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Du Y, Kobashigawa Y, Okazaki K, Ogawa M, Kawaguchi T, Sato T, Morioka H. Structure-based design, biophysical characterization, and biochemical application of the heterodimeric affinity purification tag based on the Schistosoma japonicum glutathione-S-transferase (SjGST) homodimer. J Biochem 2024; 176:69-80. [PMID: 38471515 DOI: 10.1093/jb/mvae028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 03/14/2024] Open
Abstract
Schistosoma japonicum glutathione-S-transferase (SjGST), the so-called GST-tag, is one of the most widely used protein tags for the purification of recombinant proteins by affinity chromatography. Attachment of SjGST enables the purification of a protein of interest (POI) using commercially available glutathione-immobilizing resins. Here we produced an SjGST mutant pair that forms heterodimers by adjusting the salt bridge pairs in the homodimer interface of SjGST. An MD study confirmed that the SjGST mutant pair did not disrupt the heterodimer formation. The modified SjGST protein pair coexpressed in Escherichia coli was purified by glutathione-immobilized resin. The stability of the heterodimeric form of the SjGST mutant pair was further confirmed by size exclusion chromatography. Surface plasmon resonance measurements unveiled the selective formation of heterodimers within the pair, accompanied by a significant suppression of homodimerization. The heterodimeric SjGST exhibited enzymatic activity in assays employing a commercially available fluorescent substrate. By fusing one member of the heterodimeric SjGST pair with a fluorescent protein and the other with the POI, we were able to conveniently and sensitively detect protein-protein interactions using fluorescence spectroscopy in the pull-down assays. Thus, utilization of the heterodimeric SjGST would be a useful tag for protein science.
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Affiliation(s)
- Yan Du
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Yoshihiro Kobashigawa
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Kyo Okazaki
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Mizuki Ogawa
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Tomoyuki Kawaguchi
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Takashi Sato
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Hiroshi Morioka
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
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Sekiguchi M, Fujinami Y, Takado K, Kimoto Y, Higashimura Y. Activity difference of three labdane diterpenoids on human constitutive androstane receptor. Biosci Biotechnol Biochem 2023; 87:1310-1315. [PMID: 37580155 DOI: 10.1093/bbb/zbad113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/11/2023] [Indexed: 08/16/2023]
Abstract
The constitutive androstane receptor (CAR) regulates enzyme transcription related to drug metabolism; therefore, natural compound clarification in food that interacts with CAR is significant for drug development. We revealed that 13-epimanool, which is a compound found in the common sage, is bound to hCAR based on differential scanning fluorometry (DSF) measurements using recombinant hCAR protein. Similar labdane diterpenoids were examined, which revealed that manool and sclareol, which were both natural compounds contained in herbs, are bound to hCAR. They exhibited different effects for CAR activity in the luciferase assay despite the structural similarity. Manool was a partial agonist, 13-epimanool was a weak partial agonist, and sclareol was an antagonist. The activity of hCAR may be regulated by slight differences in the bound compound.
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Affiliation(s)
- Mitsuhiro Sekiguchi
- Department of Food Science, Faculty of Bioresources and Environmental Science, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
| | - Yui Fujinami
- Department of Food Science, Faculty of Bioresources and Environmental Science, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
| | - Keiyu Takado
- Department of Food Science, Faculty of Bioresources and Environmental Science, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
| | - Yuu Kimoto
- Department of Food Science, Faculty of Bioresources and Environmental Science, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
| | - Yasuki Higashimura
- Department of Food Science, Faculty of Bioresources and Environmental Science, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
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Okazaki K, Kobashigawa Y, Morita H, Yamauchi S, Fukuda N, Liu C, Toyota Y, Sato T, Morioka H. Molecular Dynamics-Based Design and Biophysical Evaluation of Thermostable Single-Chain Fv Antibody Mutants Derived from Pharmaceutical Antibodies. ACS OMEGA 2023; 8:22945-22954. [PMID: 37396255 PMCID: PMC10308585 DOI: 10.1021/acsomega.3c01948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 05/26/2023] [Indexed: 07/04/2023]
Abstract
Antibody drugs are denatured under physical stress, e.g., friction, heat, and freezing, which triggers formation of aggregates and resultant allergic reactions. Design of a stable antibody is thus critical for the development of antibody drugs. Here, we obtained a thermostable single-chain Fv (scFv) antibody clone by rigidifying the flexible region. We first conducted a short molecular dynamics (MD) simulation (3 runs of 50 ns) to search for weak spots in the scFv antibody, i.e., flexible regions located outside the CDR (complementarity determining region) and the interface between the heavy-chain and light-chain variable regions. We then designed a thermostable mutant and evaluated it by means of a short MD simulation (3 runs of 50 ns) based on reductions in the root-mean-square fluctuation (RMSF) values and formation of new hydrophilic interactions around the weak spot. Finally, we designed the VL-R66G mutant by applying our strategy to scFv derived from trastuzumab. Trastuzumab scFv variants were prepared by using an Escherichia coli expression system, and the melting temperature-measured as a thermostability index-was 5 °C higher than that of the wild-type trastuzumab scFv, while the antigen-binding affinity was unchanged. Our strategy required few computational resources, and would be applicable to antibody drug discovery.
