in porcine circovirus type 2 (PCV2) vaccines by high-performance size-exclusion chromatography (HPSEC) coupled with multi-angle laser light scattering (MALLS). With purified inactivated PCV2 and PCV2 virus-like particles (VLP) as references, two inactivated vaccines (a and b) and two VLP vaccines (c and d) for PCV2 from four manufacturers were analyzed by HPSEC-MALLS after demulsification. The antigen peaks in HPSEC-MALLS were identified by PCV2 antigen test strips, Western blotting and transmission electron microscope (TEM). The repeatability and linearity of the method were investigated. The results showed the virus antigens in the two inactivated vaccines were eluted at about 13.3 min in HPSEC. The molecular weight of these antigens was 2.61×106 (±4.34%) Da and 2.40×106 (±2.51%) Da, respectively, as calculated by MALLS. The antigen peaks of the two VLP vaccines also appeared at 13.3 min and the molecular weight was 2.09×106 (±2.94%) Da and 2.88×106 (±11.85%) Da, respectively, which was close to the theoretical molecular weight of PCV2. Moreover, an antigen peak of VLP vaccine c was observed at 11.4 min and the molecular weight was 4.37×106 (±0.42%) Da. The antigen was verified to be the dimer of VLP by TEM. Vaccine d and purified Cap VLP antigens were tested repeatedly, and the RSD of the peak area (n=3) was all < 1.5%, indicating that the method was repeatable. The purified VLP were diluted in serial and tested for linearity. The result suggested good linear relationship between the peak area of VLP or VLP aggregates and the protein concentration of the sample with R2 of 0.999 and 0.997, respectively. Thus, the method met the requirement for quantification and aggregate analysis. This method is accurate and efficient in in vitro quality evaluation and improvement of PCV2 vaccine.


Assuntos
Infecções por Circoviridae , Circovirus , Vacinas de Partículas Semelhantes a Vírus , Vacinas Virais , Animais , Anticorpos Antivirais , Proteínas do Capsídeo , Cromatografia em Gel , Infecções por Circoviridae/prevenção & controle , Lasers , Suínos , Vacinas de Produtos Inativados
8.
Anal Chem ; 94(32): 11192-11200, 2022 08 16.
Artigo em Inglês | MEDLINE | ID: mdl-35926134

RESUMO

An external-cavity quantum cascade laser (EC-QCL)-based flow-through mid-infrared (IR) spectrometer was placed in line with a preparative size exclusion chromatography system to demonstrate real-time analysis of protein elutions with strongly overlapping chromatographic peaks. Two different case studies involving three and four model proteins were performed under typical lab-scale purification conditions. The large optical path length (25 µm), high signal-to-noise ratios, and wide spectral coverage (1350 to 1750 cm-1) of the QCL-IR spectrometer allow for robust spectra acquisition across both the amide I and II bands. Chemometric analysis by self-modeling mixture analysis and multivariate curve resolution enabled accurate quantitation and structural fingerprinting across the protein elution transient. The acquired concentration profiles were found to be in excellent agreement with the off-line high-performance liquid chromatography reference analytics performed on the collected effluent fractions. These results demonstrate that QCL-IR detectors can be used effectively for in-line, real-time analysis of protein elutions, providing critical quality attribute data that are typically only accessible through time-consuming and resource-intensive off-line methods.


Assuntos
Quimiometria , Lasers Semicondutores , Cromatografia em Gel , Proteínas , Espectrofotometria Infravermelho/métodos
9.
Molecules ; 27(15)2022 Jul 30.
Artigo em Inglês | MEDLINE | ID: mdl-35956840

RESUMO

Molecular interaction analysis is an essential technique for the study of biomolecular functions and the development of new drugs. Most current methods generally require manipulation to immobilize or label molecules, and require advance identification of at least one of the two molecules in the reaction. In this study, we succeeded in detecting the interaction of low-molecular-weight (LMW) compounds with a membrane protein mixture derived from cultured cells expressing target membrane proteins by using the size exclusion chromatography-mass spectrometry (SEC-MS) method under the condition of 0.001% lauryl maltose neopentyl glycol as detergent and atmospheric pressure chemical ionization. This method allowed us to analyze the interaction of a mixture of medicinal herbal ingredients with a mixture of membrane proteins to identify the two interacting ingredients. As it does not require specialized equipment (e.g., a two-dimensional liquid chromatography system), this SEC-MS method enables the analysis of interactions between LMW compounds and relatively high-expressed membrane proteins without immobilization or derivatization of the molecules.


