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He X, Lin T, Xie Y, Li J, Ge Y, Zhang S, Fan J. Backbone cyclization of Salmonella typhimurium diaminopropionate ammonia-lyase to enhance the activity and stability. Protein Expr Purif 2024; 218:106447. [PMID: 38369031 DOI: 10.1016/j.pep.2024.106447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 01/11/2024] [Accepted: 02/15/2024] [Indexed: 02/20/2024]
Abstract
Diaminopropionate ammonia-lyase transforms D and L isomers of 2,3-diaminopropionate to pyruvate and ammonia. It catalyzes D- and l-serine less effectively. L-2,3-diaminopropionate is a precursor in the biosynthesis of oxalyl diaminopropionate as a neurotoxin in certain legume species. In this work, we cyclized the diaminopropionate ammonia-lyase from Salmonella typhimurium in vitro using the redox-responsive split intein, and identified that backbone cyclization afforded the enzyme with the improved activity, thermal stability and resistance to the exopeptidase proteolysis, different from effects of the incorporated sequence recognized by tobacco vein mottling virus protease at C-terminus. Using analyses of three fluorescent dyes including 8-anilino-1-naphthalenesulfonic acid, N-phenyl-1-naphthylamine, and thioflavin T, the same amounts of the cyclic protein displayed less fluorescence than those of the linear protein upon the heat treatment. The cyclic enzyme displayed the enhanced activity in Escherichia coli cells using the designed novel reporter. In this system, d-serine was added to the culture and transported into the cytoplasm. It was transformed by pre-overexpression of the diaminopropionate ammonia-lyase, and untransformed d-serine was oxidized by the coproduced human d-amino acid oxidase to generate hydrogen peroxide. This oxidant is monitored by the HyPer indicator. The current results presented that the cyclized enzyme could be applied as a better candidate to block the neurotoxin biosynthesis in certain plant species.
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Affiliation(s)
- Xiaomei He
- College of Biology and Pharmaceutical Engineering, West Anhui University, Lu'an, 237012, PR China
| | - Tingting Lin
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, PR China
| | - Yuying Xie
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, PR China
| | - Jinjing Li
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, PR China
| | - Yuanyuan Ge
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, PR China
| | - Shuncheng Zhang
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, PR China
| | - Jun Fan
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, PR China.
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Lin T, Ge Y, Gao Q, Zhang D, Chen X, Hu Y, Fan J. Backbone Cyclization of Flavin Mononucleotide-Based Fluorescent Protein Increases Fluorescence and Stability. J Microbiol Biotechnol 2023; 33:1681-1691. [PMID: 37789714 PMCID: PMC10772547 DOI: 10.4014/jmb.2305.05011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/31/2023] [Accepted: 08/17/2023] [Indexed: 10/05/2023]
Abstract
Flavin mononucleotide-binding proteins or domains emit cyan-green fluorescence under aerobic and anaerobic conditions, but relatively low fluorescence and less thermostability limit their application as reporters. In this work, we incorporated the codon-optimized fluorescent protein from Chlamydomonas reinhardtii with two different linkers independently into the redox-responsive split intein construct, overexpressed the precursors in hyperoxic Escherichia coli SHuffle T7 strain, and cyclized the target proteins in vitro in the presence of the reducing agent. Compared with the purified linear protein, the cyclic protein with the short linker displayed enhanced fluorescence. In contrast, cyclized protein with incorporation of the long linker including the myc-tag and human rhinovirus 3C protease cleavable sequence emitted slightly increased fluorescence compared with the protein linearized with the protease cleavage. The cyclic protein with the short linker also exhibited increased thermal stability and exopeptidase resistance. Moreover, induction of the target proteins in an oxygen-deficient culture rendered fluorescent E. coli BL21 (DE3) cells brighter than those overexpressing the linear construct. Thus, the cyclic reporter can hopefully be used in certain thermophilic anaerobes.
