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Nakahara Y, Kawaguchi T, Matsuda Y, Endo Y, Date M, Takahashi K, Kato K, Okasora T, Ejima D, Nagaki A. Spatiotemporal Control of Protein Refolding through Flash-Change Reaction Conditions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:8483-8492. [PMID: 38618876 DOI: 10.1021/acs.langmuir.4c00024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Recombinant protein production is an essential aspect of biopharmaceutical manufacturing, with Escherichia coli serving as a primary host organism. Protein refolding is vital for protein production; however, conventional refolding methods face challenges such as scale-up limitations and difficulties in controlling protein conformational changes on a millisecond scale. In this study, we demonstrate the novel application of flow microreactors (FMR) in controlling protein conformational changes on a millisecond scale, enabling efficient refolding processes and opening up new avenues in the science of FMR technology. FMR technology has been primarily employed for small-molecule synthesis, but our novel approach successfully expands its application to protein refolding, offering precise control of the buffer pH and solvent content. Using interleukin-6 as a model, the system yielded an impressive 96% pure refolded protein and allowed for gram-scale production. This FMR system allows flash changes in the reaction conditions, effectively circumventing protein aggregation during refolding. To the best of our knowledge, this is the first study to use FMR for protein refolding, which offers a more efficient and scalable method for protein production. The study results highlight the utility of the FMR as a high-throughput screening tool for streamlined scale-up and emphasize the importance of understanding and controlling intermediates in the refolding process. The FMR technique offers a promising approach for enhancing protein refolding efficiency and has demonstrated its potential in streamlining the process from laboratory-scale research to industrial-scale production, making it a game-changing technology in the field.
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Affiliation(s)
- Yuichi Nakahara
- Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki-Ku, Kawasaki 210-8681, Kanagawa, Japan
- Department of Chemistry, Graduate School of Science, Hokkaido University, Kita-10 Nishi-8, Kita-ku, Sapporo 060-0810, Hokkaido, Japan
| | - Tomoko Kawaguchi
- Department of Chemistry, Graduate School of Science, Hokkaido University, Kita-10 Nishi-8, Kita-ku, Sapporo 060-0810, Hokkaido, Japan
| | - Yutaka Matsuda
- Ajinomoto Bio-Pharma Services, 11040 Roselle Street, San Diego, California 92121, United States
| | - Yuta Endo
- Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki-Ku, Kawasaki 210-8681, Kanagawa, Japan
| | - Masayo Date
- Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki-Ku, Kawasaki 210-8681, Kanagawa, Japan
| | - Kazutoshi Takahashi
- Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki-Ku, Kawasaki 210-8681, Kanagawa, Japan
| | - Keisuke Kato
- Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki-Ku, Kawasaki 210-8681, Kanagawa, Japan
| | - Takahiro Okasora
- Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki-Ku, Kawasaki 210-8681, Kanagawa, Japan
| | - Daisuke Ejima
- Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki-Ku, Kawasaki 210-8681, Kanagawa, Japan
| | - Aiichiro Nagaki
- Department of Chemistry, Graduate School of Science, Hokkaido University, Kita-10 Nishi-8, Kita-ku, Sapporo 060-0810, Hokkaido, Japan
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2
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Arakawa T, Niikura T, Kita Y, Akuta T. Sodium Dodecyl Sulfate Analogs as a Potential Molecular Biology Reagent. Curr Issues Mol Biol 2024; 46:621-633. [PMID: 38248342 PMCID: PMC10814491 DOI: 10.3390/cimb46010040] [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: 12/14/2023] [Revised: 01/03/2024] [Accepted: 01/05/2024] [Indexed: 01/23/2024] Open
Abstract
In this study, we review the properties of three anionic detergents, sodium dodecyl sulfate (SDS), Sarkosyl, and sodium lauroylglutamate (SLG), as they play a critical role in molecular biology research. SDS is widely used in electrophoresis and cell lysis for proteomics. Sarkosyl and, more frequently, SDS are used for the characterization of neuropathological protein fibrils and the solubilization of proteins. Many amyloid fibrils are resistant to SDS or Sarkosyl to different degrees and, thus, can be readily isolated from detergent-sensitive proteins. SLG is milder than the above two detergents and has been used in the solubilization and refolding of proteins isolated from inclusion bodies. Here, we show that both Sarkosyl and SLG have been used for protein refolding, that the effects of SLG on the native protein structure are weaker for SLG, and that SLG readily dissociates from the native proteins. We propose that SLG may be effective in cell lysis for functional proteomics due to no or weaker binding of SLG to the native proteins.
