Method For Isolation Of Proteins Research Articles

A Highly Efficient Procedure for the Extraction of Soluble Proteins from Bacterial Cells with Mild Chaotropic Solutions

AbstractThe development of methods for rapid and effective isolation of proteins from Escherichia coli is of considerable interest for biotechnology. The ability of buffer solutions containing low concentrations of detergents and chaotropic agents to extract intracellular proteins of E. coli cells was studied. We have shown that the solutions containing Triton X‐100 or sodium deoxycholate and the mixtures of these detergents with urea are the most effective for this purpose. During the extraction of proteins from bacterial cells under the conditions studied, the release of RNA into solution also occurs, while DNA mostly remains inside the cells. The proposed treatment does not break the bacterial cell walls; proteins probably are supposed to penetrate through the pores of the murein network. In efficiency, our buffer mixtures are comparable to the commercial reagent, CelLytic B, and can be used in different scale purification projects.

Removal of Lipids and Diarrhetic Shellfish Poisoning Toxins from Blue Mussels (Mytilus edulis) during Acid and Alkaline Isolation of Proteins

Diarrhetic shellfish poisoning (DSP) toxins pose a serious health risk for consumers of bivalves and other shellfish, as well as a huge economic burden for the bivalve-producing farmers. In this work, the aim was to utilize a solubilization-based protein-isolation method to produce a low-DSP toxin protein isolate from toxic blue mussels that are unsuitable for the whole shellfish market. A homogenate of whole mussel meat was solubilized at low pH (2.8) or high pH (11.1), followed by centrifugation and reprecipitation of the solubilized mussel proteins at the isoelectric pH. In a second centrifugation, precipitated proteins were collected. These processes resulted in 81 (acid solubilization) and 72% (alkaline solubilization) reduction in the initial DTX-1 toxin content of the mussel meat. No other DSP toxins were found in the protein isolates. Acid processing of mussel meat resulted in 50% reduction in the total lipid content, while alkaline treatment did not significantly affect the lipid content. The effect of citric acid and calcium chloride addition to the mussel meat-water homogenate on lipid and toxin content was also investigated. A poor correlation factor was surprisingly obtained between reductions in DTX-1 toxin and lipids in protein isolates from processed toxic mussels. Results from an analytical mass balance of the DTX-1 toxin during acid processing showed that 61% of this toxin ended up in the aqueous supernatant after the second centrifugation. The present study presents a promising alternative way of utilizing mussels for food production in periods when they are toxic.

Investigation of the effects of 2‐naphthylamine on the protein expression of Pseudomonas putida KT2440

Two‐dimensional gel electrophoresis can be used in proteomics to study changes in protein expression. Currently, this tool is being employed to determine the impact of 2‐Naphthylamine, a known carcinogen, on the growth and protein expression of Pseudomonas putida KT2440. In order to grow strong cells and to increase gel resolution, modifications were made to growth media concentrations and protein isolation methods. Following this adapted procedure, a control was produced using Succinic Acid in Hutner's Growth media and new two‐dimensional control gels were analyzed. The optimal concentration at which to grow the bacteria in the presence of 2‐Naphthylamine was determined to be 0.25mM. The proteins from the 2‐Naphthylamine variable are similarly separated using two‐dimensional gel electrophoresis and the gels are analyzed using the PDQuest Software. A comparison is made between the 2‐napthylamine gels and the Succinic Acid control gels to look for changes in the bacteria's protein expression. Changes in protein expression in the 2‐Naphthylamine gels (when compared to the master control gel) can be new proteins, missing proteins, and under or over‐expression of proteins. Financial support by the Rochester Institute of Technology College of Science Dean's Office and the Department of Chemistry.