Assuntos
Proteínas de Membrana , Cromatografia em Gel , Cromatografia Líquida/métodos , Espectrometria de Massas/métodos , Peso Molecular
10.
Eur J Pharm Biopharm ; 178: 131-139, 2022 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-35961566

RESUMO

Non-enzymatic hinge fragmentation of monoclonal antibodies (mAb) is considered a critical quality attribute since it changes the primary sequence of the proteins, thereby leading to structural changes which can affect stability, function, and efficacy. While peptide bonds are exceptionally stable under physiological conditions, reactive side chains of a few residues, the flexibility of the backbone, and physicochemical parameters such as pH, temperature, and the reaction of radicals and metal ions can promote the cleavage of peptide bonds. In this study, the relative extent and rate of fragmentation are compared with respect to the presence of several different factors (including hydrogen peroxide, metal ion, and temperature) as measured by size exclusion chromatography. A kinetic model of monomer degradation as a function of time (mAb only) is created. In the presence of either H2O2 or Cu2+, or both, the reaction kinetics follow different orders depending on the reaction conditions. The half-life for peptide bond cleavage of the mAb hinge region was 385 days at 40 °C and decreases to 250, 48, and 45 days in the presence of H2O2, Cu2+, and a combination of H2O2 and Cu2+, respectively. A temperature dependence of peptide bond cleavage at 35 °C, 40 °C, 45 °C, and 50 °C showed Arrhenius behavior with an apparent activation energy of 76.9 ± 16.4 kJ/mol. The reaction rates obtained from the Arrhenius equation were then extrapolated to predict fragmentation rates under real storage conditions (e.g., at 2-8 °C). We demonstrate that trace levels of impurities including peroxide left after surface sterilization or degradation of non-ionic surfactants or metal ions from the buffer components can significantly affect the stability of a mAb.


Assuntos
Anticorpos Monoclonais , Peróxido de Hidrogênio , Anticorpos Monoclonais/química , Cromatografia em Gel , Peróxido de Hidrogênio/química , Concentração de Íons de Hidrogênio , Cinética , Peptídeos , Temperatura
11.
J Extracell Vesicles ; 11(8): e12256, 2022 08.
Artigo em Inglês | MEDLINE | ID: mdl-35942823

RESUMO

We developed a novel asymmetric depth filtration (DF) approach to isolate extracellular vesicles (EVs) from biological fluids that outperforms ultracentrifugation and size-exclusion chromatography in purity and yield of isolated EVs. By these metrics, a single-step DF matches or exceeds the performance of multistep protocols with dedicated purification procedures in the isolation of plasma EVs. We demonstrate the selective transit and capture of biological nanoparticles in asymmetric pores by size and elasticity, low surface binding to the filtration medium, and the ability to cleanse EVs held by the filter before their recovery with the reversed flow all contribute to the achieved purity and yield of preparations. We further demonstrate the method's versatility by applying it to isolate EVs from different biofluids (plasma, urine, and cell culture growth medium). The DF workflow is simple, fast, and inexpensive. Only standard laboratory equipment is required for its implementation, making DF suitable for low-resource and point-of-use locations. The method may be used for EV isolation from small biological samples in diagnostic and treatment guidance applications. It can also be scaled up to harvest therapeutic EVs from large volumes of cell culture medium.


Assuntos
Vesículas Extracelulares , Cromatografia em Gel , Vesículas Extracelulares/metabolismo , Filtração , Plasma , Ultracentrifugação/métodos
12.
Molecules ; 27(14)2022 Jul 15.
Artigo em Inglês | MEDLINE | ID: mdl-35889395