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Affiliation(s)
- Tsutomu Arakawa
- Alliance Protein Labs, 13380 Pantera Rd., San Diego, CA 92130, USA;
| | - Takako Niikura
- Department of Information and Communication Sciences, Faculty of Science and Technology, Sophia University, Tokyo 102-8554, Japan;
| | - Yoshiko Kita
- Alliance Protein Labs, 13380 Pantera Rd., San Diego, CA 92130, USA;
| | - Teruo Akuta
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna, Takahagi-shi 318-0004, Japan;
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3
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Lyles KV, Thomas LS, Ouellette C, Cook LCC, Eichenbaum Z. HupZ, a Unique Heme-Binding Protein, Enhances Group A Streptococcus Fitness During Mucosal Colonization. Front Cell Infect Microbiol 2022; 12:867963. [PMID: 35774404 PMCID: PMC9237417 DOI: 10.3389/fcimb.2022.867963] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 05/09/2022] [Indexed: 11/13/2022] Open
Abstract
Group A Streptococcus (GAS) is a major pathogen that causes simple and invasive infections. GAS requires iron for metabolic processes and pathogenesis, and heme is its preferred iron source. We previously described the iron-regulated hupZ in GAS, showing that a recombinant HupZ-His6 protein binds and degrades heme. The His6 tag was later implicated in heme iron coordination by HupZ-His6. Hence, we tested several recombinant HupZ proteins, including a tag-free protein, for heme binding and degradation in vitro. We established that HupZ binds heme but without coordinating the heme iron. Heme-HupZ readily accepted exogenous imidazole as its axial heme ligand, prompting degradation. Furthermore, HupZ bound a fragment of heme c (whose iron is coordinated by the cytochrome histidine residue) and exhibited limited degradation. GAS, however, did not grow on a heme c fragment as an iron source. Heterologous HupZ expression in Lactococcus lactis increased heme b iron use. A GAS hupZ mutant showed reduced growth when using hemoglobin as an iron source, increased sensitivity to heme toxicity, and decreased fitness in a murine model for vaginal colonization. Together, the data demonstrate that HupZ contributes to heme metabolism and host survival, likely as a heme chaperone. HupZ is structurally similar to the recently described heme c-degrading enzyme, Pden_1323, suggesting that the GAS HupZ might be divergent to play a new role in heme metabolism.
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Affiliation(s)
- Kristin V. Lyles
- Department of Biology, Georgia State University, Atlanta, GA, United States
| | - Lamar S. Thomas
- Binghamton Biofilm Research Center, Department of Biology, Binghamton University, Binghamton, NY, United States
| | - Corbett Ouellette
- Department of Biology, Georgia State University, Atlanta, GA, United States
| | - Laura C. C. Cook
- Binghamton Biofilm Research Center, Department of Biology, Binghamton University, Binghamton, NY, United States
| | - Zehava Eichenbaum
- Department of Biology, Georgia State University, Atlanta, GA, United States
- *Correspondence: Zehava Eichenbaum,
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Sorokina I, Mushegian AR, Koonin EV. Is Protein Folding a Thermodynamically Unfavorable, Active, Energy-Dependent Process? Int J Mol Sci 2022; 23:521. [PMID: 35008947 PMCID: PMC8745595 DOI: 10.3390/ijms23010521] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/30/2021] [Accepted: 12/31/2021] [Indexed: 02/04/2023] Open
Abstract
The prevailing current view of protein folding is the thermodynamic hypothesis, under which the native folded conformation of a protein corresponds to the global minimum of Gibbs free energy G. We question this concept and show that the empirical evidence behind the thermodynamic hypothesis of folding is far from strong. Furthermore, physical theory-based approaches to the prediction of protein folds and their folding pathways so far have invariably failed except for some very small proteins, despite decades of intensive theory development and the enormous increase of computer power. The recent spectacular successes in protein structure prediction owe to evolutionary modeling of amino acid sequence substitutions enhanced by deep learning methods, but even these breakthroughs provide no information on the protein folding mechanisms and pathways. We discuss an alternative view of protein folding, under which the native state of most proteins does not occupy the global free energy minimum, but rather, a local minimum on a fluctuating free energy landscape. We further argue that ΔG of folding is likely to be positive for the majority of proteins, which therefore fold into their native conformations only through interactions with the energy-dependent molecular machinery of living cells, in particular, the translation system and chaperones. Accordingly, protein folding should be modeled as it occurs in vivo, that is, as a non-equilibrium, active, energy-dependent process.