녹용으로부터 Insulin-like Growth Factor-I의 일부정제 및 정량

사슴뿔은 동물세계에서 가장 빨리 성장하는 조직이다. 따라서 성장중인 사슴뿔은 뼈 성장을 촉진하는 인자가 풍부하게 포함된 것으로 생각된다. 이들 성장인자들 중 IGF-1은 뼈를 자라게 하는 조골세포의 대사에 중요한 역할을 한다고 알려져 있어 이를 정제하고자 하였다. IGF-1의 정제는 상대라고 불리는 신선한 사슴뿔을 유안침전, DEAE-Sepharose CL-6B 이온교환수지, CM-Sepharose CL-6B 양이온교환수지, Sephadex G-50의 순차적인 방법으로 할 수 있었다. 각 과정마다 IGF-1의 거동을 HPLC, SDS-PAGE, Dot blot, 그리고 western blot으로 분석하였다. IGF-1의 정량은 ELISA기술로 재조합 인간 IGF-1을 이용하여 계산되었으며, 최종 분별 액은 두 개의 단백질을 보였으나, Western-blot에서 작은 분자량인 12 kDa으로 최종 판명할 수 있었다. 정제된 단백질은 HPLC에서 retention 시간 8분만에 검출되었으며, 총 농도는 2910 ng/ml 이고 중량은 0.291 g 이었다. Deer antler tissue contains the most rapidly growing bone in the animal kingdom. Thus, it is likely that growing antler tissue is a rich source of local paracrine bone-stimulating factors. Growth factors, at least the insulin-like growth factor (IGF), control the bone-remodelling process. In this study, we tried to isolate and purify IGF-I from fresh antler tissue by the routine isolation and purification of protein. The purification involved ammonium sulfate precipitation, DEAE-Sepharose CL-60 ion-exchange chromatography, CM-Sepharose CL-6B ion-exchange chromatography, and Sephadex G-50 chromatography. Purified fractions from each step were analyzed by high-performance liquid chromatography (HPLC), SDS polyacrylamide gel electrophoresis (SDS-PACE), Dot-blot, and Western-blot methods. Furthermore, the quantification of partially purified IGF-I was calculated by enzyme-linked immunosorbent assays (ELISA) using antibody to human recombinant IGF-1. SDS-PAGE analysis of the final fraction yielded two molecular bands and the signal band was at 12 kDa on the Western-blot film. This purified IGF-I fraction showed a peak at retention time of eight min. The quantity of IGF-I in 20 g deer antler tissue as starting weight was calculated using a standard curve to be 2910 ng/ml, and total IGF-I amount is 0.291 g. The results show that IGF-I, which can be found in deer antler, can be partially purified and quantified by classic protein isolation methods.

Conversion of α1,2-mannosidase E-I from Candida albicans to α1,2-mannosidase E-II by limited proteolysis

Previous studies demonstrated the presence in Candida albicans ATCC 26555 of two soluble alpha1,2-mannosidases: E-I and E-II. In contrast, in the C. albicans CAI-4 mutant only E-I was detected and it could be processed by a membrane-bound proteolytic activity from the ATCC 26555 strain, generating an active 43 kDa polypeptide. Here, alpha1,2-mannosidase E-I from strain ATCC 26555 was purified by conventional methods of protein isolation and affinity chromatography in Concanavalin A-Sepharose 4B. Analytical electrophoresis of the purified enzyme revealed two polypeptides of 52 and 23 kDa, the former being responsible for enzyme activity as revealed by zymogram analysis. Time course proteolysis with an aspartyl protease from Aspergillus saitoi, converted alpha1,2-mannosidase E-I into an active polypeptide of 43 kDa which trimmed Man(9)GlcNAc(2), generating Man(8)GlcNAc(2) isomer B and mannose. Trimming was inhibited preferentially by 1-deoxymannojirimycin. Both, the molecular mass and the enzyme properties of the proteolytic product were identical to those described for alpha1,2-mannosidase E-II therefore supporting the notion that E-I is the precursor of E-II.

RepTAGs: Universal tags for isolation and labeling of proteins, for labeling live mammalian cells and for drug discovery

Methods for specific immobilization, isolation and labeling of proteins are central to the elucidation of cellular functions. Based on bacterial repressor proteins, which bind to specific target sequences in response to small molecules (macrolide and tetracycline antibiotics) or environmental parameters (temperature), we have developed a set of protein tags (RepTAGs), which enable reversible immobilization of the protein of interest on a solid support for the isolation and quantification as well as for the specific labeling of target proteins with fluorescent dyes for tracking them within a complex protein mixture. Similarly, live mammalian cells were specifically labeled with a fluorescent operator sequence bound to RepTAGs, which were directed towards the cell surface for easy discrimination between transfected and untransfected cell populations. Based on the drug-responsive RepTAG-DNA interactions, it was also possible to quantify or discover antibiotics in environmental samples or compound libraries by means of rapid, sensitive detection methods involving fluorescence polarization and bioluminescence. We believe that the universally applicable RepTAGs will become essential for the analysis and manipulation of proteins in the most diverse areas of protein chemistry and cell biology.

