101
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Perperopoulou F, Pouliou F, Labrou NE. Recent advances in protein engineering and biotechnological applications of glutathione transferases. Crit Rev Biotechnol 2017; 38:511-528. [PMID: 28936894 DOI: 10.1080/07388551.2017.1375890] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Glutathione transferases (GSTs, EC 2.5.1.18) are a widespread family of enzymes that play a central role in the detoxification, metabolism, and transport or sequestration of endogenous or xenobiotic compounds. During the last two decades, delineation of the important structural and catalytic features of GSTs has laid the groundwork for engineering GSTs, involving both rational and random approaches, aiming to create new variants with new or altered properties. These approaches have expanded the usefulness of native GSTs, not only for understanding the fundamentals of molecular detoxification mechanisms, but also for the development medical, analytical, environmental, and agricultural applications. This review article attempts to summarize successful examples and current developments on GST engineering, highlighting in parallel the recent knowledge gained on their phylogenetic relationships, structural/catalytic features, and biotechnological applications.
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Affiliation(s)
- Fereniki Perperopoulou
- a Department of Biotechnology, Laboratory of Enzyme Technology , School of Food, Biotechnology and Development, Agricultural University of Athens , Athens , Greece
| | - Fotini Pouliou
- a Department of Biotechnology, Laboratory of Enzyme Technology , School of Food, Biotechnology and Development, Agricultural University of Athens , Athens , Greece
| | - Nikolaos E Labrou
- a Department of Biotechnology, Laboratory of Enzyme Technology , School of Food, Biotechnology and Development, Agricultural University of Athens , Athens , Greece
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102
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Abstract
Streptomyces are of great biological and industrial significance due to their complex morphological development and ability to produce numerous secondary metabolites. However, the intrinsic biochemical mechanisms underlying morphogenesis and secondary metabolism are rarely revealed, partially because of the limited availability of the biochemical tools in Streptomyces. Here we provided series of integrative vectors with various affinity tags, including single tags 3×FLAG, 3×HA, 3×Strep-tag II, 18×His, 13×Myc, and dual tags, all of which were driven from a strong constitutive promoter ermEp*. Using a sigma factor SigT from S. coelicolor as a model, we successfully expressed and immuno-detected SigT fused with all tags. Moreover, after SigT was N-terminally tagged with 3×FLAG and C-terminally tagged with 18×His, we isolated SigT-interactive proteins from the S. coelicolor lysate based on the tandem affinity purification (TAP). Particularly, among the proteins purified, the SigT cognate anti-sigma factor RstA ranked the top with the most total independent spectra. These data suggested the feasibility of these affinity tags in Streptomyces, which will be widely employed to explore the biochemical mechanisms to further understand the dynamic and elaborate regulation in this genus.
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103
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Vargas-Cortez T, Morones-Ramirez JR, Balderas-Renteria I, Zarate X. Production of recombinant proteins in Escherichia coli tagged with the fusion protein CusF3H+. Protein Expr Purif 2017; 132:44-49. [DOI: 10.1016/j.pep.2017.01.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 01/07/2017] [Accepted: 01/10/2017] [Indexed: 01/05/2023]
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104
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Ectopic Expression of Plant RNA Chaperone Offering Multiple Stress Tolerance in E. coli. Mol Biotechnol 2017; 59:66-72. [DOI: 10.1007/s12033-017-9992-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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105
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Kosobokova EN, Skrypnik KA, Kosorukov VS. Overview of Fusion Tags for Recombinant Proteins. BIOCHEMISTRY (MOSCOW) 2017; 81:187-200. [PMID: 27262188 DOI: 10.1134/s0006297916030019] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Virtually all recombinant proteins are now prepared using fusion domains also known as "tags". The use of tags helps to solve some serious problems: to simplify procedures of protein isolation, to increase expression and solubility of the desired protein, to simplify protein refolding and increase its efficiency, and to prevent proteolysis. In this review, advantages and disadvantages of such fusion tags are analyzed and data on both well-known and new tags are generalized. The authors own data are also presented.
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Affiliation(s)
- E N Kosobokova
- Blokhin Russian Cancer Research Center, Moscow, 115478, Russia.
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106
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Arora S, Saxena V, Ayyar BV. Affinity chromatography: A versatile technique for antibody purification. Methods 2016; 116:84-94. [PMID: 28012937 DOI: 10.1016/j.ymeth.2016.12.010] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 12/16/2016] [Accepted: 12/17/2016] [Indexed: 12/19/2022] Open
Abstract
Antibodies continue to be extremely utilized entities in myriad applications including basic research, imaging, targeted delivery, chromatography, diagnostics, and therapeutics. At production stage, antibodies are generally present in complex matrices and most of their intended applications necessitate purification. Antibody purification has always been a major bottleneck in downstream processing of antibodies, due to the need of high quality products and associated high costs. Over the years, extensive research has focused on finding better purification methodologies to overcome this holdup. Among a plethora of different techniques, affinity chromatography is one of the most selective, rapid and easy method for antibody purification. This review aims to provide a detailed overview on affinity chromatography and the components involved in purification. An array of support matrices along with various classes of affinity ligands detailing their underlying working principles, together with the advantages and limitations of each system in purifying different types of antibodies, accompanying recent developments and important practical methodological considerations to optimize purification procedure are discussed.