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Affiliation(s)
| | - Arcady R. Mushegian
- Division of Molecular and Cellular Biosciences, National Science Foundation, Alexandria, VA 22314, USA;
- Clare Hall College, University of Cambridge, Cambridge CB3 9AL, UK
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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Kibria MG, Fukutani A, Akazawa-Ogawa Y, Hagihara Y, Kuroda Y. Anti-EGFR V HH Antibody under Thermal Stress Is Better Solubilized with a Lysine than with an Arginine SEP Tag. Biomolecules 2021; 11:biom11060810. [PMID: 34072518 PMCID: PMC8229009 DOI: 10.3390/biom11060810] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/15/2021] [Accepted: 05/26/2021] [Indexed: 02/06/2023] Open
Abstract
In this study, we assessed the potential of arginine and lysine solubility-enhancing peptide (SEP) tags to control the solubility of a model protein, anti-EGFR VHH-7D12, in a thermally denatured state at a high temperature. We produced VHH-7D12 antibodies attached with a C-terminal SEP tag made of either five or nine arginines or lysines (7D12-C5R, 7D12-C9R, 7D12-C5K and 7D12-C9K, respectively). The 5-arginine and 5-lysine SEP tags increased the E. coli expression of VHH-7D12 by over 80%. Biophysical and biochemical analysis confirmed the native-like secondary and tertiary structural properties and the monomeric nature of all VHH-7D12 variants. Moreover, all VHH-7D12 variants retained a full binding activity to the EGFR extracellular domain. Finally, thermal stress with 45-minute incubation at 60 and 75 °C, where VHH-7D12 variants are unfolded, showed that the untagged VHH-7D12 formed aggregates in all of the four buffers, and the supernatant protein concentration was reduced by up to 35%. 7D12-C5R and 7D12-C9R did not aggregate in Na-acetate (pH 4.7) and Tris-HCl (pH 8.5) but formed aggregates in phosphate buffer (PB, pH 7.4) and phosphate buffer saline (PBS, pH 7.4). The lysine tags (either C5K or C9K) had the strongest solubilization effect, and both 7D12-C5K and 7D12-C9K remained in the supernatant. Altogether, our results indicate that, under a thermal stress condition, the lysine SEP tags solubilization effect is more potent than that of an arginine SEP tags, and the SEP tags did not affect the structural and functional properties of the protein.
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Affiliation(s)
- Md. Golam Kibria
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Nakamachi, Koganei-shi, Tokyo 184-8588, Japan; (M.G.K.); (A.F.)
| | - Akari Fukutani
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Nakamachi, Koganei-shi, Tokyo 184-8588, Japan; (M.G.K.); (A.F.)
| | - Yoko Akazawa-Ogawa
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-8-31, Midorigaoka, Ikeda, Osaka 563-8577, Japan; (Y.A.-O.); (Y.H.)
| | - Yoshihisa Hagihara
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-8-31, Midorigaoka, Ikeda, Osaka 563-8577, Japan; (Y.A.-O.); (Y.H.)
| | - Yutaka Kuroda
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Nakamachi, Koganei-shi, Tokyo 184-8588, Japan; (M.G.K.); (A.F.)
- Correspondence: ; Tel./Fax: +81-42-388-7794
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6
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Pauk JN, Raju Palanisamy J, Kager J, Koczka K, Berghammer G, Herwig C, Veiter L. Advances in monitoring and control of refolding kinetics combining PAT and modeling. Appl Microbiol Biotechnol 2021; 105:2243-2260. [PMID: 33598720 PMCID: PMC7954745 DOI: 10.1007/s00253-021-11151-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 01/19/2021] [Accepted: 01/27/2021] [Indexed: 12/21/2022]
Abstract
Overexpression of recombinant proteins in Escherichia coli results in misfolded and non-active protein aggregates in the cytoplasm, so-called inclusion bodies (IB). In recent years, a change in the mindset regarding IBs could be observed: IBs are no longer considered an unwanted waste product, but a valid alternative to produce a product with high yield, purity, and stability in short process times. However, solubilization of IBs and subsequent refolding is necessary to obtain a correctly folded and active product. This protein refolding process is a crucial downstream unit operation-commonly done as a dilution in batch or fed-batch mode. Drawbacks of the state-of-the-art include the following: the large volume of buffers and capacities of refolding tanks, issues with uniform mixing, challenging analytics at low protein concentrations, reaction kinetics in non-usable aggregates, and generally low re-folding yields. There is no generic platform procedure available and a lack of robust control strategies. The introduction of Quality by Design (QbD) is the method-of-choice to provide a controlled and reproducible refolding environment. However, reliable online monitoring techniques to describe the refolding kinetics in real-time are scarce. In our view, only monitoring and control of re-folding kinetics can ensure a productive, scalable, and versatile platform technology for re-folding processes. For this review, we screened the current literature for a combination of online process analytical technology (PAT) and modeling techniques to ensure a controlled refolding process. Based on our research, we propose an integrated approach based on the idea that all aspects that cannot be monitored directly are estimated via digital twins and used in real-time for process control. KEY POINTS: • Monitoring and a thorough understanding of refolding kinetics are essential for model-based control of refolding processes. • The introduction of Quality by Design combining Process Analytical Technology and modeling ensures a robust platform for inclusion body refolding.
