1
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Santos EM, Chandra I, Assar Z, Sheng W, Ghanbarpour A, Bingham C, Vasileiou C, Geiger JH, Borhan B. Regulation of Absorption and Emission in a Protein/Fluorophore Complex. ACS Chem Biol 2024. [PMID: 39046136 DOI: 10.1021/acschembio.4c00125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
Human cellular retinol binding protein II (hCRBPII) was used as a protein engineering platform to rationally regulate absorptive and emissive properties of a covalently bound fluorogenic dye. We demonstrate the binding of a thio-dapoxyl analog via formation of a protonated imine between an active site lysine residue and the chromophore's aldehyde. Rational manipulation of the electrostatics of the binding pocket results in a 204 nm shift in absorption and a 131 nm shift in emission. The protein is readily expressed in mammalian systems and binds with exogenously delivered fluorophore as demonstrated by live-cell imaging experiments.
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Affiliation(s)
- Elizabeth M Santos
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Ishita Chandra
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Zahra Assar
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Wei Sheng
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Alireza Ghanbarpour
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Courtney Bingham
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Chrysoula Vasileiou
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - James H Geiger
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Babak Borhan
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
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2
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Minoshima M, Reja SI, Hashimoto R, Iijima K, Kikuchi K. Hybrid Small-Molecule/Protein Fluorescent Probes. Chem Rev 2024; 124:6198-6270. [PMID: 38717865 DOI: 10.1021/acs.chemrev.3c00549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Hybrid small-molecule/protein fluorescent probes are powerful tools for visualizing protein localization and function in living cells. These hybrid probes are constructed by diverse site-specific chemical protein labeling approaches through chemical reactions to exogenous peptide/small protein tags, enzymatic post-translational modifications, bioorthogonal reactions for genetically incorporated unnatural amino acids, and ligand-directed chemical reactions. The hybrid small-molecule/protein fluorescent probes are employed for imaging protein trafficking, conformational changes, and bioanalytes surrounding proteins. In addition, fluorescent hybrid probes facilitate visualization of protein dynamics at the single-molecule level and the defined structure with super-resolution imaging. In this review, we discuss development and the bioimaging applications of fluorescent probes based on small-molecule/protein hybrids.
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Affiliation(s)
- Masafumi Minoshima
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Shahi Imam Reja
- Immunology Frontier Research Center, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Ryu Hashimoto
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Kohei Iijima
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Kazuya Kikuchi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
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3
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Wang J, Liu Q, Li Y, Pang Y. An environmentally sensitive zinc-selective two-photon NIR fluorescent turn-on probe and zinc sensing in stroke. J Pharm Anal 2024; 14:100903. [PMID: 38655400 PMCID: PMC11035362 DOI: 10.1016/j.jpha.2023.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 11/01/2023] [Accepted: 11/21/2023] [Indexed: 04/26/2024] Open
Abstract
A two-photon near infrared (NIR) fluorescence turn-on sensor with high selectivity and sensitivity for Zn2+ detection has been developed. This sensor exhibits a large Stokes' shift (∼300 nm) and can be excited from 900 to 1000 nm, with an emission wavelength of ∼785 nm, making it ideal for imaging in biological tissues. The sensor's high selectivity for Zn2+ over other structurally similar cations, such as Cd2+, makes it a promising tool for monitoring zinc ion levels in biological systems. Given the high concentration of zinc in thrombi, this sensor could provide a useful tool for in vivo thrombus imaging.
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Affiliation(s)
- Junfeng Wang
- Department of Chemistry, The University of Akron, Akron, OH 44325, USA
- Gordon Center for Medical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Qibing Liu
- Department of Pharmacy, The First Affiliated Hospital of Hainan Medical University, Haikou, 570100, China
- Engineering Research Center of Tropical Medicine, Ministry of Education, Hainan Medical University, Haikou, 571199, China
| | - Yingbo Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Yi Pang
- Department of Chemistry, The University of Akron, Akron, OH 44325, USA
- Maurice Morton Institute of Polymer Science, The University of Akron, Akron, OH 44325, USA
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4
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Cole MS, Hegde PV, Aldrich CC. β-Lactamase-Mediated Fragmentation: Historical Perspectives and Recent Advances in Diagnostics, Imaging, and Antibacterial Design. ACS Infect Dis 2022; 8:1992-2018. [PMID: 36048623 DOI: 10.1021/acsinfecdis.2c00315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The discovery of β-lactam (BL) antibiotics in the early 20th century represented a remarkable advancement in human medicine, allowing for the widespread treatment of infectious diseases that had plagued humanity throughout history. Yet, this triumph was followed closely by the emergence of β-lactamase (BLase), a bacterial weapon to destroy BLs. BLase production is a primary mechanism of resistance to BL antibiotics, and the spread of new homologues with expanded hydrolytic activity represents a pressing threat to global health. Nonetheless, researchers have developed strategies that take advantage of this defense mechanism, exploiting BLase activity in the creation of probes, diagnostic tools, and even novel antibiotics selective for resistant organisms. Early discoveries in the 1960s and 1970s demonstrating that certain BLs expel a leaving group upon BLase cleavage have spawned an entire field dedicated to employing this selective release mechanism, termed BLase-mediated fragmentation. Chemical probes have been developed for imaging and studying BLase-expressing organisms in the laboratory and diagnosing BL-resistant infections in the clinic. Perhaps most promising, new antibiotics have been developed that use BLase-mediated fragmentation to selectively release cytotoxic chemical "warheads" at the site of infection, reducing off-target effects and allowing for the repurposing of putative antibiotics against resistant organisms. This Review will provide some historical background to the emergence of this field and highlight some exciting recent reports that demonstrate the promise of this unique release mechanism.