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Affiliation(s)
- Sushrut Arora
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Vikas Saxena
- Center for Vascular and Inflammatory Diseases, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
| | - B Vijayalakshmi Ayyar
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
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107
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Chen X, Wong YK, Wang J, Zhang J, Lee YM, Shen HM, Lin Q, Hua ZC. Target identification with quantitative activity based protein profiling (ABPP). Proteomics 2016; 17. [PMID: 27723264 DOI: 10.1002/pmic.201600212] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 09/14/2016] [Accepted: 10/06/2016] [Indexed: 12/20/2022]
Abstract
As many small bioactive molecules fulfill their functions through interacting with protein targets, the identification of such targets is crucial in understanding their mechanisms of action (MOA) and side effects. With technological advancements in target identification, it has become possible to accurately and comprehensively study the MOA and side effects of small molecules. While small molecules with therapeutic potential were derived solely from nature in the past, the remodeling and synthesis of such molecules have now been made possible. Presently, while some small molecules have seen successful application as drugs, the majority remain undeveloped, requiring further understanding of their MOA and side effects to fully tap into their potential. Given the typical promiscuity of many small molecules and the complexity of the cellular proteome, a high-flux and high-accuracy method is necessary. While affinity chromatography approaches combined with MS have had successes in target identification, limitations associated with nonspecific results remain. To overcome these complications, quantitative chemical proteomics approaches have been developed including metabolic labeling, chemical labeling, and label-free methods. These new approaches are adopted in conjunction with activity-based protein profiling (ABPP), allowing for a rapid process and accurate results. This review will briefly introduce the principles involved in ABPP, then summarize current advances in quantitative chemical proteomics approaches as well as illustrate with examples how ABPP coupled with quantitative chemical proteomics has been used to detect the targets of drugs and other bioactive small molecules including natural products.
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Affiliation(s)
- Xiao Chen
- The State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, P. R., China
| | - Yin Kwan Wong
- Department of Biological Sciences, National University of Singapore, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jigang Wang
- The State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, P. R., China.,Department of Biological Sciences, National University of Singapore, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Interdisciplinary Research Group in Infectious Diseases, Singapore-MIT Alliance for Research & Technology (SMART), Singapore
| | - Jianbin Zhang
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Clinical Research Institute, Zhejiang Provincial People's Hospital, Hangzhou, P. R., China
| | - Yew-Mun Lee
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Han-Ming Shen
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore
| | - Qingsong Lin
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Zi-Chun Hua
- The State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, P. R., China
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108
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Abstract
Affinity capture is an effective technique for isolating endogenous protein complexes for further study. When used in conjunction with an antibody, this technique is also frequently referred to as immunoprecipitation. Affinity capture can be applied in a bench-scale and in a high-throughput context. When coupled with protein mass spectrometry, affinity capture has proven to be a workhorse of interactome analysis. Although there are potentially many ways to execute the numerous steps involved, the following protocols implement our favored methods. Two features are distinctive: the use of cryomilled cell powder to produce cell extracts, and antibody-coupled paramagnetic beads as the affinity medium. In many cases, we have obtained superior results to those obtained with more conventional affinity capture practices. Cryomilling avoids numerous problems associated with other forms of cell breakage. It provides efficient breakage of the material, while avoiding denaturation issues associated with heating or foaming. It retains the native protein concentration up to the point of extraction, mitigating macromolecular dissociation. It reduces the time extracted proteins spend in solution, limiting deleterious enzymatic activities, and it may reduce the non-specific adsorption of proteins by the affinity medium. Micron-scale magnetic affinity media have become more commonplace over the last several years, increasingly replacing the traditional agarose- and Sepharose-based media. Primary benefits of magnetic media include typically lower non-specific protein adsorption; no size exclusion limit because protein complex binding occurs on the bead surface rather than within pores; and ease of manipulation and handling using magnets.
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Affiliation(s)
- John LaCava
- Laboratory of Cellular and Structural Biology, The Rockefeller University; Institute for Systems Genetics, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine;
| | - Hua Jiang
- Laboratory of Cellular and Structural Biology, The Rockefeller University
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University
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109
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Shin MK, Kang B, Yoon NK, Kim MH, Ki J, Han S, Ahn JO, Haam S. Synthesis of Fe 3O 4@nickel-silicate core-shell nanoparticles for His-tagged enzyme immobilizing agents. NANOTECHNOLOGY 2016; 27:495705. [PMID: 27831938 DOI: 10.1088/0957-4484/27/49/495705] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Immobilizing enzymes on artificially fabricated carriers for their efficient use and easy removal from reactants has attracted enormous interest for decades. Specifically, binding platforms using inorganic nanoparticles have been widely explored because of the benefits of their large surface area, easy surface modification, and high stability in various pH and temperatures. Herein, we fabricated Fe3O4 encapsulated 'sea-urchin' shaped nickel-silicate nanoparticles with a facile synthetic route. The enzymes were then rapidly and easily immobilized with poly-histidine tags (His-tags) and nickel ion affinity. Porous nickel silicate covered nanoparticles achieved a high immobilization capacity (85 μg mg-1) of His-tagged tobacco etch virus (TEV) protease. To investigate immobilized TEV protease enzymatic activity, we analyzed the cleaved quantity of maltose binding protein-exendin-fused immunoglobulin fusion protein, which connected with the TEV protease-specific cleavage peptide sequence. Moreover, TEV protease immobilized nanocomplexes conveniently removed and recollected from the reactant by applying an external magnetic field, maintained their enzymatic activity after reuse. Therefore, our newly developed nanoplatform for His-tagged enzyme immobilization provides advantageous features for biotechnological industries including recombinant protein processing.
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Affiliation(s)
- Moo-Kwang Shin
- Department of Chemical and Biomolecular Engineering, Yonsei University, Seoul 120-749, Korea
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110
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Production of Computationally Designed Small Soluble- and Membrane-Proteins: Cloning, Expression, and Purification. Methods Mol Biol 2016. [PMID: 27914046 DOI: 10.1007/978-1-4939-6637-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
This book chapter focuses on expression and purification of computationally designed small soluble proteins and membrane proteins that are ordinarily difficult to express in good amounts for experiments. Over-expression of such proteins can be achieved by using the solubility tag such as maltose binding protein (MBP), Thioredoxin (Trx), and Gultathione-S-transferase (GST) fused to the protein of interest. Here, we describe and provide the protocols for cloning, expression and purification of such proteins using the solubility tag.
