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Buscajoni L, Martinetz MC, Berkemeyer M, Brocard C. Refolding in the modern biopharmaceutical industry. Biotechnol Adv 2022; 61:108050. [PMID: 36252795 DOI: 10.1016/j.biotechadv.2022.108050] [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: 06/07/2022] [Revised: 10/07/2022] [Accepted: 10/11/2022] [Indexed: 11/02/2022]
Abstract
Inclusion bodies (IBs) often emerge upon overexpression of recombinant proteins in E. coli. From IBs, refolding is necessary to generate the native protein that can be further purified to obtain pure and active biologicals. This work focusses on refolding as a significant process step during biopharmaceutical manufacturing with an industrial perspective. A theoretical and historical background on protein refolding gives the reader a starting point for further insights into industrial process development. Quality requirements on IBs as starting material for refolding are discussed and further economic and ecological aspects are considered with regards to buffer systems and refolding conditions. A process development roadmap shows the development of a refolding process starting from first exploratory screening rounds to scale-up and implementation in manufacturing plant. Different aspects, with a direct influence on yield, such as the selection of chemicals including pH, ionic strength, additives, etc., and other often neglected aspects, important during scale-up, such as mixing, and gas-fluid interaction, are highlighted with the use of a quality by design (QbD) approach. The benefits of simulation sciences (process simulation and computer fluid dynamics) and process analytical technology (PAT) for seamless process development are emphasized. The work concludes with an outlook on future applications of refolding and highlights open research inquiries.
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Affiliation(s)
- Luisa Buscajoni
- Boehringer-Ingelheim RCV GmbH & Co KG, Biopharma Austria, Process Science Downstream Development, Dr. Boehringer-Gasse 5- 11, 1120 Vienna, Austria.
| | - Michael C Martinetz
- Boehringer-Ingelheim RCV GmbH & Co KG, Biopharma Austria, Process Science Downstream Development, Dr. Boehringer-Gasse 5- 11, 1120 Vienna, Austria.
| | - Matthias Berkemeyer
- Boehringer-Ingelheim RCV GmbH & Co KG, Biopharma Austria, Process Science Downstream Development, Dr. Boehringer-Gasse 5- 11, 1120 Vienna, Austria.
| | - Cécile Brocard
- Boehringer-Ingelheim RCV GmbH & Co KG, Biopharma Austria, Process Science Downstream Development, Dr. Boehringer-Gasse 5- 11, 1120 Vienna, Austria.
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2
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Zhang A, Piechocka-Trocha A, Li X, Walker BD. A Leucine Zipper Dimerization Strategy to Generate Soluble T Cell Receptors Using the Escherichia coli Expression System. Cells 2022; 11:cells11030312. [PMID: 35159122 PMCID: PMC8834513 DOI: 10.3390/cells11030312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 01/13/2022] [Accepted: 01/14/2022] [Indexed: 12/10/2022] Open
Abstract
T cell-mediated adaptive immunity plays a key role in immunological surveillance and host control of infectious diseases. A better understanding of T cell receptor (TCR) recognition of pathogen-derived epitopes or cancer-associated neoantigens is the basis for developing T cell-based vaccines and immunotherapies. Studies on the interaction between soluble TCR α:β heterodimers and peptide-bound major histocompatibility complexes (pMHCs) inform underlying mechanisms driving TCR recognition, but not every isolated TCR can be prepared in soluble form for structural and functional studies using conventional methods. Here, taking a challenging HIV-specific TCR as a model, we designed a general leucine zipper (LZ) dimerization strategy for soluble TCR preparation using the Escherichia coli expression system. We report details of TCR construction, inclusion body expression and purification, and protein refolding and purification. Measurements of binding affinity between the TCR and its specific pMHC using surface plasmon resonance (SPR) verify its activity. We conclude that this is a feasible approach to produce challenging TCRs in soluble form, needed for studies related to T cell recognition.
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Affiliation(s)
- Angela Zhang
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; (A.Z.); (A.P.-T.)