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Affiliation(s)
- Malcolm S Cole
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard St SE, Minneapolis, Minnesota 55455, United States
| | - Pooja V Hegde
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard St SE, Minneapolis, Minnesota 55455, United States
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard St SE, Minneapolis, Minnesota 55455, United States
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5
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Mizukami S. Development of Photoresponsive Probes to Investigate Cellular Functions. YAKUGAKU ZASSHI 2022; 142:503-511. [DOI: 10.1248/yakushi.21-00203-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Shin Mizukami
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University
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6
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Yang XQ, Bai LW, Chen Y, Lin YX, Xiang H, Xiang TT, Zhu SX, Zhou L, Li K, Lei X. Peptide probes with high affinity to target protein selection by phage display and characterization using biophysical approaches. NEW J CHEM 2022. [DOI: 10.1039/d2nj00621a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein, phage display was utilized to screen the affinity of peptides against dihydrofolate reductase and a positive peptide was obtained, and the verification of the affinity was tested by multiple in vitro biophysical methods.
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Affiliation(s)
- Xiao-Qin Yang
- School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan, 430074, P. R. China
| | - Li-Wen Bai
- School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan, 430074, P. R. China
| | - Yu Chen
- School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan, 430074, P. R. China
| | - Yue-Xiao Lin
- School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan, 430074, P. R. China
| | - Hua Xiang
- School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan, 430074, P. R. China
| | - Ting-Ting Xiang
- College of Life Sciences, South-Central Minzu University, Wuhan, 430074, P. R. China
| | - Shuang-Xing Zhu
- College of Life Sciences, South-Central Minzu University, Wuhan, 430074, P. R. China
| | - Li Zhou
- School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan, 430074, P. R. China
| | - Kai Li
- College of Life Sciences, South-Central Minzu University, Wuhan, 430074, P. R. China
| | - Xinxiang Lei
- School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan, 430074, P. R. China
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7
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Kowada T, Arai K, Yoshimura A, Matsui T, Kikuchi K, Mizukami S. Optical Manipulation of Subcellular Protein Translocation Using a Photoactivatable Covalent Labeling System. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Toshiyuki Kowada
- Institute of Multidisciplinary Research for Advanced Materials Tohoku University Sendai Miyagi 980-8577 Japan
- Graduate School of Life Sciences Tohoku University Sendai Miyagi 980-8577 Japan
| | - Keisuke Arai
- Graduate School of Life Sciences Tohoku University Sendai Miyagi 980-8577 Japan
| | - Akimasa Yoshimura
- Graduate School of Engineering Osaka University 2-1 Yamadaoka, Suita Osaka 565-0871 Japan
| | - Toshitaka Matsui
- Institute of Multidisciplinary Research for Advanced Materials Tohoku University Sendai Miyagi 980-8577 Japan
- Graduate School of Life Sciences Tohoku University Sendai Miyagi 980-8577 Japan
| | - Kazuya Kikuchi
- Graduate School of Engineering Osaka University 2-1 Yamadaoka, Suita Osaka 565-0871 Japan
- Immunology Frontier Research Center Osaka University 2-1 Yamadaoka, Suita Osaka 565-0871 Japan
- Center for Quantum Information and Quantum Biology Osaka University 2-1 Yamadaoka, Suita Osaka 565-0871 Japan
| | - Shin Mizukami
- Institute of Multidisciplinary Research for Advanced Materials Tohoku University Sendai Miyagi 980-8577 Japan
- Graduate School of Life Sciences Tohoku University Sendai Miyagi 980-8577 Japan
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8
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Kowada T, Arai K, Yoshimura A, Matsui T, Kikuchi K, Mizukami S. Optical Manipulation of Subcellular Protein Translocation Using a Photoactivatable Covalent Labeling System. Angew Chem Int Ed Engl 2021; 60:11378-11383. [PMID: 33644979 DOI: 10.1002/anie.202016684] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/15/2021] [Indexed: 12/21/2022]
Abstract
The photoactivatable chemically induced dimerization (photo-CID) technique for tag-fused proteins is one of the most promising methods for regulating subcellular protein translocations and protein-protein interactions. However, light-induced covalent protein dimerization in living cells has yet to be established, despite its various advantages. Herein, we developed a photoactivatable covalent protein-labeling technology by applying a caged ligand to the BL-tag system, a covalent protein labeling system that uses mutant β-lactamase. We further developed CBHD, a caged protein dimerizer, using caged BL-tag and HaloTag ligands, and achieved light-induced protein translocation from the cytoplasm to subcellular regions. In addition, this covalent photo-CID system enabled quick protein translocation to a laser-illuminated microregion. These results indicate that the covalent photo-CID system will expand the scope of CID applications in the optical manipulation of cellular functions.