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111
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Separating full-length protein from aggregating proteolytic products using filter flow-through purification. Anal Biochem 2016; 514:8-11. [PMID: 27623435 DOI: 10.1016/j.ab.2016.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 09/04/2016] [Accepted: 09/09/2016] [Indexed: 11/20/2022]
Abstract
Separation of full-length protein from proteolytic products is challenging, since the properties used to isolate the protein can also be present in proteolytic products. Many separation techniques risk non-specific protein adhesion and/or require a lot of time, enabling continued proteolysis and aggregation after lysis. We demonstrate that proteolytic products aggregate for two different proteins. As a result, full-length protein can be rapidly separated from these fragments by filter flow-through purification, resulting in a substantial protein purity enhancement. This rapid approach is likely to be useful for intrinsically disordered proteins, whose repetitive sequence composition and flexible nature can facilitate aggregation.
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112
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Axarli I, Muleta AW, Chronopoulou EG, Papageorgiou AC, Labrou NE. Directed evolution of glutathione transferases towards a selective glutathione-binding site and improved oxidative stability. Biochim Biophys Acta Gen Subj 2016; 1861:3416-3428. [PMID: 27612661 DOI: 10.1016/j.bbagen.2016.09.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 08/28/2016] [Accepted: 09/04/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND Glutathione transferases (GSTs) are a family of detoxification enzymes that catalyze the conjugation of glutathione (GSH) to electrophilic compounds. METHODS A library of alpha class GSTs was constructed by DNA shuffling using the DNA encoding the human glutathione transferase A1-1 (hGSTA1-1) and the rat glutathione transferase A1-1 (rGSTA1-1). RESULTS Activity screening of the library allowed the selection of a chimeric enzyme variant (GSTD4) that displayed high affinity towards GSH and GSH-Sepharose affinity adsorbent, higher kcat/Km and improved thermal stability, compared to the parent enzymes. The crystal structures of the GSTD4 enzyme in free form and in complex with GSH were determined to 1.6Å and 2.3Å resolution, respectively. Analysis of the GSTD4 structure showed subtle conformational changes in the GSH-binding site and in electron-sharing network that may contribute to the increased GSH affinity. The shuffled variant GSTD4 was further optimized for improved oxidative stability employing site-saturation mutagenesis. The Cys112Ser mutation confers optimal oxidative stability and kinetic properties in the GSTD4 enzyme. CONCLUSIONS DNA shuffling allowed the creation of a chimeric enzyme variant with improved properties, compared to the parent enzymes. X-ray crystallography shed light on how recombination of a specific segment from homologous GSTA1-1 together with point mutations gives rise to a new functionally competent enzyme with improved binding, catalytic properties and stability. GENERAL SIGNIFICANCE Such an engineered GST would be useful in biotechnology as affinity tool in affinity chromatography as well as a biocatalytic matrix for the construction of biochips or enzyme biosensors.
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Affiliation(s)
- Irine Axarli
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, 75 Iera Odos Street, GR-11855 Athens, Greece
| | - Abdi W Muleta
- Turku Centre for Biotechnology, BioCity, University of Turku and Åbo Akademi University, Turku 20521, Finland
| | - Evangelia G Chronopoulou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, 75 Iera Odos Street, GR-11855 Athens, Greece
| | - Anastassios C Papageorgiou
- Turku Centre for Biotechnology, BioCity, University of Turku and Åbo Akademi University, Turku 20521, Finland
| | - Nikolaos E Labrou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, 75 Iera Odos Street, GR-11855 Athens, Greece.
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113
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He B, Kang J, Ru B, Ding H, Zhou P, Huang J. SABinder: A Web Service for Predicting Streptavidin-Binding Peptides. BIOMED RESEARCH INTERNATIONAL 2016; 2016:9175143. [PMID: 27610387 PMCID: PMC5005764 DOI: 10.1155/2016/9175143] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 07/27/2016] [Indexed: 11/17/2022]
Abstract
Streptavidin is sometimes used as the intended target to screen phage-displayed combinatorial peptide libraries for streptavidin-binding peptides (SBPs). More often in the biopanning system, however, streptavidin is just a commonly used anchoring molecule that can efficiently capture the biotinylated target. In this case, SBPs creeping into the biopanning results are not desired binders but target-unrelated peptides (TUP). Taking them as intended binders may mislead subsequent studies. Therefore, it is important to find if a peptide is likely to be an SBP when streptavidin is either the intended target or just the anchoring molecule. In this paper, we describe an SVM-based ensemble predictor called SABinder. It is the first predictor for SBP. The model was built with the feature of optimized dipeptide composition. It was observed that 89.20% (MCC = 0.78; AUC = 0.93; permutation test, p < 0.001) of peptides were correctly classified. As a web server, SABinder is freely accessible. The tool provides a highly efficient way to exclude potential SBP when they are TUP or to facilitate identification of possibly new SBP when they are the desired binders. In either case, it will be helpful and can benefit related scientific community.