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Affiliation(s)
- Jan Niklas Pauk
- Research Area Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, Vienna University of Technology, Gumpendorferstrasse 1a/166, 1060, Vienna, Austria
- Competence Center CHASE GmbH, Altenbergerstraße 69, 4040, Linz, Austria
| | - Janani Raju Palanisamy
- Research Area Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, Vienna University of Technology, Gumpendorferstrasse 1a/166, 1060, Vienna, Austria
| | - Julian Kager
- Research Area Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, Vienna University of Technology, Gumpendorferstrasse 1a/166, 1060, Vienna, Austria
| | - Krisztina Koczka
- Bilfinger Industrietechnik Salzburg GmbH, Mooslackengasse 17, 1190, Vienna, Austria
| | - Gerald Berghammer
- Bilfinger Industrietechnik Salzburg GmbH, Mooslackengasse 17, 1190, Vienna, Austria
| | - Christoph Herwig
- Research Area Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, Vienna University of Technology, Gumpendorferstrasse 1a/166, 1060, Vienna, Austria.
| | - Lukas Veiter
- Research Area Biochemical Engineering, Institute of Chemical, Environmental and Bioscience Engineering, Vienna University of Technology, Gumpendorferstrasse 1a/166, 1060, Vienna, Austria
- Competence Center CHASE GmbH, Altenbergerstraße 69, 4040, Linz, Austria
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7
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Fathi-Roudsari M, Maghsoudi A, Maghsoudi N, Niazi S, Soleiman M. Efficient refolding of recombinant reteplase expressed in Escherichia coli strains using response surface methodology. Int J Biol Macromol 2020; 164:1321-1327. [PMID: 32698065 DOI: 10.1016/j.ijbiomac.2020.07.183] [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: 03/03/2020] [Revised: 07/12/2020] [Accepted: 07/17/2020] [Indexed: 11/19/2022]
Abstract
Reteplase is a deleted variant of human tissue plasminogen activator with a complex structure containing nine disulfide bonds. Reteplase is expressed as inclusion bodies in Escherichia coli and needs the additional step of refolding for activation. In this study an experimental design was performed to find the optimal refolding condition for reteplase. The influence of 14 chemical additives was assessed by one factor at a time method and then Taguchi design followed by response surface methodology was employed to find compounds with most significant effects on reteplase refolding and their optimum concentration. We found that 0.13 M histidine, 1.64 M methionine, 0.33 M cysteine, and 0.34 M arginine in addition to the GSH/GSSG is the optimal condition for refolding of reteplase. We also investigated the refolding yield for inclusion bodies obtained from different E. coli strains and found that BL21 (DE3) has the best recovery yield in comparison to Rosetta-gami and Shuffle T7.
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Affiliation(s)
| | | | - Nader Maghsoudi
- Neuroscience Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Sepideh Niazi
- National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Morvarid Soleiman
- National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
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8
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Takakura Y, Asano Y. Purification, characterization, and gene cloning of a novel aminoacylase from Burkholderia sp. strain LP5_18B that efficiently catalyzes the synthesis of N-lauroyl-l-amino acids. Biosci Biotechnol Biochem 2019; 83:1964-1973. [PMID: 31200632 DOI: 10.1080/09168451.2019.1630255] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
An N-lauroyl-l-phenylalanine-producing bacterium, identified as Burkholderia sp. strain LP5_18B, was isolated from a soil sample. The enzyme was purified from the cell-free extract of the strain and shown to catalyze degradation and synthesis activities toward various N-acyl-amino acids. N-lauroyl-l-phenylalanine and N-lauroyl-l-arginine were obtained with especially high yields (51% and 89%, respectively) from lauric acid and l-phenylalanine or l-arginine by the purified enzyme in an aqueous system. The gene encoding the novel aminoacylase was cloned from Burkholderia sp. strain LP5_18B and expressed in Escherichia coli. The gene contains an open reading frame of 1,323 nucleotides. The deduced protein sequence encoded by the gene has approximately 80% amino acid identity to several hydratase of Burkholderia. The addition of zinc sulfate increased the aminoacylase activity of the recombinant E. coli strain.