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Alicja Piechocka-Trocha
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; (A.Z.); (A.P.-T.)
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Xiaolong Li
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; (A.Z.); (A.P.-T.)
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Correspondence: (X.L.); (B.D.W.)
| | - Bruce D. Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; (A.Z.); (A.P.-T.)
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Institute for Medical Engineering and Science (IMES) and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Correspondence: (X.L.); (B.D.W.)
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3
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Shakya A, Imado E, Nguyen PK, Matsuyama T, Horimoto K, Hirata I, Kato K. Oriented immobilization of basic fibroblast growth factor: Bioengineered surface design for the expansion of human mesenchymal stromal cells. Sci Rep 2020; 10:8762. [PMID: 32472000 PMCID: PMC7260242 DOI: 10.1038/s41598-020-65572-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 05/05/2020] [Indexed: 01/14/2023] Open
Abstract
E. coli expressed recombinant basic fibroblast growth factor (bFGF) with histidine-tag (bFGF-His) was immobilized onto the surface of a glass plate modified with a Ni(II)-chelated alkanethiol monolayer. The immobilization is expected to take place through the coordination between Ni(II) and His-tag. The bFGF-immobilized surface was exposed to citrate buffer solution to refold in situ the surface-immobilized bFGF. The secondary structure of immobilized bFGF-His was analyzed by solid-phase circular dichroism (CD) spectroscopy. Immortalized human mesenchymal stromal cells (hMSCs) were cultured on the bFGF-His-immobilized surface to examine their proliferation. CD spectroscopy revealed that the immobilized bFGF initially exhibited secondary structure rich in α-helix and that the spectrum was gradually transformed to exhibit the formation of β-strands upon exposure to citrate buffer solution, approaching to the spectrum of native bFGF. The rate of hMSC proliferation was 1.2-fold higher on the bFGF-immobilized surface treated with in situ citrate buffer, compared to the polystyrene surface. The immobilized bFGF-His treated in situ with citrate buffer solution seemed to be biologically active because its secondary structure approached its native state. This was well demonstrated by the cell culture experiments. From these results we conclude that immobilization of bFGF on the culture substrate serves to enhance proliferation of hMSCs.
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Affiliation(s)
- Ajay Shakya
- Department of Biomaterials, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Eiji Imado
- Department of Biomaterials, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Phuong Kim Nguyen
- Department of Biomaterials, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.,Faculty of Odonto-Stomatology, Ho Chi Minh City University of Medicine and Pharmacy, Ho Chi Minh, Vietnam
| | - Tamamo Matsuyama
- Department of Biomaterials, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Kotaro Horimoto
- Department of Biomaterials, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Isao Hirata
- Department of Biomaterials, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Koichi Kato
- Department of Biomaterials, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.
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4
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A novel approach for production of an active N-terminally truncated Ulp1 (SUMO protease 1) catalytic domain from Escherichia coli inclusion bodies. Protein Expr Purif 2020; 166:105507. [DOI: 10.1016/j.pep.2019.105507] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 09/23/2019] [Accepted: 10/02/2019] [Indexed: 01/21/2023]
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5
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Abstract
In vitro protein folding can be employed to produce complex proteins expressed as insoluble inclusion bodies in E. coli from laboratory to commercial scale. Often the most challenging step is identification of renaturation conditions that will enable the denatured protein to form the native structure at an acceptable yield. Generally this requires screening a matrix of buffers and stabilizers to find an appropriate solution. Herein, we describe an automated and quantitative method to identify optimal in vitro protein folding parameters with a high rate of success.