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Affiliation(s)
- Tingting Lin
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, P.R. China
| | - Yuanyuan Ge
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, P.R. China
| | - Qing Gao
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, P.R. China
| | - Di Zhang
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, P.R. China
| | - Xiaofeng Chen
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, P.R. China
| | - Yafang Hu
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, P.R. China
| | - Jun Fan
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, P.R. China
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3
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Bacterial production of maize and human serine racemases as partially active inclusion bodies for d-serine synthesis. Enzyme Microb Technol 2020; 137:109547. [DOI: 10.1016/j.enzmictec.2020.109547] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 03/01/2020] [Accepted: 03/04/2020] [Indexed: 01/31/2023]
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Assessment of the Fusion Tags on Increasing Soluble Production of the Active TEV Protease Variant and Other Target Proteins in E. coli. Appl Biochem Biotechnol 2016; 182:769-781. [DOI: 10.1007/s12010-016-2360-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 12/05/2016] [Indexed: 10/20/2022]
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Expression platforms for producing eukaryotic proteins: a comparison of E. coli cell-based and wheat germ cell-free synthesis, affinity and solubility tags, and cloning strategies. ACTA ACUST UNITED AC 2015; 16:67-80. [PMID: 25854603 DOI: 10.1007/s10969-015-9198-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 03/25/2015] [Indexed: 10/23/2022]
Abstract
Vectors designed for protein production in Escherichia coli and by wheat germ cell-free translation were tested using 21 well-characterized eukaryotic proteins chosen to serve as controls within the context of a structural genomics pipeline. The controls were carried through cloning, small-scale expression trials, large-scale growth or synthesis, and purification. Successfully purified proteins were also subjected to either crystallization trials or (1)H-(15)N HSQC NMR analyses. Experiments evaluated: (1) the relative efficacy of restriction/ligation and recombinational cloning systems; (2) the value of maltose-binding protein (MBP) as a solubility enhancement tag; (3) the consequences of in vivo proteolysis of the MBP fusion as an alternative to post-purification proteolysis; (4) the effect of the level of LacI repressor on the yields of protein obtained from E. coli using autoinduction; (5) the consequences of removing the His tag from proteins produced by the cell-free system; and (6) the comparative performance of E. coli cells or wheat germ cell-free translation. Optimal promoter/repressor and fusion tag configurations for each expression system are discussed.
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Raran-Kurussi S, Keefe K, Waugh DS. Positional effects of fusion partners on the yield and solubility of MBP fusion proteins. Protein Expr Purif 2015; 110:159-64. [PMID: 25782741 DOI: 10.1016/j.pep.2015.03.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 03/06/2015] [Accepted: 03/08/2015] [Indexed: 11/30/2022]
Abstract
Escherichia coli maltose-binding protein (MBP) is exceptionally effective at promoting the solubility of its fusion partners. However, there are conflicting reports in the literature claiming that (1) MBP is an effective solubility enhancer only when it is joined to the N-terminus of an aggregation-prone passenger protein, and (2) MBP is equally effective when fused to either end of the passenger. Here, we endeavor to resolve this controversy by comparing the solubility of a diverse set of MBP fusion proteins that, unlike those analyzed in previous studies, are identical in every way except for the order of the two domains. The results indicate that fusion proteins with an N-terminal MBP provide an excellent solubility advantage along with more robust expression when compared to analogous fusions in which MBP is the C-terminal fusion partner. We find that only intrinsically soluble passenger proteins (i.e., those not requiring a solubility enhancer) are produced as soluble fusions when they precede MBP. We also report that even subtle differences in inter-domain linker sequences can influence the solubility of fusion proteins.
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Affiliation(s)
- Sreejith Raran-Kurussi
- Protein Engineering Section, Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Karina Keefe
- Protein Engineering Section, Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - David S Waugh
- Protein Engineering Section, Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
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Klint JK, Senff S, Saez NJ, Seshadri R, Lau HY, Bende NS, Undheim EAB, Rash LD, Mobli M, King GF. Production of recombinant disulfide-rich venom peptides for structural and functional analysis via expression in the periplasm of E. coli. PLoS One 2013; 8:e63865. [PMID: 23667680 PMCID: PMC3646780 DOI: 10.1371/journal.pone.0063865] [Citation(s) in RCA: 123] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 04/06/2013] [Indexed: 11/27/2022] Open
Abstract
Disulfide-rich peptides are the dominant component of most animal venoms. These peptides have received much attention as leads for the development of novel therapeutic agents and bioinsecticides because they target a wide range of neuronal receptors and ion channels with a high degree of potency and selectivity. In addition, their rigid disulfide framework makes them particularly well suited for addressing the crucial issue of in vivo stability. Structural and functional characterization of these peptides necessitates the development of a robust, reliable expression system that maintains their native disulfide framework. The bacterium Escherichia coli has long been used for economical production of recombinant proteins. However, the expression of functional disulfide-rich proteins in the reducing environment of the E. coli cytoplasm presents a significant challenge. Thus, we present here an optimised protocol for the expression of disulfide-rich venom peptides in the periplasm of E. coli, which is where the endogenous machinery for production of disulfide-bonds is located. The parameters that have been investigated include choice of media, induction conditions, lysis methods, methods of fusion protein and peptide purification, and sample preparation for NMR studies. After each section a recommendation is made for conditions to use. We demonstrate the use of this method for the production of venom peptides ranging in size from 2 to 8 kDa and containing 2-6 disulfide bonds.