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Affiliation(s)
- Yasuaki Takakura
- Research Institute for Bioscience Product & Fine Chemicals, Ajinomoto Co., Inc ., Kawasaki , Japan
| | - Yasuhisa Asano
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University , Toyama , Japan.,Asano Active Enzyme Molecule Project, ERATO, JST , Toyama , Japan
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9
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The NT11, a novel fusion tag for enhancing protein expression in Escherichia coli. Appl Microbiol Biotechnol 2019; 103:2205-2216. [DOI: 10.1007/s00253-018-09595-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 12/20/2018] [Indexed: 02/06/2023]
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10
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Safdari Y. Engineering of single chain antibodies for solubility. Int Immunopharmacol 2018; 55:86-97. [DOI: 10.1016/j.intimp.2017.11.046] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 11/16/2017] [Accepted: 11/30/2017] [Indexed: 11/30/2022]
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11
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Computer Simulation and Additive-Based Refolding Process of Cysteine-Rich Proteins: VEGF-A as a Model. Int J Pept Res Ther 2017. [DOI: 10.1007/s10989-017-9644-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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12
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Yoshizawa S, Arakawa T, Shiraki K. Thermal aggregation of human immunoglobulin G in arginine solutions: Contrasting effects of stabilizers and destabilizers. Int J Biol Macromol 2017. [DOI: 10.1016/j.ijbiomac.2017.06.085] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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13
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Krishnamoorthy A, Witkowski A, Tran JJ, Weers PMM, Ryan RO. Characterization of secondary structure and lipid binding behavior of N-terminal saposin like subdomain of human Wnt3a. Arch Biochem Biophys 2017; 630:38-46. [PMID: 28754322 DOI: 10.1016/j.abb.2017.07.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 07/14/2017] [Accepted: 07/24/2017] [Indexed: 02/06/2023]
Abstract
Wnt signaling is essential for embryonic development and adult homeostasis in multicellular organisms. A conserved feature among Wnt family proteins is the presence of two structural domains. Within the N-terminal (NT) domain there exists a motif that is superimposable upon saposin-like protein (SAPLIP) family members. SAPLIPs are found in plants, microbes and animals and possess lipid surface seeking activity. To investigate the function of the Wnt3a saposin-like subdomain (SLD), recombinant SLD was studied in isolation. Bacterial expression of this Wnt fragment was achieved only when the core SLD included 82 NT residues of Wnt3a (NT-SLD). Unlike SAPLIPs, NT-SLD required the presence of detergent to achieve solubility at neutral pH. Deletion of two hairpin loop extensions present in NT-SLD, but not other SAPLIPs, had no effect on the solubility properties of NT-SLD. Far UV circular dichroism spectroscopy of NT-SLD yielded 50-60% α-helix secondary structure. Limited proteolysis of isolated NT-SLD in buffer and detergent micelles showed no differences in cleavage kinetics. Unlike prototypical saposins, NT-SLD exhibited weak membrane-binding affinity and lacked cell lytic activity. In cell-based canonical Wnt signaling assays, NT-SLD was unable to induce stabilization of β-catenin or modulate the extent of β-catenin stabilization induced by full-length Wnt3a. Taken together, the results indicate neighboring structural elements within full-length Wnt3a affect SLD conformational stability. Moreover, SLD function(s) in Wnt proteins appear to have evolved away from those commonly attributed to SAPLIP family members.
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Affiliation(s)
- Aparna Krishnamoorthy
- Department of Nutritional Sciences and Toxicology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Andrzej Witkowski
- Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr. Way, Oakland, CA 94609, USA
| | - Jesse J Tran
- Department of Chemistry and Biochemistry, California State University, Long Beach, CA 90840, USA
| | - Paul M M Weers
- Department of Chemistry and Biochemistry, California State University, Long Beach, CA 90840, USA
| | - Robert O Ryan
- Department of Nutritional Sciences and Toxicology, University of California Berkeley, Berkeley, CA 94720, USA; Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr. Way, Oakland, CA 94609, USA.
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15
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Fan J, Wang Z, Huang L, Shen Y. Efficient refolding of the bifunctional therapeutic fusion protein VAS-TRAIL by a triple agent solution. Protein Expr Purif 2015; 125:68-73. [PMID: 26358405 DOI: 10.1016/j.pep.2015.09.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 09/04/2015] [Accepted: 09/05/2015] [Indexed: 11/15/2022]
Abstract
VAS-TRAIL is a bifunctional fusion protein that combines anti-angiogenic activity with tumor-selective apoptotic activity for enhanced anti-tumor efficacy. VAS-TRAIL is expressed as inclusion body in Escherichia coli, but protein refolding is difficult to achieve and results in low yields of bioactive protein. In this study, we describe an efficient method for VAS-TRAIL refolding. The solubilization of aggregated VAS-TRAIL was achieved by a triple agent solution, which consists of an alkaline solution (pH 11.5) containing 0.4M l-arginine and 2M urea. The solubilized protein showed high purity and preserved secondary structure according to fluorescence properties. VAS-TRAIL refolding was performed through stepwise dialysis and resulted in more than 50% recovery of the soluble protein. The function of l-arginine was additive with alkaline pH, as shown by the significant improvement in refolding yield (≈30%) by l-arginine-containing solubilization solutions compared with alkaline solubilization solutions without l-arginine. The refolded VAS-TRAIL also showed β-sheet structures and the propensity for oligomerization. Bioassays showed that the refolded fusion protein exhibited the expected activities, including its apoptotic activities toward tumor and endothelial cells, which proposed its promising therapeutic potential.