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Affiliation(s)
- Kenneth W Walker
- Amgen Research, Amgen, Inc., One Amgen Center, Thousand Oaks, CA, USA.
| | - Philip An
- Amgen Research, Amgen, Inc., One Amgen Center, Thousand Oaks, CA, USA
| | - Dwight Winters
- Amgen Research, Amgen, Inc., One Amgen Center, Thousand Oaks, CA, USA
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6
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Zhao M, Li P, Xie Y, Liu X, Cheng L, Liu T, Kong L, Wang O, Han F. Recombinant protein of the first two ectodomains of cadherin 23 from erl mice shows impairment in Ca 2+-dependent proteolysis protection. Protein Expr Purif 2018; 147:55-60. [PMID: 29486248 DOI: 10.1016/j.pep.2018.02.009] [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: 05/12/2017] [Revised: 02/23/2018] [Accepted: 02/23/2018] [Indexed: 10/18/2022]
Abstract
The erl mouse is a mouse model of nonsyndromic autosomal recessive deafness (DFNB12) on the C57BL/6J background. This project was carried out to express the first two ectodomains of cadherin 23 (CDH23 EC1+2) of erl mice in Escherichia coli and identify the Ca2+-binding ability of the recombinant protein. DNA sequences of CDH23 EC1+2 from wild type and erl mice were synthesized and cloned into pBV220 plasmids. Recombinant plasmids were transformed into Escherichia coli and expression of CDH23 EC1+2 was induced by increasing the temperature from 30 °C to 42 °C. The proteins were analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and antigenicity of proteins was identified by Western Blotting. Inclusion bodies were denatured in 8 M urea, purified by ion-exchange and gel filtration chromatography and refolded with dialysis in buffer containing 0.1% sarkosyl. The Ca2+-binding ability of CDH23 EC1+2 was determined by Ca2+-dependent proteolysis protection. The results showed that the sizes and sequences of inserts in recombinant plasmids were consistent with expectation and that the recombinant proteins were found mainly in the form of inclusion bodies which maintain antigenicity. After refolding, the secondary structures of recombinant proteins were measured by circular dichroism (CD) spectra. Moreover, CDH23 EC1+2 from the erl mice showed less Ca2+-dependent proteolysis protection comparing with that of the wild type control. We therefore concluded that impairment of Ca2+-dependent protein interaction was likely involved in the progressive hearing loss in erl mice. The results may aid in understanding the mechanism of hearing loss in DFNB12.
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Affiliation(s)
- Mengmeng Zhao
- Key Laboratory for Genetic Hearing Disorders in Shandong, Binzhou Medical University, 346 Guanhai Road, Yantai, Shandong, 264003, PR China; Department of Biochemistry and Molecular Biology, Binzhou Medical University, 346 Guanhai Road, Yantai, Shandong, 264003, PR China
| | - Ping Li
- Key Laboratory for Genetic Hearing Disorders in Shandong, Binzhou Medical University, 346 Guanhai Road, Yantai, Shandong, 264003, PR China
| | - Yi Xie
- Key Laboratory for Genetic Hearing Disorders in Shandong, Binzhou Medical University, 346 Guanhai Road, Yantai, Shandong, 264003, PR China; Department of Biochemistry and Molecular Biology, Binzhou Medical University, 346 Guanhai Road, Yantai, Shandong, 264003, PR China
| | - Xiang Liu
- Key Laboratory for Genetic Hearing Disorders in Shandong, Binzhou Medical University, 346 Guanhai Road, Yantai, Shandong, 264003, PR China
| | - Lin Cheng
- Key Laboratory for Genetic Hearing Disorders in Shandong, Binzhou Medical University, 346 Guanhai Road, Yantai, Shandong, 264003, PR China
| | - Tingyan Liu
- Key Laboratory for Genetic Hearing Disorders in Shandong, Binzhou Medical University, 346 Guanhai Road, Yantai, Shandong, 264003, PR China
| | - Lijun Kong
- Key Laboratory for Genetic Hearing Disorders in Shandong, Binzhou Medical University, 346 Guanhai Road, Yantai, Shandong, 264003, PR China; Department of Biochemistry and Molecular Biology, Binzhou Medical University, 346 Guanhai Road, Yantai, Shandong, 264003, PR China
| | - Oumei Wang
- Key Laboratory for Genetic Hearing Disorders in Shandong, Binzhou Medical University, 346 Guanhai Road, Yantai, Shandong, 264003, PR China.
| | - Fengchan Han
- Key Laboratory for Genetic Hearing Disorders in Shandong, Binzhou Medical University, 346 Guanhai Road, Yantai, Shandong, 264003, PR China; Department of Biochemistry and Molecular Biology, Binzhou Medical University, 346 Guanhai Road, Yantai, Shandong, 264003, PR China.