RESUMO

A low molecular weight fucosylated glycosaminoglycan sodium (LFG-Na) is a novel anticoagulant candidate from the sea cucumber Holothuria fuscopunctata that selectively inhibits intrinsic tenase (iXase). The molecular weight, molecular weight distribution and bioactivities are the critical quality attributes of LFG-Na. The determination of these quality attributes of such an oligosaccharides mixture drug is challenging but critical for the quality control process to ensure its safety and efficacy in clinical use. Herein, the molecular weight and molecular weight distribution of LFG-Na were successfully determined using high performance size exclusion chromatography coupled with multi angle laser light scattering and refractive index detector (HPSEC-MALLS-RID). Comparing to the conventional method, HPSEC-MALLS-RID based on the refractive index increment (dn/dc) did not require the reference substances to establish the calibration curve. The acceptance criteria of LFG-Na were established, the weight-average molecular weight (Mw) should be 4000 to 6000 Da, the polydispersity (Mw/Mn) < 1.40, and the fraction with molecular weights of 1500 to 8000 Da should be no less than 80% of the total. HPSEC-MALLS-RID was also utilized for the determination of the starting material native fucosylated glycosaminoglycan (NFG) to choose a better manufacturing process. Furthermore, APTT assay was selected and the potency of anti-iXase, referring to the parallel line assay (PLA) method, was established to clarify the consistency of its biological activities. The results suggest that HPSEC-MALLS-RID and bioactivity assays are critical quality control methods for multi-component glycosaminoglycan LFG-Na. The methods also provide a feasible strategy to control the quality of other polysaccharide medicines.


Assuntos
Anticoagulantes , Glicosaminoglicanos , Animais , Anticoagulantes/química , Anticoagulantes/farmacologia , Cromatografia em Gel , Glicosaminoglicanos/farmacologia , Peso Molecular , Controle de Qualidade , Sódio
13.
J Pharm Biomed Anal ; 219: 114905, 2022 Sep 20.
Artigo em Inglês | MEDLINE | ID: mdl-35843185

RESUMO

The solution properties of hydroxyethyl starch (HES) vary significantly owing to different measurement parameters adopted and sample structures. Here, a round-robin study was conducted to compare inter-laboratory measurements of solution properties, weight-average molecular weight (Mw), and molecular weight distribution of four HES candidates covering the low- and medium-molecular-weight range, and 50 commercially available HES 130/0.4 drug samples. Analysis was performed using size exclusion chromatography (SEC) combined with multi-angle laser light scattering (MALLS) and differential refractive index (dRI) detectors. The results indicate that HES molecules in the Mw range of 17,000-130,000, with varying degrees of substitution (between 0.4 and 0.8), yielded a refractive index increment (dn/dc) value of 0.145 ± 0.003 mL/g (solvent: acetic acid-sodium acetate buffer; wavelength: 658 nm) and that the second virial coefficient (A2) is correlated with Mw. The SEC-MALLS-dRI method for Mw determination of HES demonstrated good inter-laboratory reproducibility; however, the study findings suggest that column specifications should be added for HES quality standards. Comparing Mw results obtained using common and experimentally corrected dn/dc and A2 values revealed an influence of dn/dc and A2 on Mw, indicating that the Mw acceptance criteria of HES quality standards should be adjusted.


Assuntos
Derivados de Hidroxietil Amido , Refratometria , Cromatografia em Gel , Derivados de Hidroxietil Amido/química , Lasers , Luz , Peso Molecular , Reprodutibilidade dos Testes , Espalhamento de Radiação
14.
Chem Biodivers ; 19(9): e202200506, 2022 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-35853836

RESUMO

The utilization of bamboo industry exhibits varied but still needs to be improved. Bamboo leaf flavonoid (BLF) is an important resource of bamboo which has become a research focus. However, the isolation and purification techniques of four flavonoid carbon glycosides (orientin, isoorientin, vitexin, and isovitexin) from BLF were still confronted with difficulties due to their complex and similar structures, which obstructed the development of bamboo utilization. In this article, a purification technology of four flavonoid carbon glycosides from BLF by Sephadex LH-20 was improved. The results were evaluated by HPLC and pharmacological activity. Specifically, the eluent, flow rate, and loading amount were investigated, respectively. According to the results, the eluent would dominate the isolation effect among three factors. High concentration of isoorientin and four flavonoid carbon glycosides would be obtained under the optimized condition (The eluent was 70 % methanol, the loading amount was 1.5 g, and the flow rate was 0.5 mL/min). Meanwhile, the link between flavonoid carbon glycosides content and their antioxidant activity in vitro was also revealed. Overall, the results suggested that BLF may serve as potential functional food additives and medicine.