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Affiliation(s)
- Jiying Fan
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, China
| | - Zhanqing Wang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, China
| | - Liying Huang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, China
| | - Yaling Shen
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, China.
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16
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Singh A, Upadhyay V, Upadhyay AK, Singh SM, Panda AK. Protein recovery from inclusion bodies of Escherichia coli using mild solubilization process. Microb Cell Fact 2015; 14:41. [PMID: 25889252 PMCID: PMC4379949 DOI: 10.1186/s12934-015-0222-8] [Citation(s) in RCA: 287] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 03/06/2015] [Indexed: 11/13/2022] Open
Abstract
Formation of inclusion bodies in bacterial hosts poses a major challenge for large scale recovery of bioactive proteins. The process of obtaining bioactive protein from inclusion bodies is labor intensive and the yields of recombinant protein are often low. Here we review the developments in the field that are targeted at improving the yield, as well as quality of the recombinant protein by optimizing the individual steps of the process, especially solubilization of the inclusion bodies and refolding of the solubilized protein. Mild solubilization methods have been discussed which are based on the understanding of the fact that protein molecules in inclusion body aggregates have native-like structure. These methods solubilize the inclusion body aggregates while preserving the native-like protein structure. Subsequent protein refolding and purification results in high recovery of bioactive protein. Other parameters which influence the overall recovery of bioactive protein from inclusion bodies have also been discussed. A schematic model describing the utility of mild solubilization methods for high throughput recovery of bioactive protein has also been presented.
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Affiliation(s)
- Anupam Singh
- Product Development Cell, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India.
| | - Vaibhav Upadhyay
- Product Development Cell, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India.
| | - Arun Kumar Upadhyay
- Product Development Cell, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India.
| | - Surinder Mohan Singh
- Product Development Cell, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India.
| | - Amulya Kumar Panda
- Product Development Cell, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Qi X, Sun Y, Xiong S. A single freeze-thawing cycle for highly efficient solubilization of inclusion body proteins and its refolding into bioactive form. Microb Cell Fact 2015; 14:24. [PMID: 25879903 PMCID: PMC4343044 DOI: 10.1186/s12934-015-0208-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 02/13/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mild solubilization of inclusion bodies has attracted attention in recent days, with an objective to preserve the existing native-like secondary structure of proteins, reduce protein aggregation during refolding and recovering high amount of bioactive proteins from inclusion bodies. RESULTS Here we presented an efficient method for mild solubilization of inclusion bodies by using a freeze-thawing process in the presence of low concentration of urea. We used two different proteins to demonstrate the advantage of this method over the traditional urea-denatured method: enhanced green fluorescent protein (EGFP) and the catalytic domain of human macrophage metalloelastase (MMP-12_CAT). Firstly, PBS buffer at pH 8 containing different molar concentration of urea (0-8 M) were used to solubilize EGFP and MMP-12-CAT inclusion bodies and the solubility achieved in 2 M urea in PBS buffer by freeze-thawing method was comparable to that of PBS buffer containing 8 M urea by traditional urea-denatured method. Secondly, different solvents were used to solubilize EGFP and MMP-12_CAT from inclusion bodies and the results indicated that a wide range of buffers containing 2 M urea could efficiently solubilize EGFP and MMP-12_CAT inclusion bodies by freeze-thawing method. Thirdly, the effect of pH and freezing temperature on the solubility of EGFP and MMP-12_CAT inclusion bodies were studied, revealing that solubilization of inclusion bodies by freeze-thawing method is pH dependent and the optimal freezing temperature indicated here is -20°C. Forth, the solubilized EGFP and MMP-12_CAT from inclusion bodies were refolded by rapid dilution and dialysis, respectively. The results showed that the refolded efficiency is much higher (more than twice) from freeze-thawing method than the traditional urea-denatured method. The freeze-thawing method containing 2 M urea also effectively solubilized a number of proteins as inclusion bodies in E.coli. CONCLUSIONS Mild solubilization of inclusion body proteins using the freeze-thawing method is simple, highly efficient and generally applicable. The method can be utilized to prepare large quantities of bioactive soluble proteins from inclusion bodies for basic research and industrial purpose.