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7
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Mizutani H, Sugawara H, Buckle AM, Sangawa T, Miyazono KI, Ohtsuka J, Nagata K, Shojima T, Nosaki S, Xu Y, Wang D, Hu X, Tanokura M, Yura K. REFOLDdb: a new and sustainable gateway to experimental protocols for protein refolding. BMC STRUCTURAL BIOLOGY 2017; 17:4. [PMID: 28438161 PMCID: PMC5402662 DOI: 10.1186/s12900-017-0074-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 04/11/2017] [Indexed: 01/22/2023]
Abstract
Background More than 7000 papers related to “protein refolding” have been published to date, with approximately 300 reports each year during the last decade. Whilst some of these papers provide experimental protocols for protein refolding, a survey in the structural life science communities showed a necessity for a comprehensive database for refolding techniques. We therefore have developed a new resource – “REFOLDdb” that collects refolding techniques into a single, searchable repository to help researchers develop refolding protocols for proteins of interest. Results We based our resource on the existing REFOLD database, which has not been updated since 2009. We redesigned the data format to be more concise, allowing consistent representations among data entries compared with the original REFOLD database. The remodeled data architecture enhances the search efficiency and improves the sustainability of the database. After an exhaustive literature search we added experimental refolding protocols from reports published 2009 to early 2017. In addition to this new data, we fully converted and integrated existing REFOLD data into our new resource. REFOLDdb contains 1877 entries as of March 17th, 2017, and is freely available at http://p4d-info.nig.ac.jp/refolddb/. Conclusion REFOLDdb is a unique database for the life sciences research community, providing annotated information for designing new refolding protocols and customizing existing methodologies. We envisage that this resource will find wide utility across broad disciplines that rely on the production of pure, active, recombinant proteins. Furthermore, the database also provides a useful overview of the recent trends and statistics in refolding technology development.
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Affiliation(s)
- Hisashi Mizutani
- Center for Information Biology, National Institute of Genetics, 1111 Yata Mishima, Shizuoka, 411-8540, Japan
| | - Hideaki Sugawara
- Center for Information Biology, National Institute of Genetics, 1111 Yata Mishima, Shizuoka, 411-8540, Japan.
| | - Ashley M Buckle
- The Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Takeshi Sangawa
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Ken-Ichi Miyazono
- Laboratory of Structural Biology and Food Biotechnology, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Jun Ohtsuka
- Laboratory of Structural Biology and Food Biotechnology, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Koji Nagata
- Laboratory of Structural Biology and Food Biotechnology, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Tomoki Shojima
- Laboratory of Structural Biology and Food Biotechnology, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Shohei Nosaki
- Laboratory of Structural Biology and Food Biotechnology, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yuqun Xu
- Laboratory of Structural Biology and Food Biotechnology, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Delong Wang
- Laboratory of Structural Biology and Food Biotechnology, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Xiao Hu
- Laboratory of Structural Biology and Food Biotechnology, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Masaru Tanokura
- Laboratory of Structural Biology and Food Biotechnology, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Kei Yura
- Center for Information Biology, National Institute of Genetics, 1111 Yata Mishima, Shizuoka, 411-8540, Japan.,Graduate School of Humanities and Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo, Tokyo, 112-8610, Japan.,Center for Simulation Science and Informational Biology, Ochanomizu University, 2-1-1 Otsuka, Bunkyo, Tokyo, 112-8610, Japan.,School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjyuku, Tokyo, 169-8555, Japan
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8