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Affiliation(s)
- Bifang He
- Key Laboratory for Neuroinformation of Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Juanjuan Kang
- Key Laboratory for Neuroinformation of Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Beibei Ru
- Key Laboratory for Neuroinformation of Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Hui Ding
- Key Laboratory for Neuroinformation of Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Peng Zhou
- Key Laboratory for Neuroinformation of Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Jian Huang
- Key Laboratory for Neuroinformation of Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
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114
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Boumaiza M, Chahed H, Ezzine A, Jaouen M, Gianoncelli A, Longhi G, Carmona F, Arosio P, Sari MA, Marzouki MN. Recombinant overexpression of camel hepcidin cDNA in Pichia pastoris: purification and characterization of the polyHis-tagged peptide HepcD-His. J Mol Recognit 2016; 30. [PMID: 27507710 DOI: 10.1002/jmr.2561] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 06/20/2016] [Accepted: 07/15/2016] [Indexed: 11/09/2022]
Abstract
Hepcidin, a liver-expressed antimicrobial peptide, has been demonstrated to act as an iron regulatory hormone as well as to exert a wide spectrum of antimicrobial activity. The aim of this work was the expression, as secreted peptide, purification, and characterization of a new recombinant polyHis-tagged camel hepcidin (HepcD-His) in yeast Pichia pastoris. The use of this eukaryotic expression system, for the production of HepcD-His, having 6 histidine residues at its C terminus, was simpler and more efficient compared with the use of the prokaryotic system Escherichia coli. Indeed, a single purification step was required to isolate the soluble hepcidin with purity estimated more that 94% and a yield of 2.8 against 0.2 mg/L for the E coli system. Matrix-assisted laser desorption/ionization time-of-flight (TOF)/TOF mass spectrometry of the purified HepcD-His showed 2 major peaks at m/z 4524.64 and 4634.56 corresponding to camel hepcidin with 39 and 40 amino acids. Evaluation of disulfide bond connectivity with the Ellman method showed an absence of free thiol groups, testifying that the 8 cysteine residues in the peptide are displayed, forming 4 disulfide bridges. Circular dichroism spectroscopy showed that camel hepcidin structure was significantly modified at high temperature of 90°C and returns to its original structure when incubation temperature drops back to 20°C. Interestingly, this peptide showed also a greater bactericidal activity, at low concentration of 9.5μM, against E coli, than the synthetic analog DH3. Thus, the production, at a large scale, of the recombinant camel hepcidin, HepcD-His, may be helpful for future therapeutic applications including bacterial infection diseases.
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Affiliation(s)
- Mohamed Boumaiza
- Laboratoire d'ingénierie des protéines et des molécules bioactives (LIP-MB), Institut National des Sciences Appliquées et de Technologie, Université de Carthage, BP 676, 1080, Tunis Cedex, Tunis, Tunisia
| | - Haifa Chahed
- Laboratoire d'ingénierie des protéines et des molécules bioactives (LIP-MB), Institut National des Sciences Appliquées et de Technologie, Université de Carthage, BP 676, 1080, Tunis Cedex, Tunis, Tunisia
| | - Aymen Ezzine
- Laboratoire d'ingénierie des protéines et des molécules bioactives (LIP-MB), Institut National des Sciences Appliquées et de Technologie, Université de Carthage, BP 676, 1080, Tunis Cedex, Tunis, Tunisia
| | - Maryse Jaouen
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601, Université Paris Descartes, CNRS, 45 rue des Saints Pères, 75270, Paris Cedex 06, Paris, France
| | - Alessandra Gianoncelli
- Department of Molecular and Translational Medicine, DMMT, University of Brescia, Viale Europa 11, 25123, Brescia, Brescia, Italy
| | - Giovanna Longhi
- Department of Molecular and Translational Medicine, DMMT, University of Brescia, Viale Europa 11, 25123, Brescia, Brescia, Italy
| | - Fernando Carmona
- Department of Molecular and Translational Medicine, DMMT, University of Brescia, Viale Europa 11, 25123, Brescia, Brescia, Italy
| | - Paolo Arosio
- Department of Molecular and Translational Medicine, DMMT, University of Brescia, Viale Europa 11, 25123, Brescia, Brescia, Italy
| | - Marie-Agnès Sari
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601, Université Paris Descartes, CNRS, 45 rue des Saints Pères, 75270, Paris Cedex 06, Paris, France
| | - Mohamed Nejib Marzouki
- Laboratoire d'ingénierie des protéines et des molécules bioactives (LIP-MB), Institut National des Sciences Appliquées et de Technologie, Université de Carthage, BP 676, 1080, Tunis Cedex, Tunis, Tunisia
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115
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Milewski MC, Broger T, Kirkpatrick J, Filomena A, Komadina D, Schneiderhan-Marra N, Wilmanns M, Parret AHA. A standardized production pipeline for high profile targets from Mycobacterium tuberculosis. Proteomics Clin Appl 2016; 10:1049-1057. [PMID: 27400835 PMCID: PMC5095800 DOI: 10.1002/prca.201600033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 05/23/2016] [Accepted: 07/07/2016] [Indexed: 01/21/2023]
Abstract
Purpose Tuberculosis is still a major threat to global health. New tools and strategies to produce disease‐related proteins are quintessential for the development of novel vaccines and diagnostic markers. Experimental design To obtain recombinant proteins from Mycobacterium tuberculosis (Mtb) for use in clinical applications, a standardized procedure was developed that includes subcloning, protein expression in Mycobacterium smegmatis and protein purification using chromatography. The potential for the different protein targets to serve as diagnostic markers for tuberculosis was established using multiplex immunoassays. Results Twelve soluble proteins from Mtb, including one protein complex, were purified to near‐homogeneity following recombinant expression in M. smegmatis. Protein purity was assessed both by size exclusion chromatography and MS. Multiplex serological testing of the final protein preparations showed that all but one protein displayed a clear antibody response in serum samples from 278 tuberculosis patients. Conclusion and clinical relevance The established workflow comprises a simple, cost‐effective, and scalable pipeline for production of soluble proteins from Mtb and can be used to prioritize immunogenic proteins suitable for use as diagnostic markers.
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Affiliation(s)
- Morlin C Milewski
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, Hamburg, Germany
| | - Tobias Broger
- Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland
| | - Joanna Kirkpatrick
- European Molecular Biology Laboratory (EMBL), Proteomics Core Facility, Heidelberg, Germany
| | - Angela Filomena
- Natural and Medical Sciences Institute, University of Tübingen, Reutlingen, Germany
| | - Dana Komadina
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, Hamburg, Germany
| | | | - Matthias Wilmanns
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, Hamburg, Germany.,University of Hamburg Clinical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Annabel H A Parret
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, Hamburg, Germany.