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Affiliation(s)
- Xingmei Qi
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, Jiangsu, 215123, China.
| | - Yifan Sun
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, Jiangsu, 215123, China.
| | - Sidong Xiong
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, Jiangsu, 215123, China.
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18
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19
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Refolding techniques for recovering biologically active recombinant proteins from inclusion bodies. Biomolecules 2014; 4:235-51. [PMID: 24970214 PMCID: PMC4030991 DOI: 10.3390/biom4010235] [Citation(s) in RCA: 157] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 01/23/2014] [Accepted: 02/10/2014] [Indexed: 02/02/2023] Open
Abstract
Biologically active proteins are useful for studying the biological functions of genes and for the development of therapeutic drugs and biomaterials in a biotechnology industry. Overexpression of recombinant proteins in bacteria, such as Escherichia coli, often results in the formation of inclusion bodies, which are protein aggregates with non-native conformations. As inclusion bodies contain relatively pure and intact proteins, protein refolding is an important process to obtain active recombinant proteins from inclusion bodies. However, conventional refolding methods, such as dialysis and dilution, are time consuming and, often, recovered yields of active proteins are low, and a trial-and-error process is required to achieve success. Recently, several approaches have been reported to refold these aggregated proteins into an active form. The strategies largely aim at reducing protein aggregation during the refolding procedure. This review focuses on protein refolding techniques using chemical additives and laminar flow in microfluidic chips for the efficient recovery of active proteins from inclusion bodies.
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20
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Ramón A, Señorale-Pose M, Marín M. Inclusion bodies: not that bad…. Front Microbiol 2014; 5:56. [PMID: 24592259 PMCID: PMC3924032 DOI: 10.3389/fmicb.2014.00056] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Accepted: 01/28/2014] [Indexed: 12/03/2022] Open
Abstract
The formation of inclusion bodies (IBs) constitute a frequent event during the production of heterologous proteins in bacterial hosts. Although the mechanisms leading to their formation are not completely understood, empirical data have been exploited trying to predict the aggregation propensity of specific proteins while a great number of strategies have been developed to avoid the generation of IBs. However, in many cases, the formation of such aggregates can be considered an advantage for basic research as for protein production. In this review, we focus on this positive side of IBs formation in bacteria. We present a compilation on recent advances on the understanding of IBs formation and their utilization as a model to understand protein aggregation and to explore strategies to control this process. We include recent information about their composition and structure, their use as an attractive approach to produce low cost proteins and other promising applications in Biomedicine.
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Affiliation(s)
- Ana Ramón
- Sección Bioquímica, Facultad de Ciencias, Universidad de la República Montevideo, Uruguay
| | - Mario Señorale-Pose
- Sección Bioquímica, Facultad de Ciencias, Universidad de la República Montevideo, Uruguay
| | - Mónica Marín
- Sección Bioquímica, Facultad de Ciencias, Universidad de la República Montevideo, Uruguay
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21
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Efficient production of anti-fluorescein and anti-lysozyme as single-chain anti-body fragments (scFv) by Brevibacillus expression system. Protein Expr Purif 2013; 91:184-91. [PMID: 23973803 DOI: 10.1016/j.pep.2013.08.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 08/02/2013] [Accepted: 08/06/2013] [Indexed: 11/21/2022]
Abstract
Expression of scFv in Brevibacillus choshinensis was tested using combinations of three different promoters and four different secretion signals. Two model scFv constructs, i.e., His-scFvFLU and His-scFvHEL, were successfully expressed with some of the combinations. Ni Sepharose column and size exclusion chromatography resulted in fairly pure preparations of these two proteins. The purified His-scFvFLU inhibited fluorescence from fluorescein, while the purified His-scFvHEL inhibited lysozyme activity. Relatively high yield of His-scFvFLU (∼40%) and His-scFvHEL (∼30%) was achieved with the expression and purification system described here.