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Chen LH, Cai F, Zhang DJ, Zhang L, Zhu P, Gao S. Large-scale purification and characterization of recombinant human stem cell factor in Escherichia coli. Biotechnol Appl Biochem 2017; 64:509-518. [PMID: 27301759 DOI: 10.1002/bab.1517] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 06/06/2016] [Indexed: 11/07/2022]
Abstract
The pharmacological importance of recombinant human stem cell factor (rhSCF) has increased the demand to establish effective and large-scale production and purification processes. A good source of bioactive recombinant protein with capability of being scaled-up without losing activity has always been a challenge. The objectives of the study were the rapid and efficient pilot-scale expression and purification of rhSCF. The gene encoding stem cell factor (SCF) was cloned into pBV220 and transformed into Escherichia coli. The recombinant SCF was expressed and isolated using a procedure consisting of isolation of inclusion bodies (IBs), denaturation, and refolding followed by chromatographic steps toward purification. The yield of rhSCF reached 835.6 g/20 L, and the expression levels of rhSCF were about 33.9% of the total E. coli protein content. rhSCF was purified by isolation of IBs, denaturation, and refolding, followed by SP-Sepharose chromatography, Source 30 reversed-phase chromatography, and Q-Sepharose chromatography. This procedure was developed to isolate 5.5 g of rhSCF (99.5% purity) with specific activity at 0.96 × 106 IU/mg, endotoxin levels of pyrogen at 1.0 EU/mg, and bacterial DNA at 10 ng/mg. Pilot-scale fermentations and purifications were set up for the production of rhSCF that can be upscaled for industry.
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Affiliation(s)
- Liang-Hua Chen
- Institute of Ecological Forestry, Faculty of Forestry, Sichuan Agricultural University, Chengdu, Sichuan, People's Republic of China
| | - Feng Cai
- College of Life Sciences, Sichuan University, Chengdu, People's Republic of China
| | - Dan-Ju Zhang
- Institute of Ecological Forestry, Faculty of Forestry, Sichuan Agricultural University, Chengdu, Sichuan, People's Republic of China
| | - Li Zhang
- Institute of Ecological Forestry, Faculty of Forestry, Sichuan Agricultural University, Chengdu, Sichuan, People's Republic of China
| | - Peng Zhu
- Institute of Ecological Forestry, Faculty of Forestry, Sichuan Agricultural University, Chengdu, Sichuan, People's Republic of China
| | - Shun Gao
- Institute of Ecological Forestry, Faculty of Forestry, Sichuan Agricultural University, Chengdu, Sichuan, People's Republic of China.,State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, People's Republic of China
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9
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Ni H, Guo PC, Jiang WL, Fan XM, Luo XY, Li HH. Expression of nattokinase in Escherichia coli and renaturation of its inclusion body. J Biotechnol 2016; 231:65-71. [PMID: 27234878 DOI: 10.1016/j.jbiotec.2016.05.034] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 05/18/2016] [Accepted: 05/23/2016] [Indexed: 11/26/2022]
Abstract
Nattokinase is an important fibrinolytic enzyme with therapeutic applications for cardiovascular diseases. The full-length and mature nattokinase genes were cloned from Bacillus subtilis var. natto and expressed in pQE30 vector in Escherichia coli. The full-length gene expressed low nattokinase activity in the intracellular soluble and the medium fractions. The mature gene expressed low soluble nattokinase activity and large amount insoluble protein in inclusion bodies without enzyme activity. Large amount of refolding solutions (RSs) at different pH values were screening and RS-10 and RS-11 at pH 9 were selected to refold nattokinase inclusion bodies. The recombinant cells were lysed with 0.1mg/mL lysozyme and ultrasonic treatment. After centrifugation, the pellete was washed twice with 20mM Tris-HCl buffer (pH 7.5) containing 1% Triton X-100 to purify the inclusion bodies. The inclusion bodies were dissolved in water at pH 12.0 and refolded with RS-10. The refolded proteins showed 42.8IU/mg and 79.3IU/mg fibrinolytic activity by the traditional dilution method (20-fold dilution into RS-10) and the directly mixing the protein solution with equal volume RS-10, respectively, compared to the 52.0IU/mg of total water-soluble proteins from B. subtilis var. natto. This work demonstrated that the inclusion body of recombinant nattokinase expressed in E. coli could be simply refolded to the natural enzyme activity level by directly mixing the protein solution with equal volume refolding solution.