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Affiliation(s)
- Toshiyuki Kowada
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi, 980-8577, Japan.,Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8577, Japan
| | - Keisuke Arai
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8577, Japan
| | - Akimasa Yoshimura
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Toshitaka Matsui
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi, 980-8577, Japan.,Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8577, Japan
| | - Kazuya Kikuchi
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Immunology Frontier Research Center, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Center for Quantum Information and Quantum Biology, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Shin Mizukami
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi, 980-8577, Japan.,Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8577, Japan
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9
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Abstract
Systematically dissecting the molecular basis of the cell surface as well as its related biological activities is considered as one of the most cutting-edge fields in fundamental sciences. The advent of various advanced cell imaging techniques allows us to gain a glimpse of how the cell surface is structured and coordinated with other cellular components to respond to intracellular signals and environmental stimuli. Nowadays, cell surface-related studies have entered a new era featured by a redirected aim of not just understanding but artificially manipulating/remodeling the cell surface properties. To meet this goal, biologists and chemists are intensely engaged in developing more maneuverable cell surface labeling strategies by exploiting the cell's intrinsic biosynthetic machinery or direct chemical/physical binding methods for imaging, sensing, and biomedical applications. In this review, we summarize the recent advances that focus on the visualization of various cell surface structures/dynamics and accurate monitoring of the microenvironment of the cell surface. Future challenges and opportunities in these fields are discussed, and the importance of cell surface-based studies is highlighted.
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Affiliation(s)
- Hao-Ran Jia
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, 2 Sipailou Road, Nanjing 210096, P. R. China.
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10
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Gao Y, Wang C, Chi W, Liu X. Molecular Origins of Heteroatom Engineering on the Emission Wavelength Tuning, Quantum Yield Variations and Fluorogenicity of NBD-like SCOTfluors. Chem Asian J 2020; 15:4082-4086. [PMID: 33029926 DOI: 10.1002/asia.202000966] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/29/2020] [Indexed: 01/15/2023]
Abstract
Molecular engineering of fluorophore scaffolds, especially heteroatom replacement, is a promising method to yield novel fluorophores with tailored properties for various applications. Yet, molecular origins of the distinct fluorescent properties in newly developed SCOTfluors, i. e., varied emission wavelengths, distinct quantum yields, and fluorogenicity, remain elusive. Such understanding, however, is critical for the rational molecular engineering of high-performance fluorophores. Herein, we employed quantum chemical calculations to understand the structure-property relationships of nitrobenzoxadiazole (NBD)-like SCOTfluors. Our findings are important not only for the rational deployment of SCOTfluors, but also for the effective modifications of other fluorophore scaffolds, for satisfying the increasingly diversified requirements of bioimaging and biosensing applications.