Assuntos
Antioxidantes , Metanol , Antioxidantes/química , Carbono , Cromatografia em Gel , Cromatografia Líquida de Alta Pressão , Flavonoides/química , Glicosídeos , Extratos Vegetais/química , Folhas de Planta/química
15.
J Chromatogr A ; 1676: 463262, 2022 Aug 02.
Artigo em Inglês | MEDLINE | ID: mdl-35779389

RESUMO

Size exclusion chromatography has become an essential tool for the protein therapeutics industry. Conceptually, it is a simple form of chromatography that is driven by entropy and sieving effects. An ideal size exclusion column would exhibit no adsorptive interactions between its internal surfaces and the solutes being analysed, but that is not easily achieved. To this end, we have studied the utility of three unique packing materials in pursuit of additional column chemistries that might be less prone to interacting with proteins. These packing materials were each prepared from bridged ethylene hybrid organic/inorganic particles but uniquely derivatized into either hydroxy terminated PEO bonded, methoxy terminated PEO bonded, or diol bonded packing materials. All three materials were packed into column hardware modified with hydrophilic hybrid surface technology (h-HST) so that packing material effects could be more clearly observed without any influence from the secondary interactions that can originate from metal hardware. Non-specific interactions were compared for various challenging protein samples in the presence of ammonium acetate (volatile) and phosphate buffered saline (non-volatile) buffers. It was reconfirmed that the h-HST column hardware mitigates a majority of non-desired secondary interactions. However, during studies on hydrophobic interactions, the new hydroxy terminated PEO packing material showed clear benefit to obtaining higher apparent recoveries to better ensure accurate aggregate quantitation. Further experiments were explored to show that a hydroxy terminated PEO column could be effectively paired with a mobile phase comprised of standard strength phosphate buffered saline to make a fast platform method capable of baseline resolving monoclonal antibody monomer and aggregate peaks within a 3 min analysis time.


Assuntos
Fosfatos , Proteínas , Cromatografia em Gel , Interações Hidrofóbicas e Hidrofílicas , Indicadores e Reagentes
16.
Sci Rep ; 12(1): 9218, 2022 06 02.
Artigo em Inglês | MEDLINE | ID: mdl-35654960

RESUMO

Hen eggs are rich in proteins and are an important source of protein for humans. Pasteurized frozen whole hen eggs are widely used in cooking and confectionery and can be stored for long periods. However, processed eggs differ from raw eggs in properties such as viscosity, foaming ability, and thermal aggregation. To develop pasteurized frozen whole egg products with properties similar to those of unpasteurized whole eggs, it is necessary to establish a method that can differentiate between the two egg types with respect to the structures of their proteins. In this study, size-exclusion chromatography (SEC) and SEC coupled with small-angle X-ray scattering (SEC-SAXS) were successfully used to differentiate between the proteins in unpasteurized and pasteurized frozen whole eggs. We found that proteins in the plasma fraction of egg yolk, especially apovitellenins I and II, formed large aggregates in the pasteurized eggs, indicating that their structures are sensitive to temperature changes during pasteurization, freezing, and thawing. The results suggest that SEC and SEC-SAXS can be used to differentiate between unpasteurized and pasteurized frozen whole eggs. Additionally, they may be useful in determining molecular sizes and shapes of multiple components in various complex biological systems such as whole eggs.


Assuntos
Galinhas , Animais , Cromatografia em Gel , Feminino , Congelamento , Espalhamento a Baixo Ângulo , Difração de Raios X , Raios X
17.
J Sep Sci ; 45(15): 2845-2854, 2022 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-35675540

RESUMO

Aqueous extract of toad skin (named as Cinobufacini or Huachansu) provides plentiful sources of bioactive peptides that remain undetected and unidentified. High-resolution mass spectrometry-based peptidomics platforms have developed into a major approach to the discovery of natural peptides, with data-dependent acquisition modes providing a wealth of peptide profiling information. In this study, we used a gel- and HLB (a solid phase extraction cartridge)-based two-dimensional separation and purification system and nano-liquid chromatography-tandem mass spectrometry-based peptidomic studies with homology matching for the identification of peptides from Cinobufacini. We evaluated 232 multi-charged peptides and found several specific peptides, some of which were validated by target parallel reaction monitoring mode. These peptides are the first to be identified in Cinobufacini and are completely different from ones identified in toad venom. So, this mapping provides key peptide information for the quality control of Bufo bufo gargarizans skin and its preparation.