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Affiliation(s)
- He Ni
- Guangdong Provincial Key Lab of Biotechnology for Plant Development, College of Life Sciences, and Research and Development Center for Rare Animals, South China Normal University, Guangzhou 510631, China
| | - Peng-Cheng Guo
- Guangdong Provincial Key Lab of Biotechnology for Plant Development, College of Life Sciences, and Research and Development Center for Rare Animals, South China Normal University, Guangzhou 510631, China
| | - Wei-Ling Jiang
- Guangdong Provincial Key Lab of Biotechnology for Plant Development, College of Life Sciences, and Research and Development Center for Rare Animals, South China Normal University, Guangzhou 510631, China
| | - Xiao-Min Fan
- Guangdong Provincial Key Lab of Biotechnology for Plant Development, College of Life Sciences, and Research and Development Center for Rare Animals, South China Normal University, Guangzhou 510631, China
| | - Xiang-Yu Luo
- Guangdong Provincial Key Lab of Biotechnology for Plant Development, College of Life Sciences, and Research and Development Center for Rare Animals, South China Normal University, Guangzhou 510631, China; Guangzhou Huichuan Medical Technology Ltd., 211 Jinfu Building, 90 Qifu Road, Baiyun District, Guangzhou 510410, China
| | - Hai-Hang Li
- Guangdong Provincial Key Lab of Biotechnology for Plant Development, College of Life Sciences, and Research and Development Center for Rare Animals, South China Normal University, Guangzhou 510631, China.
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10
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Automated high-throughput dense matrix protein folding screen using a liquid handling robot combined with microfluidic capillary electrophoresis. Protein Expr Purif 2015; 120:138-47. [PMID: 26678961 DOI: 10.1016/j.pep.2015.11.015] [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: 09/24/2015] [Revised: 11/06/2015] [Accepted: 11/17/2015] [Indexed: 01/31/2023]
Abstract
Modern molecular genetics technology has made it possible to swiftly sequence, clone and mass-produce recombinant DNA for the purpose of expressing heterologous genes of interest; however, recombinant protein production systems have struggled to keep pace. Mammalian expression systems are typically favored for their ability to produce and secrete proteins in their native state, but bacterial systems benefit from rapid cell line development and robust growth. The primary drawback to prokaryotic expression systems are that recombinant proteins are generally not secreted at high levels or correctly folded, and are often insoluble, necessitating post-expression protein folding to obtain the active product. In order to harness the advantages of prokaryotic expression, high-throughput methods for executing protein folding screens and the subsequent analytics to identify lead conditions are required. Both of these tasks can be accomplished using a Biomek 3000 liquid handling robot to prepare the folding screen and to subsequently prepare the reactions for assessment using Caliper microfluidic capillary electrophoresis. By augmenting a protein folding screen with automation, the primary disadvantage of Escherichia coli expression has been mitigated, namely the labor intensive identification of the required protein folding conditions. Furthermore, a rigorous, quantitative method for identifying optimal protein folding buffer aids in the rapid development of an optimal production process.