Quantitative proteomic profiling of membrane proteins from the mouse brain cortex, hippocampus, and cerebellum using the HysTag reagent: Mapping of neurotransmitter receptors and ion channels

Analysis of the brain proteome and studying brain diseases through clinical biopsies and animal disease models require methods of quantitative proteomics that are sensitive and allow identification and quantification of low abundant membrane proteins from minute amount of tissue. Taking advantage of recently developed methods for isolation of membrane proteins from 10–20 mg brain tissue [Nielsen, P.Aa., Olsen, J.V., Podtelejnokov, A.V., Andersen, J.R., Mann, M., Wiśniewski, J.R., 2005. Proteomic mapping of brain plasma membrane proteins. Mol. Cell. Proteomics 4, 402--408] and the HysTag-quantification method [Olsen, J.V., Andersen, J.R., Nielsen, P.Aa., Nielsen, M.L., Figeys, D., Mann, M., Wiśniewski, J.R., 2004. HysTag---A novel proteomic qualification tool applied to differential analysis of membrane proteins from distinct areas of mouse brain. Mol. Cell. Proteomics 3, 82--92] we performed quantitative proteomic analysis of three functionally distinct compartments of mouse brain: cortex, hippocampus, and cerebellum. In total, 976 unique peptides corresponding to 555 unique proteins were quantified. Up to 20-fold differences in the levels of some proteins between brain areas were measured. For many quantified proteins – as for glutamate receptors, calcium channel subunits, and ATP-ases – an excellent correlation between our proteomic data and previously published mRNA expression levels or intensity of immunostaining was found. Our results clearly demonstrate differences in levels of membrane proteins mapped in distinct brain compartments and offer a technology that allows in depth study of brain membrane proteomes, such as mouse models of neurological diseases.

A fully automated robotic system for purification of polyhistidine‐tagged proteins

A protein isolation method that results in rapid and high yield proteins is essential for protein sample preparation in proteomics. A magnetic bead-based automated method to purify both soluble and insoluble 6x histidine-tag (His-tag) proteins from cell lysates has been developed employing PSS Magtration® technology. Magtration® is a PSS patented technique that traps magnetic particles against the sidewall of a disposable pipette tip, resulting in superior washing and recovery compared to other magnetic particle-separation systems. We have extended this technology from immunoassay and nucleic acid purification to His-tag protein purification using Magtration® 12GC robotic system with commercially available Ni2+ and Co2+ magnetic beads. Unlike other automated protein purification systems, Magtration®12GC allows for high volumes (up to 800 μl) of initial sample, and can run up to 12 samples at once. Experimental conditions including buffer compositions, buffer pH and various His-tag protein binding magnetic beads have been studied and optimized for the robotic purification on the Magtration® system. A two-step elution protocol has been developed for effective removal of nonspecific proteins resulting in highly pure His-tag target proteins. The yield and purity of the His-tag protein from the automated system are more successful in terms of efficiency and reproducibility compared to manual protocols due to more thorough washing, complete separation between the magnetic beads and supernatant, and consistent robotic operation.

High-throughput protein purification using an automated set-up for high-yield affinity chromatography

One of the key steps in high-throughput protein production is protein purification. A newly developed high-yield protein purification and isolation method for laboratory scale use is presented. This procedure allows fully automated purification of up to 60 cell lysates with milligram yields of pure recombinant protein in 18.5 h. The method is based on affinity chromatography and has been set up on an instrument that utilizes positive pressure for liquid transfer through columns. A protocol is presented that includes all steps of equilibration of the chromatography resin, load of sample, wash, and elution without any manual handling steps. In contrast to most existing high-throughput protein purification procedures, positive pressure is used for liquid transfer rather than vacuum. Positive pressure and individual pumps for each liquid channel contribute to controlled flow rates and eliminate the risk of introducing air in the chromatography resin and therefore ensure stable chromatography conditions. The procedure is highly reproducible and allows for high protein yield and purity.