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116
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Jussen D, Soltner H, Stute B, Wiechert W, von Lieres E, Pohl M. μMORE: A microfluidic magnetic oscillation reactor for accelerated parameter optimization in biocatalysis. J Biotechnol 2016; 231:174-182. [PMID: 27288595 DOI: 10.1016/j.jbiotec.2016.06.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 06/06/2016] [Accepted: 06/07/2016] [Indexed: 12/15/2022]
Abstract
Enzymatic parameter determination is an essential step in biocatalytic process development. Therefore higher throughput in miniaturized devices is urgently needed. An ideal microfluidic device should combine easy immobilization and retention of a minimal amount of biocatalyst with a well-mixed reaction volume. Together, all criteria are hardly met by current tools. Here we describe a microfluidic reactor (μMORE) which employs magnetic particles for both enzyme immobilization and efficient mixing using two permanent magnets placed in rotating cylinders next to the a glass chip reactor. The chip geometry and agitation speed was optimized by investigation of the mixing and retention characteristics using simulation and dye distribution analysis. Subsequently, the μMORE was successfully applied to determine critical biocatalytic process parameters in a parallelized manner for the carboligation of benzaldehyde and acetaldehyde to (S)-2-hydroxy-1-phenylpropan-1-one with less than 5μg of benzoylformate decarboxylase from Pseudomonas putida immobilized on magnetic beads. Here, one run of the device in six parallelized glass reactors took only 2-3h for an immobilized enzyme with very low activity (∼2U/mg). The optimized parameter set was finally tested in a 10mL enzyme membrane reactor, demonstrating that the μMORE provides a solid data base for biocatalytic process optimization.
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Affiliation(s)
- Daniel Jussen
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany.
| | - Helmut Soltner
- ZEA-1: Engineering and Technology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany.
| | - Birgit Stute
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany.
| | - Wolfgang Wiechert
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany.
| | - Eric von Lieres
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany.
| | - Martina Pohl
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany.
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Nakamura M, Suzuki A, Akada J, Yarimizu T, Iwakiri R, Hoshida H, Akada R. A Novel Terminator Primer and Enhancer Reagents for Direct Expression of PCR-Amplified Genes in Mammalian Cells. Mol Biotechnol 2016; 57:767-80. [PMID: 25997599 DOI: 10.1007/s12033-015-9870-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Escherichia coli plasmids are commonly used for gene expression experiments in mammalian cells, while PCR-amplified DNAs are rarely used even though PCR is a much faster and easier method to construct recombinant DNAs. One difficulty may be the limited amount of DNA produced by PCR. For direct utilization of PCR-amplified DNA in transfection experiments, efficient transfection with a smaller amount of DNA should be attained. For this purpose, we investigated two enhancer reagents, polyethylene glycol and tRNA, for a chemical transfection method. The addition of the enhancers to a commercial transfection reagent individually and synergistically exhibited higher transfection efficiency applicable for several mammalian cell culture lines in a 96-well plate. By taking advantage of a simple transfection procedure using PCR-amplified DNA, SV40 and rabbit β-globin terminator lengths were minimized. The terminator length is short enough to design in oligonucleotides; thus, terminator primers can be used for the construction and analysis of numerous mutations, deletions, insertions, and tag-fusions at the 3'-terminus of any gene. The PCR-mediated gene manipulation with the terminator primers will transform gene expression by allowing for extremely simple and high-throughput experiments with small-scale, multi-well, and mammalian cell cultures.
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Affiliation(s)
- Mikiko Nakamura
- Innovation Center, Yamaguchi University, Tokiwadai, Ube, 755-8611, Japan,
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118
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Soleimanpour S, Hassannia T, Motiee M, Amini AA, Rezaee SAR. Fcγ1 fragment of IgG1 as a powerful affinity tag in recombinant Fc-fusion proteins: immunological, biochemical and therapeutic properties. Crit Rev Biotechnol 2016; 37:371-392. [PMID: 27049690 DOI: 10.3109/07388551.2016.1163323] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Affinity tags are vital tools for the production of high-throughput recombinant proteins. Several affinity tags, such as the hexahistidine tag, maltose-binding protein, streptavidin-binding peptide tag, calmodulin-binding peptide, c-Myc tag, glutathione S-transferase and FLAG tag, have been introduced for recombinant protein production. The fragment crystallizable (Fc) domain of the IgG1 antibody is one of the useful affinity tags that can facilitate detection, purification and localization of proteins and can improve the immunogenicity, modulatory effects, physicochemical and pharmaceutical properties of proteins. Fcγ recombinant forms a group of recombinant proteins called Fc-fusion proteins (FFPs). FFPs are widely used in drug discovery, drug delivery, vaccine design and experimental research on receptor-ligand interactions. These fusion proteins have become successful alternatives to monoclonal antibodies for drug developments. In this review, the physicochemical, biochemical, immunological, pharmaceutical and therapeutic properties of recombinant FFPs were discussed as a new generation of bioengineering strategies.