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11
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Ling C, Zhang J, Lin D, Tao A. Approaches for the generation of active papain-like cysteine proteases from inclusion bodies of Escherichia coli. World J Microbiol Biotechnol 2015; 31:681-90. [PMID: 25792298 DOI: 10.1007/s11274-015-1804-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Accepted: 01/11/2015] [Indexed: 11/25/2022]
Abstract
Papain-like cysteine proteases are widely expressed, fulfill specific functions in extracellular matrix turnover, antigen presentation and processing events, and may represent viable drug targets for major diseases. In depth and rigorous studies of the potential for these proteins to be targets for drug development require sufficient amounts of protease protein that can be used for both experimental and therapeutic purposes. Escherichia coli was widely used to express papain-like cysteine proteases, but most of those proteases are produced in insoluble inclusion bodies that need solubilizing, refolding, purifying and activating. Refolding is the most critical step in the process of generating active cysteine proteases and the current approaches to refolding include dialysis, dilution and chromatography. Purification is mainly achieved by various column chromatography. Finally, the attained refolded proteases are examined regarding their protease structures and activities.
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Affiliation(s)
- Chunfang Ling
- School of Life Science, South China Normal University, 55# Zhongshan Road West, Tianhe District, Guangzhou, 510631, People's Republic of China
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12
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Calçada EO, Korsak M, Kozyreva T. Recombinant Intrinsically Disordered Proteins for NMR: Tips and Tricks. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 870:187-213. [PMID: 26387103 DOI: 10.1007/978-3-319-20164-1_6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The growing recognition of the several roles that intrinsically disordered proteins play in biology places an increasing importance on protein sample availability to allow the characterization of their structural and dynamic properties. The sample preparation is therefore the limiting step to allow any biophysical method being able to characterize the properties of an intrinsically disordered protein and to clarify the links between these properties and the associated biological functions. An increasing array of tools has been recruited to help prepare and characterize the structural and dynamic properties of disordered proteins. This chapter describes their sample preparation, covering the most common drawbacks/barriers usually found working in the laboratory bench. We want this chapter to be the bedside book of any scientist interested in preparing intrinsically disordered protein samples for further biophysical analysis.
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Affiliation(s)
- Eduardo O Calçada
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy.
| | - Magdalena Korsak
- Giotto Biotech, Via Madonna del Piano 6, 50019, Sesto Fiorentino, Italy.
| | - Tatiana Kozyreva
- Giotto Biotech, Via Madonna del Piano 6, 50019, Sesto Fiorentino, Italy.
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Tanca A, Abbondio M, Pisanu S, Pagnozzi D, Uzzau S, Addis MF. Critical comparison of sample preparation strategies for shotgun proteomic analysis of formalin-fixed, paraffin-embedded samples: insights from liver tissue. Clin Proteomics 2014; 11:28. [PMID: 25097466 PMCID: PMC4115481 DOI: 10.1186/1559-0275-11-28] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 07/03/2014] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND The growing field of formalin-fixed paraffin-embedded (FFPE) tissue proteomics holds promise for improving translational research. Direct tissue trypsinization (DT) and protein extraction followed by in solution digestion (ISD) or filter-aided sample preparation (FASP) are the most common workflows for shotgun analysis of FFPE samples, but a critical comparison of the different methods is currently lacking. EXPERIMENTAL DESIGN DT, FASP and ISD workflows were compared by subjecting to the same label-free quantitative approach three independent technical replicates of each method applied to FFPE liver tissue. Data were evaluated in terms of method reproducibility and protein/peptide distribution according to localization, MW, pI and hydrophobicity. RESULTS DT showed lower reproducibility, good preservation of high-MW proteins, a general bias towards hydrophilic and acidic proteins, much lower keratin contamination, as well as higher abundance of non-tryptic peptides. Conversely, FASP and ISD proteomes were depleted in high-MW proteins and enriched in hydrophobic and membrane proteins; FASP provided higher identification yields, while ISD exhibited higher reproducibility. CONCLUSIONS These results highlight that diverse sample preparation strategies provide significantly different proteomic information, and present typical biases that should be taken into account when dealing with FFPE samples. When a sufficient amount of tissue is available, the complementary use of different methods is suggested to increase proteome coverage and depth.