Purification of soluble α1,2-mannosidase fromCandida albicansCAI-4

A soluble alpha-mannosidase from Candida albicans CAI-4 was purified by conventional methods of protein isolation. Analytical electrophoresis of the purified preparation revealed two polypeptides of 52 and 27 kDa, the former being responsible for enzyme activity. The purified, 52 kDa enzyme trimmed Man9GlcNAc2, producing Man8GlcNAc2 isomer B and mannose, and was inhibited preferentially by 1-deoxymannojirimycin. These properties are consistent with an endoplasmic reticulum-resident alpha1,2-mannosidase of the glycosyl hydrolase family 47. Moreover, a proteolytic activity responsible for converting the 52 kDa alpha-mannosidase into a polypeptide of 43 kDa retaining full enzyme activity, was demonstrated in membranes of ATCC 26555, but not in CAI-4 strain.

Characterization and Quantification of Proteins in Lecithins

Several methods for extraction and quantification of proteins from lecithins were compared. Extraction with hexane-2-propanol-water followed by amino acid analysis is the most suitable method for isolation and quantification of proteins from lecithins. The detection limit of the method is 15 mg protein/kg lecithin, and the quantification limit is 50 mg protein/kg. The relative repeatability limits for samples containing 0-500 and 500-5000 mg protein/kg sample were 12.6 and 7.5%, respectively. The protein recovery ranged between 101 and 123%. The protein content has been determined in different kinds of lecithins. The results were as follows: standard soy lecithins (between 232 and 1338 mg/kg), deoiled soy lecithin (342 mg/kg), phosphatydylcholine-enriched soy lecithins (not detectable and 163 mg/kg), sunflower lecithins (892 and 414 mg/kg), and egg lecithin (50 mg/kg). The sodium dodecyl sulfate-polyacrylamide gel electrophoresis protein patterns of the standard soy and sunflower lecithins are very similar to those of soy flour. The protein profile of the egg lecithin shows several bands with a broad range of molecular masses. The molecular masses of the main proteins of soy lecithins and soy flour have been determined by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) and ranged from 10.5 to 52.2 kDa. Most of the major proteins from soy and sunflower lecithins identified by MALDI-MS and electrospray tandem MS belong to the 11S globulin fraction, which is one of the main fractions of soy and sunflower seeds. In addition, the seed maturation protein P34 from the 7S globulin fraction of soy proteins has also been identified in soy lecithins. This protein has been reported as the most allergenic protein in soybean.

Cell-free synthesis and in situ isolation of recombinant proteins

We present a method for rapid expression and isolation of recombinant proteins. Cell-free protein synthesis in the presence of affinity beads enables in situ isolation of translation products, which simplifies the procedures for the preparation of purified protein samples. In the present study, we have made an attempt to carry out in situ isolation of histidine-tagged proteins by using Ni–NTA magnetic agarose beads. The presence of Ni–NTA beads gave no drastic effects on the efficiency of protein synthesis and successfully captured the synthesized proteins. Purified proteins were obtained after subsequent washing and elution steps. In particular, most of the endogenous bead-binding proteins were removed by pre-treating S30 extract with affinity beads and the purity of the target proteins was enhanced up to 95%. The methods described here will provide a basis for fast and convenient preparation of purified proteins from multiple genetic sequences.

Large-scale purification of the proton pumping pyrophosphatase from Thermotoga maritima: A “Hot-Solve” method for isolation of recombinant thermophilic membrane proteins

Although several proton-pumping pyrophosphatases (H +-PPases) have been overexpressed in heterologous systems, purification of these recombinant integral membrane proteins in large amounts in order to study their structure–function relationships has proven to be a very difficult task. In this study we report a new method for large-scale production of pure and stable thermophilic H +-PPase from Thermotoga maritima. Following overexpression in yeast, a “Hot-Solve” procedure based on high-temperature solubilization and metal-affinity chromatography was used to obtain a highly purified detergent-solubilized TVP fraction with a yield around 1.5 mg of protein per litre of yeast culture. Electron microscopy showed the monodispersity of the purified protein and single particle analysis provided the first direct evidence of a dimeric structure for H +-PPases. We propose that the method developed could be useful for large-scale purification of other recombinant thermophilic membrane proteins.