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Emoto Y, Katayama R, Hibino E, Ishihara S, Goda N, Tenno T, Kobashigawa Y, Morioka H, Hiroaki H. A Cost-Effective Immobilization Method for MBP Fusion Proteins on Microtiter Plates Using a Gelatinized Starch-Agarose Mixture and Its Application for Convenient Protein-Protein Interaction Analysis. Methods Protoc 2023; 6:mps6030044. [PMID: 37218904 DOI: 10.3390/mps6030044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/14/2023] [Accepted: 04/19/2023] [Indexed: 05/24/2023] Open
Abstract
The detection and quantification of protein-protein interactions (PPIs) is a crucial technique that often involves the use of recombinant proteins with fusion protein tags, such as maltose-binding protein (MBP) and glutathione-S-transferase (GST). In this study, we improved the cohesive and sticky properties of gelatinized starch by supplementing it with agarose, resulting in a harder gel that could coat the bottom of a microtiter plate. The resulting gelatinized starch/agarose mixture allowed for the efficient immobilization of MBP-tagged proteins on the coated plates, enabling the use of indirect ELISA-like PPI assays. By using the enzymatic activity of GST as an indicator, we succeeded in determining the dissociation constants between MBP-tagged and GST-tagged proteins on 96-well microtiter plates and a microplate reader without any expensive specialized equipment.
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Affiliation(s)
- Yuri Emoto
- Laboratory of Structural Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Furocho, Chikusa-ku, Nagoya 464-8601, Aichi, Japan
| | - Ryoya Katayama
- Division of Biological Sciences, Graduate School of Science, Nagoya University, Furocho, Chikusa-ku, Nagoya 464-8601, Aichi, Japan
- Graduate Program of Transformative Chem-Bio Research, Nagoya University, Furocho, Chikusa-ku, Nagoya 464-8601, Aichi, Japan
| | - Emi Hibino
- Laboratory of Structural Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Furocho, Chikusa-ku, Nagoya 464-8601, Aichi, Japan
- WISE Program, Convolution of Informatics and Biomedical Sciences on Glocal Alliances, Nagoya University, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Aichi, Japan
| | - Sho Ishihara
- Laboratory of Structural Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Furocho, Chikusa-ku, Nagoya 464-8601, Aichi, Japan
| | - Natsuko Goda
- Laboratory of Structural Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Furocho, Chikusa-ku, Nagoya 464-8601, Aichi, Japan
| | - Takeshi Tenno
- Laboratory of Structural Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Furocho, Chikusa-ku, Nagoya 464-8601, Aichi, Japan
- BeCellBar LLC., 1 Kamimura, Showa-ku, Nagoya 466-0802, Aichi, Japan
| | - Yoshihiro Kobashigawa
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University; 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Kumamoto, Japan
| | - Hiroshi Morioka
- Department of Analytical and Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University; 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Kumamoto, Japan
| | - Hidekazu Hiroaki
- Laboratory of Structural Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Furocho, Chikusa-ku, Nagoya 464-8601, Aichi, Japan
- Graduate Program of Transformative Chem-Bio Research, Nagoya University, Furocho, Chikusa-ku, Nagoya 464-8601, Aichi, Japan
- WISE Program, Convolution of Informatics and Biomedical Sciences on Glocal Alliances, Nagoya University, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Aichi, Japan
- BeCellBar LLC., 1 Kamimura, Showa-ku, Nagoya 466-0802, Aichi, Japan
- Center for One Medicine Innovative Translational Research (COMIT), Nagoya University, Nagoya 464-8601, Aichi, Japan