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Affiliation(s)
- Saman Soleimanpour
- a Microbiology & Virology Research Center, Bu-Ali Research Institute, Mashhad University of Medical Sciences , Mashhad, Iran
| | - Tahereh Hassannia
- b Internal medicine Department, Arash Hospital, the College of Medicine, Tehran University of Medical Sciences , Tehran, Iran
| | - Mahdieh Motiee
- c Inflammation and Inflammatory Diseases Research Center, Medical School, Mashhad University of Medical Sciences , Mashhad, Iran
| | - Abbas Ali Amini
- d Department of Immunology, faculty of medicine, Kurdistan University of Medical Sciences , Sanandaj, Iran
| | - S A R Rezaee
- c Inflammation and Inflammatory Diseases Research Center, Medical School, Mashhad University of Medical Sciences , Mashhad, Iran
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119
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Sudhir PR, Chen CH. Proteomics-Based Analysis of Protein Complexes in Pluripotent Stem Cells and Cancer Biology. Int J Mol Sci 2016; 17:432. [PMID: 27011181 PMCID: PMC4813282 DOI: 10.3390/ijms17030432] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 03/08/2016] [Accepted: 03/16/2016] [Indexed: 12/24/2022] Open
Abstract
A protein complex consists of two or more proteins that are linked together through protein-protein interactions. The proteins show stable/transient and direct/indirect interactions within the protein complex or between the protein complexes. Protein complexes are involved in regulation of most of the cellular processes and molecular functions. The delineation of protein complexes is important to expand our knowledge on proteins functional roles in physiological and pathological conditions. The genetic yeast-2-hybrid method has been extensively used to characterize protein-protein interactions. Alternatively, a biochemical-based affinity purification coupled with mass spectrometry (AP-MS) approach has been widely used to characterize the protein complexes. In the AP-MS method, a protein complex of a target protein of interest is purified using a specific antibody or an affinity tag (e.g., DYKDDDDK peptide (FLAG) and polyhistidine (His)) and is subsequently analyzed by means of MS. Tandem affinity purification, a two-step purification system, coupled with MS has been widely used mainly to reduce the contaminants. We review here a general principle for AP-MS-based characterization of protein complexes and we explore several protein complexes identified in pluripotent stem cell biology and cancer biology as examples.
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Affiliation(s)
| | - Chung-Hsuan Chen
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan.
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120
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Immunogenicity and protective efficacy of recombinant Clostridium difficile flagellar protein FliC. Emerg Microbes Infect 2016; 5:e8. [PMID: 26839147 PMCID: PMC4777929 DOI: 10.1038/emi.2016.8] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 10/13/2015] [Accepted: 11/12/2015] [Indexed: 12/31/2022]
Abstract
Clostridium difficile is a Gram-positive bacillus and is the leading cause of toxin-mediated nosocomial diarrhea following antibiotic use. C. difficile flagella play a role in colonization, adherence, biofilm formation, and toxin production, which might contribute to the overall virulence of certain strains. Human and animal studies indicate that anti-flagella immune responses may play a role in protection against colonization by C. difficile and subsequent disease outcome. Here we report that recombinant C. difficile flagellin (FliC) is immunogenic and protective in a murine model of C. difficile infection (CDI) against a clinical C. difficile strain, UK1. Passive protection experiments using anti-FliC polyclonal serum in mice suggest this protection to be antibody-mediated. FliC immunization also was able to afford partial protection against CDI and death in hamsters following challenge with C. difficile 630Δerm. Additionally, immunization against FliC does not have an adverse effect on the normal gut flora of vaccinated hamsters as evidenced by comparing the fecal microbiome of vaccinated and control hamsters. Therefore, the use of FliC as a vaccine candidate against CDI warrants further testing.
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121
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Gao S, Li F, Li H, Huang Y, Liu Y, Chen Y. Effects and Molecular Mechanism of GST-Irisin on Lipolysis and Autocrine Function in 3T3-L1 Adipocytes. PLoS One 2016; 11:e0147480. [PMID: 26799325 PMCID: PMC4723061 DOI: 10.1371/journal.pone.0147480] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 01/05/2016] [Indexed: 02/01/2023] Open
Abstract
Irisin, which was recently identified as a myokine and an adipokine, transforms white adipose tissue to brown adipose tissue and has increasingly caught the attention of the medical and scientific community. However, the signaling pathway of irisin and the molecular mechanisms responsible for the lipolysis effect remain unclear. In this study, we established an efficient system for the expression and purification of GST-irisin in Escherichia coli. The biological activity of GST-irisin was verified using the cell counting kit-8 assay and by detecting the mRNA expression of uncoupling protein 1. Our data showed that GST-irisin regulates mRNA levels of lipolysis-related genes such as adipose triglyceride lipase and hormone-sensitive lipase and proteins such as the fatty acid-binding protein 4, leading to increased secretion of glycerol and decreased lipid accumulation in 3T3-L1 adipocytes. In addition, exogenous GST-irisin can increase its autocrine function in vitro by regulating the expression of fibronectin type III domain-containing protein 5. GST-irisin could regulate glucose uptake in 3T3-L1 adipocytes. Hence, we believe that recombinant GST-irisin could promote lipolysis and its secretion in vitro and can potentially prevent obesity and related metabolic diseases.
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Affiliation(s)
- Shanshan Gao
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
- School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Fangmin Li
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
- School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Huimin Li
- School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Yibing Huang
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
- School of Life Sciences, Jilin University, Changchun, 130012, China
- National Engineering Laboratory for AIDS Vaccine, Jilin University, Changchun, 130012, China
| | - Yu Liu
- Department of Endocrinology, the Second Hospital of Jilin University, Changchun, 130041, China
- * E-mail: (YXC); (YL)
| | - Yuxin Chen
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
- School of Life Sciences, Jilin University, Changchun, 130012, China
- National Engineering Laboratory for AIDS Vaccine, Jilin University, Changchun, 130012, China
- * E-mail: (YXC); (YL)
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122
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Li S, Yang K, Zhao B, Li X, Liu L, Chen Y, Zhang L, Zhang Y. Epitope imprinting enhanced IMAC (EI-IMAC) for highly selective purification of His-tagged protein. J Mater Chem B 2016; 4:1960-1967. [DOI: 10.1039/c5tb02505b] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Selectivity of epitope imprinted sites is introduced on the IMAC surface through epitope surface imprinting. The obtained epitope imprinting enhanced IMAC (EI-IMAC) could purify His-tagged proteins with high selectivity without any major interference from the host proteins.
