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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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Wang Q, Liu Y, Zhang C, Guo F, Feng C, Li X, Shi H, Su Z. High hydrostatic pressure enables almost 100% refolding of recombinant human ciliary neurotrophic factor from inclusion bodies at high concentration. Protein Expr Purif 2017; 133:152-159. [PMID: 28323167 DOI: 10.1016/j.pep.2017.03.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 03/12/2017] [Accepted: 03/14/2017] [Indexed: 11/28/2022]
Abstract
Protein refolding from inclusion bodies (IBs) often encounters a problem of low recovery at high protein concentration. In this study, we demonstrated that high hydrostatic pressure (HHP) could simultaneously achieve high refolding concentration and high refolding yield for IBs of recombinant human ciliary neurotrophic factor (rhCNTF), a potential therapeutic for neurodegenerative diseases. The use of dilution refolding obtained 18% recovery at 3 mg/mL, even in the presence of 4 M urea. In contrast, HHP refolding could efficiently increase the recovery up to almost 100% even at 4 mg/mL. It was found that in the dilution, hydrophobic aggregates were the off-path products and their amount increased with the protein concentration. However, HHP could effectively minimize the formation of hydrophobic aggregates, leading to almost complete conversion of the rhCNTF IBs to the correct configuration. The stable operation range of concentration is 0.5-4.0 mg/mL, in which the refolding yield was almost 100%. Compared with the literatures where HHP failed to increase the refolding yield beyond 90%, the reason could be attributed to the structural difference that rhCNTF has no disulfide bond and is a monomeric protein. After purification by one-step of anionic chromatography, the purity of rhCNTF reached 95% with total process recovery of 54.1%. The purified rhCNTF showed similar structure and in vitro bioactivity to the native species. The whole process featured integration of solubilization/refolding, a high refolding yield of 100%, a high concentration of 4 mg/mL, and a simple chromatography to ensure a high productivity.
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Affiliation(s)
- Qi Wang
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, No.1 Beierjie Street, Zhongguancun, Haidian District, Beijing 100190, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yongdong Liu
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, No.1 Beierjie Street, Zhongguancun, Haidian District, Beijing 100190, PR China.
| | - Chun Zhang
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, No.1 Beierjie Street, Zhongguancun, Haidian District, Beijing 100190, PR China
| | - Fangxia Guo
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, No.1 Beierjie Street, Zhongguancun, Haidian District, Beijing 100190, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Cui Feng
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, No.1 Beierjie Street, Zhongguancun, Haidian District, Beijing 100190, PR China
| | - Xiunan Li
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, No.1 Beierjie Street, Zhongguancun, Haidian District, Beijing 100190, PR China
| | - Hong Shi
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, No.1 Beierjie Street, Zhongguancun, Haidian District, Beijing 100190, PR China
| | - Zhiguo Su
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, No.1 Beierjie Street, Zhongguancun, Haidian District, Beijing 100190, PR China.
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Katayama Y, Suzuki T, Ebisawa T, Ohtsuka J, Wang S, Natsume R, Lo YH, Senda T, Nagamine T, Hull JJ, Matsumoto S, Nagasawa H, Nagata K, Tanokura M. A class-A GPCR solubilized under high hydrostatic pressure retains its ligand binding ability. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2145-2151. [PMID: 27342372 DOI: 10.1016/j.bbamem.2016.06.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 06/16/2016] [Accepted: 06/17/2016] [Indexed: 11/17/2022]
Abstract
The effect of high hydrostatic pressure (HHP) on the solubilization of a class-A G protein-coupled receptor, the silkmoth pheromone biosynthesis-activating neuropeptide receptor (PBANR), was investigated. PBANR was expressed in expresSF+ insect cells as a C-terminal fusion protein with EGFP. The membrane fraction was subjected to HHP treatment (200MPa) at room temperature for 1-16h in the presence of 0-2.0% (w/v) n-dodecyl-β-D-maltopyranoside (DDM). The solubilization yield of PBANR-EGFP in the presence of 0.6% (w/v) DDM increased to ~1.5-fold after 1h HHP treatment. Fluorescence-detection size-exclusion chromatography demonstrated that the PBANR-EGFP ligand binding ability was retained after HHP-mediated solubilization. The PBANR-EGFP solubilized with 1.0% DDM under HHP at room temperature for 6h retained ligand binding ability, whereas solubilization in the absence of HHP treatment resulted in denaturation.
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Affiliation(s)
- Yukie Katayama
- 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
| | - Tatsuya Suzuki
- 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
| | - Tatsuki Ebisawa
- 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
- 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
| | - Shipeng Wang
- 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
| | - Ryo Natsume
- Department of Green and Sustainable Chemistry, School of Engineering, Tokyo Denki University, 5 Senju Asahi-cho, Adachi-ku, Tokyo 120-8551, Japan
| | - Yu-Hua Lo
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Toshiya Senda
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Toshihiro Nagamine
- Molecular Entomology Laboratory, RIKEN Advanced Science Institute, Wako, Saitama 351-0198, Japan
| | - J Joe Hull
- USDA-ARS Arid Land Agricultural Research Center, Maricopa, AZ, USA
| | - Shogo Matsumoto
- Molecular Entomology Laboratory, RIKEN Advanced Science Institute, Wako, Saitama 351-0198, Japan
| | - Hiromichi Nagasawa
- 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; College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
| | - Koji Nagata
- 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
- 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.