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Krasitskaya VV, Kudryavtsev AN, Yaroslavtsev RN, Velikanov DA, Bayukov OA, Gerasimova YV, Stolyar SV, Frank LA. Starch-Coated Magnetic Iron Oxide Nanoparticles for Affinity Purification of Recombinant Proteins. Int J Mol Sci 2022; 23:ijms23105410. [PMID: 35628220 PMCID: PMC9140719 DOI: 10.3390/ijms23105410] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 02/04/2023] Open
Abstract
Starch-coated magnetic iron oxide nanoparticles have been synthesized by a simple, fast, and cost-effective co-precipitation method with cornstarch as a stabilizing agent. The structural and magnetic characteristics of the synthesized material have been studied by transmission electron microscopy, Mössbauer spectroscopy, and vibrating sample magnetometry. The nature of bonds between ferrihydrite nanoparticles and a starch shell has been examined by Fourier transform infrared spectroscopy. The data on the magnetic response of the prepared composite particles have been obtained by magnetic measurements. The determined magnetic characteristics make the synthesized material a good candidate for use in magnetic separation. Starch-coated magnetic iron oxide nanoparticles have been tested as an affinity sorbent for one-step purification of several recombinant proteins (cardiac troponin I, survivin, and melanoma inhibitory activity protein) bearing the maltose-binding protein as an auxiliary fragment. It has been shown that, due to the highly specific binding of this fragment to the starch shell, the target fusion protein is selectively immobilized on magnetic nanoparticles and eluted with the maltose solution. The excellent efficiency of column-free purification, high binding capacity of the sorbent (100–500 µg of a recombinant protein per milligram of starch-coated magnetic iron oxide nanoparticles), and reusability of the obtained material have been demonstrated.
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Affiliation(s)
- Vasilisa V. Krasitskaya
- Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 660036 Krasnoyarsk, Russia; (V.V.K.); (A.N.K.)
| | - Alexander N. Kudryavtsev
- Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 660036 Krasnoyarsk, Russia; (V.V.K.); (A.N.K.)
| | - Roman N. Yaroslavtsev
- Kirensky Institute of Physics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 660036 Krasnoyarsk, Russia; (R.N.Y.); (D.A.V.); (O.A.B.); (Y.V.G.); (S.V.S.)
- Federal Research Center “Krasnoyarsk Science Center SB RAS”, 660036 Krasnoyarsk, Russia
| | - Dmitry A. Velikanov
- Kirensky Institute of Physics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 660036 Krasnoyarsk, Russia; (R.N.Y.); (D.A.V.); (O.A.B.); (Y.V.G.); (S.V.S.)
| | - Oleg A. Bayukov
- Kirensky Institute of Physics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 660036 Krasnoyarsk, Russia; (R.N.Y.); (D.A.V.); (O.A.B.); (Y.V.G.); (S.V.S.)
| | - Yulia V. Gerasimova
- Kirensky Institute of Physics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 660036 Krasnoyarsk, Russia; (R.N.Y.); (D.A.V.); (O.A.B.); (Y.V.G.); (S.V.S.)
- School of Fundamental Biology and Biotechnology, Siberian Federal University, 660041 Krasnoyarsk, Russia
| | - Sergey V. Stolyar
- Kirensky Institute of Physics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 660036 Krasnoyarsk, Russia; (R.N.Y.); (D.A.V.); (O.A.B.); (Y.V.G.); (S.V.S.)
- Federal Research Center “Krasnoyarsk Science Center SB RAS”, 660036 Krasnoyarsk, Russia
- School of Fundamental Biology and Biotechnology, Siberian Federal University, 660041 Krasnoyarsk, Russia
| | - Ludmila A. Frank
- Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 660036 Krasnoyarsk, Russia; (V.V.K.); (A.N.K.)
- School of Fundamental Biology and Biotechnology, Siberian Federal University, 660041 Krasnoyarsk, Russia
- Correspondence:
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Honkakoski P. Searching for CAR modulators. Drug Metab Dispos 2022; 50:1002-1009. [DOI: 10.1124/dmd.121.000482] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 02/01/2022] [Indexed: 11/22/2022] Open
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