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Affiliation(s)
- Senwu Li
- National Chromatographic R. & A. Center
- Key Laboratory of Separation Science for Analytical Chemistry
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
| | - Kaiguang Yang
- National Chromatographic R. & A. Center
- Key Laboratory of Separation Science for Analytical Chemistry
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
| | - Baofeng Zhao
- National Chromatographic R. & A. Center
- Key Laboratory of Separation Science for Analytical Chemistry
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
| | - Xiao Li
- National Chromatographic R. & A. Center
- Key Laboratory of Separation Science for Analytical Chemistry
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
| | - Lukuan Liu
- National Chromatographic R. & A. Center
- Key Laboratory of Separation Science for Analytical Chemistry
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
| | - Yuanbo Chen
- National Chromatographic R. & A. Center
- Key Laboratory of Separation Science for Analytical Chemistry
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
| | - Lihua Zhang
- National Chromatographic R. & A. Center
- Key Laboratory of Separation Science for Analytical Chemistry
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
| | - Yukui Zhang
- National Chromatographic R. & A. Center
- Key Laboratory of Separation Science for Analytical Chemistry
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
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123
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Zhang M, Martin JL, Kumar M, Khairallah RJ, de Tombe PP. Rapid large-scale purification of myofilament proteins using a cleavable His6-tag. Am J Physiol Heart Circ Physiol 2015; 309:H1509-15. [PMID: 26386113 PMCID: PMC4666967 DOI: 10.1152/ajpheart.00598.2015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 09/15/2015] [Indexed: 11/22/2022]
Abstract
With the advent of high-throughput DNA sequencing, the number of identified cardiomyopathy-causing mutations has increased tremendously. As the majority of these mutations affect myofilament proteins, there is a need to understand their functional consequence on contraction. Permeabilized myofilament preparations coupled with protein exchange protocols are a common method for examining into contractile mechanics. However, producing large quantities of myofilament proteins can be time consuming and requires different approaches for each protein of interest. In the present study, we describe a unified automated method to produce troponin C, troponin T, and troponin I as well as myosin light chain 2 fused to a His6-tag followed by a tobacco etch virus (TEV) protease site. TEV protease has the advantage of a relaxed P1' cleavage site specificity, allowing for no residues left after proteolysis and preservation of the native sequence of the protein of interest. After expression in Esherichia coli, cells were lysed by sonication in imidazole-containing buffer. The His6-tagged protein was then purified using a HisTrap nickel metal affinity column, and the His6-tag was removed by His6-TEV protease digestion for 4 h at 30°C. The protease was then removed using a HisTrap column, and complex assembly was performed via column-assisted sequential desalting. This mostly automated method allows for the purification of protein in 1 day and can be adapted to most soluble proteins. It has the advantage of greatly increasing yield while reducing the time and cost of purification. Therefore, production and purification of mutant proteins can be accelerated and functional data collected in a faster, less expensive manner.
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Affiliation(s)
- Mengjie Zhang
- Department of Cell and Molecular Physiology, Loyola University, Chicago, Illinois
| | - Jody L Martin
- Department of Cell and Molecular Physiology, Loyola University, Chicago, Illinois
| | - Mohit Kumar
- Department of Cell and Molecular Physiology, Loyola University, Chicago, Illinois
| | - Ramzi J Khairallah
- Department of Cell and Molecular Physiology, Loyola University, Chicago, Illinois
| | - Pieter P de Tombe
- Department of Cell and Molecular Physiology, Loyola University, Chicago, Illinois
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124
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Single step purification of recombinant proteins using the metal ion-inducible autocleavage (MIIA) domain as linker for tag removal. J Biotechnol 2015; 208:22-7. [PMID: 26026704 DOI: 10.1016/j.jbiotec.2015.05.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 05/21/2015] [Accepted: 05/24/2015] [Indexed: 11/23/2022]
Abstract
For fast and easy purification, proteins are typically fused with an affinity tag, which often needs to be removed after purification. Here, we present a method for the removal of the affinity tag from the target protein in a single step protocol. The protein VIC_001052 of the coral pathogen Vibrio coralliilyticus ATCC BAA-450 contains a metal ion-inducible autocatalytic cleavage (MIIA) domain. Its coding sequence was inserted into an expression vector for the production of recombinant fusion proteins. Following, the target proteins MalE and mCherry were produced as MIIA-Strep fusion proteins in Escherichia coli. The target proteins could be separated from the MIIA-Strep part simply by the addition of calcium or manganese(II) ions within minutes. The cleavage is not affected in the pH range from 5.0 to 9.0 or at low temperatures (6°C). Autocleavage was also observed with immobilized protein on an affinity column. The protein yield was similar to that achieved with a conventional purification protocol.
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125
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Kato E, Tsuji H, Kawabata J. Selective purification of intestinal maltase complex by affinity chromatography employing an uncompetitive inhibitor as the ligand. Tetrahedron 2015. [DOI: 10.1016/j.tet.2015.01.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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126
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Panchapakesan SSS, Jeng SCY, Unrau PJ. RNA complex purification using high-affinity fluorescent RNA aptamer tags. Ann N Y Acad Sci 2015; 1341:149-55. [PMID: 25585661 DOI: 10.1111/nyas.12663] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
RNA plays important roles in cellular processes, but RNA-protein complexes are notoriously hard to isolate and study. We compare and contrast existing RNA- and protein-purification strategies with the potential of new RNA-tagging systems such as RNA Spinach and RNA Mango. Each RNA aptamer binds a small fluorophore, resulting in a highly fluorescent complex that is thousands of times brighter than the unbound fluorophore. Provided that the aptamer binding affinity is high enough, derivatized dyes can be used in conjunction with these aptamers to purify RNA complexes while simultaneously using their intrinsic fluorescence to track the complex of interest. The known strengths and weakness of these RNA tagging systems are discussed.