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Affiliation(s)
- Alessandro Tanca
- Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio, 07041 Alghero, Italy
| | - Marcello Abbondio
- Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio, 07041 Alghero, Italy
| | - Salvatore Pisanu
- Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio, 07041 Alghero, Italy
| | - Daniela Pagnozzi
- Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio, 07041 Alghero, Italy
| | - Sergio Uzzau
- Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio, 07041 Alghero, Italy ; Dipartimento di Scienze Biomediche, Università di Sassari, Viale San Pietro 43/B, 07100, Sassari, Italy
| | - Maria Filippa Addis
- Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio, 07041 Alghero, Italy
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The ToxAvapA toxin-antitoxin locus contributes to the survival of nontypeable Haemophilus influenzae during infection. PLoS One 2014; 9:e91523. [PMID: 24621787 PMCID: PMC3951411 DOI: 10.1371/journal.pone.0091523] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Accepted: 02/13/2014] [Indexed: 12/02/2022] Open
Abstract
Nontypeable Haemophilus influenzae (NTHi) is an opportunistic pathogen that is a common cause of acute and recurrent mucosal infections. One uncharacterized NTHi toxin-antitoxin (TA) module, NTHI1912-1913, is a host inhibition of growth (higBA) homologue. We hypothesized that this locus, which we designated toxAvapA, contributed to NTHi survival during infection. We deleted toxAvapA and determined that growth of the mutant in defined media was not different from the parent strain. We tested the mutant for persistence during long-term in vitro co-culture with primary human respiratory tissues, which revealed that the ΔtoxAvapA mutant was attenuated for survival. We then performed challenge studies using the chinchilla model of otitis media and determined that mutant survival was also reduced in vivo. Following purification, the toxin exhibited ribonuclease activity on RNA in vitro, while the antitoxin did not. A microarray comparison of the transcriptome revealed that the tryptophan biosynthetic regulon was significantly repressed in the mutant compared to the parent strain. HPLC studies of conditioned medium confirmed that there was no significant difference in the concentration of tryptophan remaining in the supernatant, indicating that the uptake of tryptophan by the mutant was not affected. We conclude that the role of the NTHi toxAvapA TA module in persistence following stress is multifactorial and includes effects on essential metabolic pathways.
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Lebendiker M, Danieli T. Production of prone-to-aggregate proteins. FEBS Lett 2013; 588:236-46. [DOI: 10.1016/j.febslet.2013.10.044] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 10/30/2013] [Accepted: 10/31/2013] [Indexed: 12/16/2022]
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Feng Y, Liu L, Wang J, Liu J, Hu W, Wang X, Yang Z. Integrated refolding techniques for Schistosoma japonicum MTH1 overexpressed as inclusion bodies in Escherichia coli. Protein Expr Purif 2012; 84:181-7. [PMID: 22641057 DOI: 10.1016/j.pep.2012.05.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Revised: 05/08/2012] [Accepted: 05/14/2012] [Indexed: 12/25/2022]
Abstract
The full-length cDNA of MTH1in Schistosoma japonicum was previously isolated. However, insoluble protein expression in Escherichia coli is the biggest bottleneck limiting biological and biophysical studies. Protein aggregation could not be significantly prevented using solubilization or refolding techniques, and denatured MTH1 protein could not be refolded to the native monomer form. Hence, integrating several refolding techniques within the protein refolding process of MTH1, a large amount of active MTH1 was obtained for protein crystallization. We primarily utilized the two-step-denaturing and refolding method and the protein refolding screening technique, as well as the continuous dialysis method. First, we identified the refolding buffer composition that allowed for successful refolding to overcome protein precipitation. Next, we used the two-step-denaturing and refolding method and the continuous dialysis method to suppress protein aggregation. In the end, we obtained 15 mg of active MTH1 monomer with 95% purity from 0.5l medium. Integrated refolding techniques proved to be excellent for obtaining the native monomer of S. japonicum MTH1 from inclusion bodies, paving the way for future biological and biophysical studies.
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Affiliation(s)
- Yanye Feng
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China.
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