Isolation of rodent airway epithelial cell proteins facilitates in vivo proteomics studies of lung toxicity

Recent developments in genomics, proteomics, and metabolomics hold substantial promise for understanding cellular responses to toxicants. Gene expression profiling is now considered standard procedure, but numerous publications reporting a lack of correlation between mRNA and protein expression emphasize the importance of conducting parallel proteomics studies. The cellular complexity of the lung presents great challenges for in vivo proteomics, and improved isolation methods for proteins from specific lung cell phenotypes are required. To address this issue, we have developed a novel method for isolation of rodent airway epithelial cell proteins that facilitates in vivo proteomics studies of two target-cell pheno-types of the lung, Clara cells and ciliated cells. The airway epithelial cell proteins are reproducibly solubilized, leaving the underlying basement membrane and smooth muscle intact as shown by histopathological analyses. The method yields epithelial cell-specific proteins in fivefold higher concentrations and reduces the yield of nonepithelial cell proteins 13-fold compared with homogenates from microdissected airways. In addition, 36% more protein spots were detectable by two-dimensional gel electrophoresis.

High throughput protein production for functional proteomics

A major impact of genome projects on human health will be their contribution to the understanding of protein function. Proteins are the engines of biological systems, nearly all pharmaceuticals act on proteins and increasingly proteins themselves are used therapeutically. As biology enters the post-genomic era, researchers have begun to embrace the exciting opportunity of investigating proteins in high throughput (HT) experiments. The study of proteins includes a vast array of techniques ranging from enzyme catalysis assays to interaction and structural studies. Many of these methods depend on purified proteins. The discovery of thousands of novel protein-coding sequences and the increased availability of large cDNA collections provide the opportunity to investigate protein function in a systematic manner and at an unprecedented scale. This opportunity highlights the need for development of HT methods for protein isolation. This article describes the challenges faced and the approaches taken to develop proteome-scale protein expression systems.

Protein Transduction: Generation of Full‐Length Transducible Proteins Using the TAT System

This unit describes the technology that allows an investigator to transduce full-length proteins by utilizing a minimal, eleven-amino acid, HIV-TAT transduction domain that can be fused to a protein of choice using the pTAT or pTAT-HA protein expression plasmids. Bacterial expression, followed by solubilization of protein aggregates with a denaturing agent, affords high yields of transducible fusion protein. The fusion protein, once added to the culture medium, can cross the cell membrane and then be degraded or refolded by the cellular machinery. Correct targeting and function of the fusion protein can be easily examined by fluorescent microscopy or immunohistochemistry. This strategy was established and improved to its current state by the purification and transduction of a multitude of fusion proteins. Because the pool of fusion proteins spans many different functions, the protocols cover a wide variety of commonly used protein isolation and characterization methods.

Highly-resolving two-dimensional electrophoresis for the study of insect proteins.

In this paper, we describe methods for isolation, purification and solubilization of insect proteins from various tissues, including lipid-rich fat body. An Australian locust, Oedaleus australis, and its associated dipteran parasite, Trichopsidea oestracea, provided the protein samples. Protein samples of locust fat body, haemolymph and body wall as well as parasite whole-body extracts were isolated and purified of lipids and salts using chloroform-methanol extraction. Proteins were solubilized using two types of enhanced solubilizing solutions and arrayed using two-dimensional electrophoresis. We demonstrated substantial differences between the body wall protein spectra of normal locusts and those parasitized by T. oestracea. Proteins more abundant in parasitized locusts include two 70 kDa proteins with an isoelectric point (pI) of about 5.5, one approximately 55 kDa protein cluster with a pI of about 4.7 and three 40 kDa proteins with pI values of around 5.6. Proteins that decreased in parasitized locusts include a group of 45 kDa proteins with pI values between 6 and 6.8, and a cluster of 22 to 23 kDa proteins with pI values of approximately 5.4 and 5.6.