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Takayanagi A, Miyakawa T, Asano A, Ohtsuka J, Tanokura M, Arioka M. Expression, purification, refolding, and enzymatic characterization of two secretory phospholipases A2 from Neurospora crassa. Protein Expr Purif 2015; 115:69-75. [DOI: 10.1016/j.pep.2015.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 08/06/2015] [Accepted: 08/08/2015] [Indexed: 10/23/2022]
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Lemke LS, Chura-Chambi RM, Rodrigues D, Cussiol JRR, Malavasi NV, Alegria TGP, Netto LES, Morganti L. Investigation on solubilization protocols in the refolding of the thioredoxin TsnC from Xylella fastidiosa by high hydrostatic pressure approach. Protein Expr Purif 2014; 106:72-7. [PMID: 25448595 DOI: 10.1016/j.pep.2014.10.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 10/21/2014] [Accepted: 10/23/2014] [Indexed: 01/27/2023]
Abstract
The lack of efficient refolding methodologies must be overcome to take full advantage of the fact that bacteria express high levels of aggregated recombinant proteins. High hydrostatic pressure (HHP) impairs intermolecular hydrophobic and electrostatic interactions, dissociating aggregates, which makes HHP a useful tool to solubilize proteins for subsequent refolding. A process of refolding was set up by using as a model TsnC, a thioredoxin that catalyzes the disulfide reduction to a dithiol, a useful indication of biological activity. The inclusion bodies (IB) were dissociated at 2.4 kbar. The effect of incubation of IB suspensions at 1-800 bar, the guanidine hydrochloride concentration, the oxidized/reduced glutathione (GSH/GSSG) ratios, and the additives in the refolding buffer were analyzed. To assess the yields of fully biologically active protein obtained for each tested condition, it was crucial to analyze both the TsnC solubilization yield and its enzymatic activity. Application of 2.4 kbar to the IB suspension in the presence of 9 mM GSH, 1mM GSSG, 0.75 M guanidine hydrochloride, and 0.5M arginine with subsequent incubation at 1 bar furnished high refolding yield (81%). The experience gained in this study shall help to establish efficient HHP-based protein refolding processes for other proteins.
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Affiliation(s)
- Laura Simoni Lemke
- Instituto de Pesquisas Energéticas e Nucleares, IPEN-CNEN/SP, Centro de Biotecnologia, São Paulo, Brazil
| | - Rosa Maria Chura-Chambi
- Instituto de Pesquisas Energéticas e Nucleares, IPEN-CNEN/SP, Centro de Biotecnologia, São Paulo, Brazil
| | - Daniella Rodrigues
- Instituto de Pesquisas Energéticas e Nucleares, IPEN-CNEN/SP, Centro de Biotecnologia, São Paulo, Brazil
| | - Jose Renato Rosa Cussiol
- Instituto de Biociências, Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo, Brazil
| | - Natalia Vallejo Malavasi
- Instituto de Pesquisas Energéticas e Nucleares, IPEN-CNEN/SP, Centro de Biotecnologia, São Paulo, Brazil
| | - Thiago Geronimo Pires Alegria
- Instituto de Biociências, Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo, Brazil
| | - Luis Eduardo Soares Netto
- Instituto de Biociências, Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo, Brazil
| | - Ligia Morganti
- Instituto de Pesquisas Energéticas e Nucleares, IPEN-CNEN/SP, Centro de Biotecnologia, São Paulo, Brazil.
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Miyazono KI, Tsutsumi K, Ishino Y, Tanokura M. Expression, high-pressure refolding, purification, crystallization and preliminary X-ray analysis of a novel single-strand-specific 3'-5' exonuclease PhoExo I from Pyrococcus horikoshii OT3. Acta Crystallogr F Struct Biol Commun 2014; 70:1076-9. [PMID: 25084386 PMCID: PMC4118808 DOI: 10.1107/s2053230x14012734] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 06/01/2014] [Indexed: 12/22/2022] Open
Abstract
PhoExo I is a single-strand-specific 3'-5' exonuclease from Pyrococcus horikoshii OT3 and is thought to be involved in a Thermococcales-specific DNA-repair pathway. The recombinant PhoExo I protein was produced as inclusion bodies in Escherichia coli cells. Solubilization of the inclusion bodies was performed by the high-pressure refolding method and highly purified protein was subjected to crystallization by the sitting-drop vapour-diffusion method at 20°C. A crystal of PhoExo I was obtained in a reservoir solution consisting of 0.1 M Tris-HCl pH 8.9, 27% PEG 6000 and diffracted X-rays to 1.52 Å resolution. The crystal of PhoExo I belonged to space group H32, with unit-cell parameters a = b = 112.07, c = 202.28 Å. The crystal contained two PhoExo I molecules in the asymmetric unit.
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Affiliation(s)
- Ken-ichi Miyazono
- 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
| | - Kanae Tsutsumi
- 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
| | - Yoshizumi Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, and Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Masaru Tanokura
- 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
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Assenberg R, Wan PT, Geisse S, Mayr LM. Advances in recombinant protein expression for use in pharmaceutical research. Curr Opin Struct Biol 2013; 23:393-402. [DOI: 10.1016/j.sbi.2013.03.008] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 03/24/2013] [Accepted: 03/25/2013] [Indexed: 10/26/2022]
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Zheng H, Miyakawa T, Sawano Y, Yamagoe S, Tanokura M. Expression, high-pressure refolding and purification of human leukocyte cell-derived chemotaxin 2 (LECT2). Protein Expr Purif 2013; 88:221-9. [DOI: 10.1016/j.pep.2013.01.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 12/18/2012] [Accepted: 01/08/2013] [Indexed: 11/17/2022]
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Ogura K, Kobashigawa Y, Saio T, Kumeta H, Torikai S, Inagaki F. Practical applications of hydrostatic pressure to refold proteins from inclusion bodies for NMR structural studies. Protein Eng Des Sel 2013; 26:409-16. [DOI: 10.1093/protein/gzt012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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