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127
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Ling C, Zhang J, Chen H, Zou Z, Lai H, Zhang J, Lin D, Tao A. Expression and refolding of mite allergen pro-Der f1 from inclusion bodies in Escherichia coli. Protein Expr Purif 2014; 109:93-8. [PMID: 25462803 DOI: 10.1016/j.pep.2014.11.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 10/31/2014] [Accepted: 11/17/2014] [Indexed: 10/24/2022]
Abstract
House dust mite (Dermatophagoides farinae) allergen Der f1 is one of the most important indoor allergens associated with asthma, eczema and allergic rhinitis in humans. Therefore, sufficient quantities of Der f1 cysteine protease to be used for both experimental and therapeutic purposes are very much needed. Using recombinant DNA technology, high expression rates of cysteine proteases were obtained. The cDNA sequence encoding pro-Der f1 was cloned and expressed in Escherichia coli using the T7 based expression vector pET-44a and induced by isopropyl-β-d-thiogalactoside at a final concentration of 0.2mM. Recombinant pro-Der f1 (pro-rDer f1) was expressed as an inclusion body and the isolated protease was solubilized, refolded and purified. The protease activities and IgE reactivities of pro-rDer f1 that were refolded by size-exclusion chromatography (SEC) were higher than those obtained by dilution. The pair of pro-rDer f1 polypeptides produced by this method could be used for more effective and safer allergen-specific immunotherapy or to produce enzymatically and immunologically active Der f1 for diagnostic testing and deciphering of immunotherapy mechanisms.
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Affiliation(s)
- Chunfang Ling
- Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, The State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital of Guangzhou Medical University, 250# Changgang Road East, Guangzhou 510260, Guangdong Province, PR China; School of Life Science, South China Normal University, 55# Zhongshan Road West, Tianhe District, Guangzhou 510631, PR China
| | - Junyan Zhang
- Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, The State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital of Guangzhou Medical University, 250# Changgang Road East, Guangzhou 510260, Guangdong Province, PR China
| | - Huifang Chen
- Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, The State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital of Guangzhou Medical University, 250# Changgang Road East, Guangzhou 510260, Guangdong Province, PR China
| | - Zehong Zou
- Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, The State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital of Guangzhou Medical University, 250# Changgang Road East, Guangzhou 510260, Guangdong Province, PR China
| | - He Lai
- Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, The State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital of Guangzhou Medical University, 250# Changgang Road East, Guangzhou 510260, Guangdong Province, PR China
| | - Jianguo Zhang
- Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, The State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital of Guangzhou Medical University, 250# Changgang Road East, Guangzhou 510260, Guangdong Province, PR China
| | - Deqiu Lin
- Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, The State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital of Guangzhou Medical University, 250# Changgang Road East, Guangzhou 510260, Guangdong Province, PR China; School of Life Science, South China Normal University, 55# Zhongshan Road West, Tianhe District, Guangzhou 510631, PR China.
| | - Ailin Tao
- Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, The State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital of Guangzhou Medical University, 250# Changgang Road East, Guangzhou 510260, Guangdong Province, PR China.
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128
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Harbers M. Wheat germ systems for cell-free protein expression. FEBS Lett 2014; 588:2762-73. [PMID: 24931374 DOI: 10.1016/j.febslet.2014.05.061] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 05/25/2014] [Accepted: 05/26/2014] [Indexed: 10/25/2022]
Abstract
Cell-free protein expression plays an important role in biochemical research. However, only recent developments led to new methods to rapidly synthesize preparative amounts of protein that make cell-free protein expression an attractive alternative to cell-based methods. In particular the wheat germ system provides the highest translation efficiency among eukaryotic cell-free protein expression approaches and has a very high success rate for the expression of soluble proteins of good quality. As an open in vitro method, the wheat germ system is a preferable choice for many applications in protein research including options for protein labeling and the expression of difficult-to-express proteins like membrane proteins and multiple protein complexes. Here I describe wheat germ cell-free protein expression systems and give examples how they have been used in genome-wide expression studies, preparation of labeled proteins for structural genomics and protein mass spectroscopy, automated protein synthesis, and screening of enzymatic activities. Future directions for the use of cell-free expression methods are discussed.
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Affiliation(s)
- Matthias Harbers
- RIKEN Center for Life Science Technologies, Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa 230-0045, Japan; CellFree Sciences Co., Ltd., 75-1, Ono-cho, Leading Venture Plaza 201, Tsurumi-ku, Yokohama, Kanagawa 230-0046, Japan.
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129
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Kowalczyk T, Hnatuszko-Konka K, Gerszberg A, Kononowicz AK. Elastin-like polypeptides as a promising family of genetically-engineered protein based polymers. World J Microbiol Biotechnol 2014; 30:2141-52. [PMID: 24699809 PMCID: PMC4072924 DOI: 10.1007/s11274-014-1649-5] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 03/27/2014] [Indexed: 01/01/2023]
Abstract
Elastin-like polypeptides (ELP) are artificial, genetically encodable biopolymers, belonging to elastomeric proteins, which are widespread in a wide range of living organisms. They are composed of a repeating pentapeptide sequence Val-Pro-Gly-Xaa-Gly, where the guest residue (Xaa) can be any naturally occurring amino acid except proline. These polymers undergo reversible phase transition that can be triggered by various environmental stimuli, such as temperature, pH or ionic strength. This behavior depends greatly on the molecular weight, concentration of ELP in the solution and composition of the amino acids constituting ELPs. At a temperature below the inverse transition temperature (Tt), ELPs are soluble, but insoluble when the temperature exceeds Tt. Furthermore, this feature is retained even when ELP is fused to the protein of interest. These unique properties make ELP very useful for a wide variety of biomedical applications (e.g. protein purification, drug delivery etc.) and it can be expected that smart biopolymers will play a significant role in the development of most new materials and technologies. Here we present the structure and properties of thermally responsive elastin-like polypeptides with a particular emphasis on biomedical and biotechnological application.
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Affiliation(s)
- Tomasz Kowalczyk
- Department of Genetics and Plant Molecular Biology and Biotechnology, The University of Lodz, Banacha Street 12/16, 90-237, Lodz, Poland,
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