Isolation of proteins comprising native gene-specific messenger ribonucleoprotein particles using paramagnetic beads

A method for the rapid isolation of proteins comprising native messenger ribonucleoprotein particles (mRNPs), that utilises streptavidin-coated paramagnetic beads, coupled with biotinylated oligodeoxyribonucleotides, to pull down general and transcript-specific mRNP complexes from crude cell-free extracts, is described. Two biotinylated oligo probes were tested for their efficacy in isolating mRNPs from tobacco pollen extracts; a 25-mer oligo(dT) probe for the isolation of total mRNPs, and a transcript-specific oligo complementary to the pollen-specific ntp303 mRNA sequence. Following annealing to the target mRNAs, the oligo probes, with associated ribonucleoprotein particles, were captured by streptavidin-coated paramagnetic particles and pelleted in a magnetic field. After several washing steps, the bound RNPs were released and analysed by SDS-polyacrylamide gel electrophoresis (SDS-PAGE) and Western blot immunodetection. This one-step mRNP enrichment method could be used either to enhance the detection of low-abundance mRNA-binding proteins in subsequent northwestern and RNA UV cross-linking experiments or the direct identification and biochemical characterisation of RNA-binding proteins.

Mechanisms of phase behaviour and protein partitioning in detergent/polymer aqueous two-phase systems for purification of integral membrane proteins

Detergent/polymer aqueous two-phase systems are studied as a fast, mild and efficient general separation method for isolation of labile integral membrane proteins. Mechanisms for phase behaviour and protein partitioning of both membrane-bound and hydrophilic proteins have been examined in a large number of detergent/polymer aqueous two-phase systems. Non-ionic detergents such as the Triton series (polyoxyethylene alkyl phenols), alkyl polyoxyethylene ethers (C m EO n ), Tween series (polyoxyethylene sorbitol esters) and alkylglucosides form aqueous two-phase systems in mixtures with hydrophilic polymers, such as PEG or dextran, at low and moderate temperatures. Phase diagrams for these mixtures are shown and phase behaviour is discussed from a thermodynamic model. Membrane proteins, such as bacteriorhodopsin and cholesterol oxidase, were partitioned strongly to the micelle phase, while hydrophilic proteins, BSA and lysozyme, were partitioned to the polymer phase. The partitioning of membrane protein is mainly determined by non-specific hydrophobic interactions between detergent and membrane protein. An increased partitioning of membrane proteins to the micelle phase was found with an increased detergent concentration difference between the phases, lower polymer molecular weight and increased micelle size. Partitioning of hydrophilic proteins is mainly related to excluded volume effects, i.e. increased phase component size made the hydrophilic proteins partition more to the opposite phase. Addition of ionic detergent to the system changed the partitioning of membrane proteins slightly, but had a strong effect on hydrophilic proteins, and can be used for enhanced separation between hydrophilic proteins and membrane protein.

An efficient method for simultaneous isolation of biologically active transcription factors and DNA

Transcription factors play a crucial role in gene regulation during different stages of eukaryotic development as well as in controlling various cellular disorders involving the immune system. In order to study the role of cellular DNAs and the effects of certain biologically active regulatory proteins, which can affect gene expression, we have developed a rapid and efficient method for preparing highly purified DNAs as well as nuclear and cytoplasmic proteins, simultaneously. These DNAs and proteins can be effectively analyzed to determine their genetic integrity and binding motifs to specific DNA sequences, respectively. This protocol avoids the drastic use of mechanical shearing of cells, aggressive use of detergents or high speed ultracentrifugation steps, as well as facilitating the ease of collecting samples in a sequential and effective manner with minimal time lapse during processing. Such an approach permits the analysis of a large number of samples in a short time. The current technique uses a non-ionic detergent to isolate nuclei, and obtain the cytosolic extract, a low-ionic strength buffer to wash off the detergent and a high-salt buffer to extract nuclear proteins including transcription factors. The remainder of the cellular products are processed for DNA extraction. This method will be particularly useful to evaluate the time course effects of various cell signal transducing biological modifiers such as cytokines or mitogens, as well as drugs used in therapy, especially in infectious diseases and also in immunological or neoplastic disorders, with minimal physical contact to the laboratory personnel. This rapid DNA and protein isolation method can be widely used in various systems to analyze the modulation of DNA characteristics and transcriptionally active proteins as biomarkers in different human diseases.