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Affiliation(s)
- Julie K. Klint
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Australia
| | - Sebastian Senff
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Australia
| | - Natalie J. Saez
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Australia
| | - Radha Seshadri
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Australia
| | - Ho Yee Lau
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Australia
| | - Niraj S. Bende
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Australia
| | - Eivind A. B. Undheim
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Australia
| | - Lachlan D. Rash
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Australia
| | - Mehdi Mobli
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Australia
| | - Glenn F. King
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Australia
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Kwak Y, Rhee IK, Shin JH. Expression pattern of recombinant organophosphorus hydrolase from Flavobacterium sp. ATCC 27551 in Escherichia coli. Appl Microbiol Biotechnol 2012; 97:8097-105. [PMID: 23274957 DOI: 10.1007/s00253-012-4626-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Revised: 11/26/2012] [Accepted: 11/28/2012] [Indexed: 12/01/2022]
Affiliation(s)
- Yunyoung Kwak
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, 702-701, Republic of Korea
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Wei L, Cai X, Qi Z, Rong L, Cheng B, Fan J. In vivo and in vitro characterization of TEV protease mutants. Protein Expr Purif 2012; 83:157-63. [DOI: 10.1016/j.pep.2012.03.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 03/13/2012] [Accepted: 03/15/2012] [Indexed: 11/15/2022]
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Kim SG, Min WK, Rho YT, Seo JH. Electrostatic interaction-induced inclusion body formation of glucagon-like peptide-1 fused with ubiquitin and cationic tag. Protein Expr Purif 2012; 84:38-46. [PMID: 22564875 DOI: 10.1016/j.pep.2012.04.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2012] [Revised: 04/14/2012] [Accepted: 04/16/2012] [Indexed: 10/28/2022]
Abstract
In an attempt to produce glucagon-like peptide-1 (GLP-1) using recombinant Escherichia coli, ubiquitin (Ub) as a fusion partner was fused to GLP-1 with the 6-lysine tag (K6) for simple purification. Despite the high solubility of ubiquitin, the fusion protein K6UbGLP-1 was expressed mainly as insoluble inclusion bodies in E. coli. In order to elucidate this phenomenon, various N- and C-terminal truncates and GLP-1 mutants of K6UbGLP-1 were constructed and analyzed for their characteristics by various biochemical and biophysical methods. The experiment results obtained in this study clearly demonstrated that the insoluble aggregation of K6UbGLP-1 was attributed to the electrostatic interaction between the N-terminal 6-lysine tag and the C-terminal GLP-1 before the completion of folding which might be one of the reasons for protein misfolding frequently observed in many foreign proteins introduced with charged amino acid residues such as the His tag and the protease recognition sites. The application of a cation exchanger for neutralizing the positive charge of the 6-lysine tag in solid-phase refolding of K6UbGLP-1 successfully suppressed the electrostatic interaction-driven aggregation even at a high protein concentration, resulting in properly folded K6UbGLP-1 for GLP-1 production.
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Affiliation(s)
- Sung-Gun Kim
- Department of Biomedical Science, Youngdong University, Chungbuk 370-701, Republic of Korea
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Solovyov KV, Polyakov DS, Grudinina NA, Egorov VV, Morozova IV, Aleynikova TD, Shavlovsky MM. Expression in E. coli and purification of the fibrillogenic fusion proteins TTR-sfGFP and β2M-sfGFP. Prep Biochem Biotechnol 2012; 41:337-49. [PMID: 21967335 DOI: 10.1080/10826068.2010.548433] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The possibility of obtaining recombinant fibrillogenic fusion proteins such as transthyretin (TTR) and β2-microglobulin (β2M) with a superfolder green fluorescent protein (sfGFP) was studied. According to the literature data, sfGFP is resistant to denaturating influences, does not aggregate during renaturation, possesses improved kinetic characteristics of folding, and folds well when fused to different polypeptides. The corresponding DNA constructs for expression in Escherichia coli were created. It could be shown that during expression of these constructs in E. coli, soluble forms of the fusion proteins are synthesized. Efficient isolation of the fusion proteins was performed with the help of nickel-affinity chromatography. For this purpose a polyhistidine sequence (6-His-tag) was incorporated into the C-terminus of the sfGFP. We could show that the purified fusion proteins contained full-size sequences of the most amyloidogenic TTR variant, TTR(L55P) and β2M, and also sfGFP possessing fluorescent properties. In the course of fibrillogenesis both fusion proteins demonstrated their ability to form fibrils that were clearly detectable by atomic force microscopy. Furthermore, with the help of confocal microscopy we were able to reveal structures (exhibiting fluorescence) that are formed during fibrillogenesis. Thus, the use of sfGFP has made it possible to avoid formation of inclusion bodies (IB) during the synthesis of recombinant fusion proteins and to obtain soluble forms of TTR(L55P) and β2M that are suitable for further studies.