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22
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Congyu K, Wujuan S, Qunzheng Z, Xindu G. Refolding of urea-denaturedα-chymotrypsin by protein-folding liquid chromatography. Biomed Chromatogr 2012; 27:433-9. [DOI: 10.1002/bmc.2810] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2012] [Revised: 08/01/2012] [Accepted: 08/01/2012] [Indexed: 11/10/2022]
Affiliation(s)
- Ke Congyu
- College of Chemistry & Chemical Engineering; Xi' An ShiYou University; Xi'an; 710065; China
| | - Sun Wujuan
- College of Chemistry & Chemical Engineering; Xi' An ShiYou University; Xi'an; 710065; China
| | - Zhang Qunzheng
- College of Chemistry & Chemical Engineering; Xi' An ShiYou University; Xi'an; 710065; China
| | - Geng Xindu
- Institute of Modern Separation Science, Shaanxi Key Laboratory of Modern Separation Science; Northwest University; Xi'an; 710069; China
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23
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Refolding Technology for scFv Using a New Detergent, N-Lauroyl-L-glutamate and Arginine. Antibodies (Basel) 2012. [DOI: 10.3390/antib1020215] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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24
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Suzuki M, Yokoyama KI, Lee YH, Goto Y. A Two-Step Refolding of Acid-Denatured Microbial Transglutaminase Escaping from the Aggregation-Prone Intermediate. Biochemistry 2011; 50:10390-8. [DOI: 10.1021/bi2010619] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mototaka Suzuki
- Institute for Innovation, Ajinomoto Co., Inc., Suzuki-cho 1-1, Kawasaki-ku, Kawasaki
210-8681, Japan
- Institute
for Protein Research, Osaka University,
Yamadaoka 3-2, Suita, Osaka 565-0871,
Japan
| | - Kei-ichi Yokoyama
- Institute for Innovation, Ajinomoto Co., Inc., Suzuki-cho 1-1, Kawasaki-ku, Kawasaki
210-8681, Japan
| | - Young-Ho Lee
- Institute
for Protein Research, Osaka University,
Yamadaoka 3-2, Suita, Osaka 565-0871,
Japan
| | - Yuji Goto
- Institute
for Protein Research, Osaka University,
Yamadaoka 3-2, Suita, Osaka 565-0871,
Japan
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25
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Ariki R, Hirano A, Arakawa T, Shiraki K. Drug solubilization effect of lauroyl-L-glutamate. J Biochem 2011; 151:27-33. [PMID: 21949409 DOI: 10.1093/jb/mvr117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
This article proposes a new technique for the solubilization of poorly soluble drugs using lauroyl-L-glutamate, which is one of the amino acid detergents, with additional small additives. Lauroyl-L-glutamate was highly effective in solubilizing long-chain alkyl gallates, e.g. dodecyl gallate. Furthermore, lauroyl-L-glutamate and small additives, particularly arginine, acted to increase the solubility of alkyl gallates. The synergistic effect was not observed by sodium dodecyl sulphate with arginine. The solubilizing system can be applied to other drugs because of the low toxicity of both lauroyl-L-glutamate and arginine.
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Affiliation(s)
- Ryosuke Ariki
- Institute of Applied Physics, University of Tsukuba, Tsukuba, Ibaraki 305-8573, Japan
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26
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Singh SM, Sharma A, Upadhyay AK, Singh A, Garg LC, Panda AK. Solubilization of inclusion body proteins using n-propanol and its refolding into bioactive form. Protein Expr Purif 2011; 81:75-82. [PMID: 21964443 DOI: 10.1016/j.pep.2011.09.004] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Revised: 09/05/2011] [Accepted: 09/08/2011] [Indexed: 11/28/2022]
Abstract
Inclusion bodies of recombinant human growth hormone (r-hGH) were isolated from Escherichia coli, enriched and solubilized in 100mM Tris buffer containing 6M n-propanol and 2M urea. Around 4 mg/ml of r-hGH from inclusion bodies were solubilized in 6M n-propanol-based buffer containing 2M urea. Existence of native-like secondary structure of r-hGH in 6M n-propanol solution was confirmed by CD and fluorescence spectra. Solubilized r-hGH was subsequently refolded by pulsatile dilution, purified to homogeneity and found to be functionally active. Tris buffer containing 6M n-propanol and 2M urea also effectively solubilized a number of proteins expressed as inclusion bodies in E. coli. Mild solubilization of inclusion body proteins, chaotropic effect of n-propanol at high concentration and kosmotropic effect at lower concentration helped in improved refolding of the solubilized protein. Around 40% of the r-hGH in the form of inclusion body aggregates was refolded into bioactive form while using n-propanol as solubilization agent. Solubilization with 6M n-propanol solution thus can be a viable alternative for achieving high throughput recovery of bioactive protein from inclusion bodies of E. coli.
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Affiliation(s)
- Surinder M Singh
- Product Development Cell, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Aparna Sharma
- Product Development Cell, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Arun K Upadhyay
- Product Development Cell, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Anupam Singh
- Product Development Cell, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Lalit C Garg
- Product Development Cell, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Amulya K Panda
- Product Development Cell, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India.
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27
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Kudou M, Ejima D, Sato H, Yumioka R, Arakawa T, Tsumoto K. Refolding single-chain antibody (scFv) using lauroyl-l-glutamate as a solubilization detergent and arginine as a refolding additive. Protein Expr Purif 2011; 77:68-74. [DOI: 10.1016/j.pep.2010.12.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Revised: 12/10/2010] [Accepted: 12/13/2010] [Indexed: 01/29/2023]
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