Assuntos
Venenos de Anfíbios , Cromatografia em Gel , Cromatografia Líquida de Alta Pressão/métodos , Cromatografia Líquida/métodos , Peptídeos/química
18.
J Vis Exp ; (183)2022 05 19.
Artigo em Inglês | MEDLINE | ID: mdl-35661678

RESUMO

The role of extracellular vesicles (EVs) in the context of bacterial infection has emerged as a new avenue for understanding microbial physiology. Specifically, Mycobacterium tuberculosis (Mtb) EVs play a role in the host-pathogen interaction and response to environmental stress. Mtb EVs are also highly antigenic and show potential as vaccine components. The most common method for purifying Mtb EVs is density gradient ultracentrifugation. This process has several limitations, including low throughput, low yield, reliance on expensive equipment, technical challenges, and it can negatively impact the resulting preparation. Size exclusion chromatography (SEC) is a gentler alternative method that combats many of the limitations of ultracentrifugation. This protocol demonstrates that SEC is effective for Mtb EV enrichment and produces high-quality Mtb EV preparations of increased yield in a rapid and scalable manner. Additionally, a comparison to density gradient ultracentrifugation by quantification and qualification procedures demonstrates the benefits of SEC. While the evaluation of EV quantity (nanoparticle tracking analysis), phenotype (transmission electron microscopy), and content (Western blotting) is tailored to Mtb EVs, the workflow provided can be applied to other mycobacteria.


Assuntos
Vesículas Extracelulares , Mycobacterium tuberculosis , Western Blotting , Cromatografia em Gel , Vesículas Extracelulares/química , Ultracentrifugação/métodos
19.
MAbs ; 14(1): 2080628, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35771588

RESUMO

Approaches for antibody discovery have seen substantial improvement and success in recent years. Yet, advancing antibodies into the clinic remains difficult because therapeutic developability concerns are challenging to predict. We developed a computational model to simplify antibody developability assessment and enable accelerated early-stage screening. To this end, we quantified the ability of hundreds of sequence- and structure-based descriptors to differentiate clinical antibodies that have undergone rigorous screening and characterization for drug-like properties from antibodies in the human repertoire that are not natively paired. This analysis identified 144 descriptors capable of distinguishing clinical from repertoire antibodies. Five descriptors were selected and combined based on performance and orthogonality into a single model referred to as the Therapeutic Antibody Developability Analysis (TA-DA). On a hold-out test set, this tool separated clinical antibodies from repertoire antibodies with an AUC = 0.8, demonstrating the ability to identify developability attributes unique to clinical antibodies. Based on our results, the TA-DA score may serve as an approach for selecting lead antibodies for further development.Abbreviations: Affinity-Capture Self-Interaction Nanoparticle Spectroscopy (AC-SINS), Area Under the Curve (AUC), Complementary-Determining Region (CDR), Clinical-Stage Therapeutics (CST), Framework (FR), Monoclonal Antibodies (mAbs), Observed Antibody Space (OAS), Receiver Operating Characteristic (ROC), Size-Exclusion Chromatography (SEC), Structural Aggregation Propensity (SAP), Therapeutic Antibody Developability Analysis (TA-DA), Therapeutic Antibody Profiler (TAP), Therapeutic Structural Antibody Database (Thera-SAbDab), Variable Heavy (VH), Variable Light (VL).


Assuntos
Anticorpos Monoclonais , Anticorpos Monoclonais/química , Cromatografia em Gel , Humanos
20.
Methods Mol Biol ; 2500: 15-30, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35657584

RESUMO

Top-down mass spectrometry (MS)-based analysis of larger proteoforms (>50 kDa) is typically challenging due to an exponential decay in the signal-to-noise ratio with increasing protein molecular weight (MW) and coelution with low-MW proteoforms. Size exclusion chromatography (SEC) fractionates proteins based on their size, separating larger proteoforms from those of smaller size in the proteome. In this protocol, we initially describe the use of SEC to fractionate high-MW proteoforms from low-MW proteoforms. Subsequently, the SEC fractions containing the proteoforms of interest are subjected to reverse-phase liquid chromatography (RPLC) coupled online with high-resolution MS. Finally, proteoforms are characterized using MASH Explorer, a user-friendly software environment for in-depth proteoform characterization.


Assuntos
Proteômica , Espectrometria de Massas em Tandem , Cromatografia em Gel , Cromatografia de Fase Reversa/métodos , Proteoma/análise , Proteômica/métodos
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