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Affiliation(s)
- K V Solovyov
- Department of Molecular Genetics, Institute of Experimental Medicine, Nord-West Branch of Russian Academy of Medical Sciences, Saint Petersburg, Russia.
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Austin RJ, Smidansky HM, Holstein CA, Chang DK, Epp A, Josephson NC, Martin DB. Proteomic analysis of the androgen receptor via MS-compatible purification of biotinylated protein on streptavidin resin. Proteomics 2011; 12:43-53. [PMID: 22116683 DOI: 10.1002/pmic.201100348] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Revised: 09/19/2011] [Accepted: 10/25/2011] [Indexed: 11/09/2022]
Abstract
The strength of the streptavidin/biotin interaction poses challenges for the recovery of biotinylated molecules from streptavidin resins. As an alternative to high-temperature elution in urea-containing buffers, we show that mono-biotinylated proteins can be released with relatively gentle heating in the presence of biotin and 2% SDS/Rapigest, avoiding protein carbamylation and minimizing streptavidin dissociation. We demonstrate the utility of this mild elution strategy in two studies of the human androgen receptor (AR). In the first, in which formaldehyde cross-linked complexes are analyzed in yeast, a mass spectrometry-based comparison of the AR complex using SILAC reveals an association between the androgen-activated AR and the Hsp90 chaperonin, while Hsp70 chaperonins associate specifically with the unliganded complex. In the second study, the endogenous AR is quantified in the LNCaP cell line by absolute SILAC and MRM-MS showing approximately 127,000 AR copies per cell, substantially more than previously measured using radioligand binding.
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Affiliation(s)
- Ryan J Austin
- Institute for Systems Biology, Seattle, WA 98109, USA
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Exploiting the interactions between poly-histidine fusion tags and immobilized metal ions. Biotechnol Lett 2011; 33:1075-84. [PMID: 21318632 DOI: 10.1007/s10529-011-0554-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Accepted: 01/24/2011] [Indexed: 10/18/2022]
Abstract
Immobilized metal affinity chromatography (IMAC) of proteins containing poly-histidine fusion tags is an efficient research tool for purifying recombinant proteins from crude cellular feedstocks at laboratory scale. Nevertheless, to achieve successful purification of large amounts of the target protein for critical therapeutic applications that demand the precise removal of fusion tags, it is important to also take into consideration issues such as protein quality, efficiency, cost effectiveness, and optimal affinity tag choice and design. Despite the many considerations described in this article, it is expected that enhanced selectivity, the primary consideration in the field of protein separation, will continue to see the use of IMAC in solving new purification challenges. In addition, the platform nature of this technology makes it an ideal choice in purifying proteins with unknown properties. Finally, the unique interaction between immobilized metal ions and poly-histidine fusion tag has enabled new developments in the areas of biosensor, immunoassay, and other analytical technologies.
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Expression of the human soluble epoxide hydrolase in Escherichia coli by auto-induction for the study of high-throughput inhibition assays. Protein Expr Purif 2009; 69:34-8. [PMID: 19782755 DOI: 10.1016/j.pep.2009.09.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2009] [Revised: 09/16/2009] [Accepted: 09/21/2009] [Indexed: 11/24/2022]
Abstract
Soluble epoxide hydrolase (sEH) is a key enzyme involved in the metabolism of epoxy fatty acid mediators such as epoxyeicosatrienoic acids with emerging roles in the regulations of hypertension and inflammation. Inhibitors of human sEH (hsEH) are effective drug candidates for the treatment of cardiovascular diseases. Preparation of hsEH for enzyme inhibition studies has been carried out by using baculovirus expression system. We herein explored the feasibility of expression of hsEH in Escherichia coli cells for the study of high-throughput screening assays of enzyme inhibitors, because the bacterial expression system is easier to handle and more cost-effective than the baculovirus expression system. The functional target enzyme was successfully produced in prokaryotic expression system by an auto-induction method and exhibited comparable enzyme activity to that yielded in baculovirus expression system. The bacterial-hsEH showed similar sensitivity to the baculovirus-hsEH against six reported inhibitors. Overalls indicate that bacterial expression of hsEH employed in the present study is useful for preparing enzymatically active hsEH, leading to effective performance of high-throughput screening assay of hsEH inhibitors and to rapid identification of novel drug candidates for the treatment of cardiovascular diseases.
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