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Sato R, Minamihata K, Wakabayashi R, Goto M, Kamiya N. Molecular crowding elicits the acceleration of enzymatic crosslinking of macromolecular substrates. Org Biomol Chem 2023; 21:306-314. [PMID: 36342388 DOI: 10.1039/d2ob01549h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Cytoplasm contains high concentrations of biomacromolecules. Protein behavior under such crowded conditions is reportedly different from that in an aqueous buffer solution, mainly owing to the effect of volume exclusion caused by the presence of macromolecules. Using a crosslinking reaction catalyzed by microbial transglutaminase (MTG) as a model, we herein systematically determined how the substrate size affects enzymatic activity in both dilute and crowded solutions of dextran. We first observed a threefold reduction in MTG-mediated crosslinking of a pair of small peptide substrates in 15 wt% dextran solution. In contrast, when proteinaceous substrates were involved, the crosslinking rates in 15 wt% dextran solutions accelerated markedly to levels comparable with the level in the absence of dextran. Our results provide new insights into the action of enzymes with regard to macromolecular substrates under crowded conditions, of which the potential utility was demonstrated by the formation of highly crosslinked protein polymers.
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Affiliation(s)
- Ryo Sato
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan.
| | - Kosuke Minamihata
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan.
| | - Rie Wakabayashi
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan.
| | - Masahiro Goto
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan. .,Division of Biotechnology, Center for Future Chemistry, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan
| | - Noriho Kamiya
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan. .,Division of Biotechnology, Center for Future Chemistry, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan
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Dong J, Ueda H. Recent Advances in Quenchbody, a Fluorescent Immunosensor. SENSORS 2021; 21:s21041223. [PMID: 33572319 PMCID: PMC7916128 DOI: 10.3390/s21041223] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 01/27/2021] [Accepted: 02/06/2021] [Indexed: 12/29/2022]
Abstract
The detection of viruses, disease biomarkers, physiologically active substances, drugs, and chemicals is of great significance in many areas of our lives. Immunodetection technology is based on the specificity and affinity of antigen–antibody reactions. Compared with other analytical methods such as liquid chromatography coupled with mass spectrometry, which requires a large and expensive instrument, immunodetection has the advantages of simplicity and good selectivity and is thus widely used in disease diagnosis and food/environmental monitoring. Quenchbody (Q-body), a new type of fluorescent immunosensor, is an antibody fragment labeled with fluorescent dyes. When the Q-body binds to its antigen, the fluorescence intensity increases. The detection of antigens by changes in fluorescence intensity is simple, easy to operate, and highly sensitive. This review comprehensively discusses the principle, construction, application, and current progress related to Q-bodies.
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Affiliation(s)
- Jinhua Dong
- Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan;
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
- School of Life Science and Technology, Weifang Medical University, Weifang 261053, China
| | - Hiroshi Ueda
- Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan;
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
- Correspondence: ; Tel.: +81-45-924-5256
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3
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Islam J, Riley BT, Fercher C, Jones ML, Buckle AM, Howard CB, Cox RP, Bell TDM, Mahler S, Corrie SR. Wavelength-Dependent Fluorescent Immunosensors via Incorporation of Polarity Indicators near the Binding Interface of Antibody Fragments. Anal Chem 2019; 91:7631-7638. [DOI: 10.1021/acs.analchem.9b00445] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jiaul Islam
- Department of Chemical Engineering, ARC Centre of Excellence in Convergent BioNano Science and Technology, Monash University, Clayton VIC 3800, Australia
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia QLD 4072, Australia
| | - Blake T. Riley
- Dept. of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton VIC 3800, Australia
| | - Christian Fercher
- Department of Chemical Engineering, ARC Centre of Excellence in Convergent BioNano Science and Technology, Monash University, Clayton VIC 3800, Australia
- ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia QLD 4072, Australia
| | - Martina L. Jones
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia QLD 4072, Australia
- ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia QLD 4072, Australia
| | - Ashley M. Buckle
- Dept. of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton VIC 3800, Australia
| | - Christopher B. Howard
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia QLD 4072, Australia
- ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia QLD 4072, Australia
| | - Rosalind P. Cox
- School of Chemistry, Monash University, Clayton VIC 3800, Australia
| | - Toby D. M. Bell
- School of Chemistry, Monash University, Clayton VIC 3800, Australia
| | - Stephen Mahler
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia QLD 4072, Australia
- ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia QLD 4072, Australia
| | - Simon R. Corrie
- Department of Chemical Engineering, ARC Centre of Excellence in Convergent BioNano Science and Technology, Monash University, Clayton VIC 3800, Australia
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia QLD 4072, Australia
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4
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Zhou X, Cui Z, Liu L, Sun Z, Lin M, Hu Q, Wang H, Xiao X. Small molecule-protein interactions in branch migration thermodynamics: modelling and application in the homogeneous detection of proteins and small molecules. Analyst 2018; 143:2755-2759. [PMID: 29850719 DOI: 10.1039/c8an00555a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We have disclosed the unique inhibition effect of small molecule-protein interactions toward the DNA branch migration process and constructed a complete thermodynamic model for it. The disclosed effect was further coupled with the steric hindrance effect to establish a homogeneous assay for proteins and small molecules with ultra-high inhibition factors and sensitivity.
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Affiliation(s)
- Xing Zhou
- Centre of Reproductive Medicine/Family Planning Research Institute, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, PR China.
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Fukunaga K, Watanabe T, Novitasari D, Ohashi H, Abe R, Hohsaka T. Antigen-responsive fluorescent antibody probes generated by selective N-terminal modification of IgGs. Chem Commun (Camb) 2018; 54:12734-12737. [DOI: 10.1039/c8cc07827k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Fluorescent antibody probes showing antigen-dependent fluorescence responses were developed by N-terminal-selective reductive alkylation of IgGs.
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Affiliation(s)
- Keisuke Fukunaga
- School of Materials Science
- Japan Advanced Institute of Science and Technology (JAIST)
- Ishikawa 923-1292
- Japan
| | - Takayoshi Watanabe
- School of Materials Science
- Japan Advanced Institute of Science and Technology (JAIST)
- Ishikawa 923-1292
- Japan
| | - Dian Novitasari
- School of Materials Science
- Japan Advanced Institute of Science and Technology (JAIST)
- Ishikawa 923-1292
- Japan
| | | | - Ryoji Abe
- Ushio Incorporated
- Yokohama 225-0004
- Japan
| | - Takahiro Hohsaka
- School of Materials Science
- Japan Advanced Institute of Science and Technology (JAIST)
- Ishikawa 923-1292
- Japan
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6
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Ohashi H, Matsumoto T, Jeong HJ, Dong J, Abe R, Ueda H. Insight into the Working Mechanism of Quenchbody: Transition of the Dye around Antibody Variable Region That Fluoresces upon Antigen Binding. Bioconjug Chem 2016; 27:2248-2253. [DOI: 10.1021/acs.bioconjchem.6b00217] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hiroyuki Ohashi
- Department
of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Ushio Incorporated, 6409 Motoishikawa-cho, Aoba-ku, Yokohama 225-0004, Japan
| | - Takashi Matsumoto
- Department
of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Hee-Jin Jeong
- Department
of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Laboratory
for Chemistry and Life Science, Tokyo Institute of Technology, 4259-R1-18,
Nagatsuta-cho, Midori-ku, Yokoyama, Kanagawa 226-8503, Japan
| | - Jinhua Dong
- Laboratory
for Chemistry and Life Science, Tokyo Institute of Technology, 4259-R1-18,
Nagatsuta-cho, Midori-ku, Yokoyama, Kanagawa 226-8503, Japan
| | - Ryoji Abe
- Ushio Incorporated, 6409 Motoishikawa-cho, Aoba-ku, Yokohama 225-0004, Japan
| | - Hiroshi Ueda
- Department
of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Laboratory
for Chemistry and Life Science, Tokyo Institute of Technology, 4259-R1-18,
Nagatsuta-cho, Midori-ku, Yokoyama, Kanagawa 226-8503, Japan
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