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Affiliation(s)
- Ying Gao
- Jilin Engineering Normal University, Kaixuan Road 3050, Changchun, 130052, P. R. China.,Fluorescence Research Group, Singapore University of Technology and Design, 8 Somapah Road, Singapore, 487372, Singapore
| | - Chao Wang
- Fluorescence Research Group, Singapore University of Technology and Design, 8 Somapah Road, Singapore, 487372, Singapore
| | - Weijie Chi
- Fluorescence Research Group, Singapore University of Technology and Design, 8 Somapah Road, Singapore, 487372, Singapore
| | - Xiaogang Liu
- Fluorescence Research Group, Singapore University of Technology and Design, 8 Somapah Road, Singapore, 487372, Singapore
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11
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Liu F, Zhang L, Li F, Zhang X, Zou L, Chai J, Xin X, Xu J, Zhang G. A noteworthy interface-targeting fluorescent probe for long-term tracking mitochondria and visualizing mitophagy. Biosens Bioelectron 2020; 168:112526. [DOI: 10.1016/j.bios.2020.112526] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 08/16/2020] [Accepted: 08/18/2020] [Indexed: 12/20/2022]
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12
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Reja SI, Minoshima M, Hori Y, Kikuchi K. Near-infrared fluorescent probes: a next-generation tool for protein-labeling applications. Chem Sci 2020; 12:3437-3447. [PMID: 34163617 PMCID: PMC8179524 DOI: 10.1039/d0sc04792a] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/18/2020] [Indexed: 12/21/2022] Open
Abstract
The development of near-infrared (NIR) fluorescent probes over the past few decades has changed the way that biomolecules are imaged, and thus represents one of the most rapidly progressing areas of research. Presently, NIR fluorescent probes are routinely used to visualize and understand intracellular activities. The ability to penetrate tissues deeply, reduced photodamage to living organisms, and a high signal-to-noise ratio characterize NIR fluorescent probes as efficient next-generation tools for elucidating various biological events. The coupling of self-labeling protein tags with synthetic fluorescent probes is one of the most promising research areas in chemical biology. Indeed, at present, protein-labeling techniques are not only used to monitor the dynamics and localization of proteins but also play a more diverse role in imaging applications. For instance, one of the dominant technologies employed in the visualization of protein activity and regulation is based on protein tags and their associated NIR fluorescent probes. In this mini-review, we will discuss the development of several NIR fluorescent probes used for various protein-tag systems.
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Affiliation(s)
- Shahi Imam Reja
- Graduate School of Engineering, Osaka University Suita Osaka 565-0871 Japan
| | - Masafumi Minoshima
- Graduate School of Engineering, Osaka University Suita Osaka 565-0871 Japan
| | - Yuichiro Hori
- Graduate School of Engineering, Osaka University Suita Osaka 565-0871 Japan
- Immunology Frontier Research Center, Osaka University Osaka 565-0871 Japan
| | - Kazuya Kikuchi
- Graduate School of Engineering, Osaka University Suita Osaka 565-0871 Japan
- Immunology Frontier Research Center, Osaka University Osaka 565-0871 Japan
- Quantum Information and Quantum Biology Division, Osaka University Suita Osaka 565-0871 Japan
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13
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Hoelzel CA, Zhang X. Visualizing and Manipulating Biological Processes by Using HaloTag and SNAP-Tag Technologies. Chembiochem 2020; 21:1935-1946. [PMID: 32180315 PMCID: PMC7367766 DOI: 10.1002/cbic.202000037] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/27/2020] [Indexed: 12/25/2022]
Abstract
Visualizing and manipulating the behavior of proteins is crucial to understanding the physiology of the cell. Methods of biorthogonal protein labeling are important tools to attain this goal. In this review, we discuss advances in probe technology specific for self-labeling protein tags, focusing mainly on the application of HaloTag and SNAP-tag systems. We describe the latest developments in small-molecule probes that enable fluorogenic (no wash) imaging and super-resolution fluorescence microscopy. In addition, we cover several methodologies that enable the perturbation or manipulation of protein behavior and function towards the control of biological pathways. Thus, current technical advances in the HaloTag and SNAP-tag systems means that they are becoming powerful tools to enable the visualization and manipulation of biological processes, providing invaluable scientific insights that are difficult to obtain by traditional methodologies. As the multiplex of self-labeling protein tag systems continues to be developed and expanded, the utility of these protein tags will allow researchers to address previously inaccessible questions at the forefront of biology.
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Affiliation(s)
- Conner A Hoelzel
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania, PA 16802, USA
| | - Xin Zhang
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania, PA 16802, USA
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14
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Thiel Z, Nguyen J, Rivera‐Fuentes P. Genetically Encoded Activators of Small Molecules for Imaging and Drug Delivery. Angew Chem Int Ed Engl 2020; 59:7669-7677. [PMID: 31898373 PMCID: PMC7318188 DOI: 10.1002/anie.201915521] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Indexed: 12/30/2022]
Abstract
Chemical biologists have developed many tools based on genetically encoded macromolecules and small, synthetic compounds. The two different approaches are extremely useful, but they have inherent limitations. In this Minireview, we highlight examples of strategies that combine both concepts to tackle challenging problems in chemical biology. We discuss applications in imaging, with a focus on super-resolved techniques, and in probe and drug delivery. We propose future directions in this field, hoping to inspire chemical biologists to develop new combinations of synthetic and genetically encoded probes.
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Affiliation(s)
- Zacharias Thiel
- Institute of Chemical Sciences and EngineeringEPF LausanneCH C2 425, Station 61015LausanneSwitzerland
- Laboratory of Organic ChemistryETH ZurichVladimir-Prelog-Weg 38093ZurichSwitzerland
| | - Jade Nguyen
- Institute of Chemical Sciences and EngineeringEPF LausanneCH C2 425, Station 61015LausanneSwitzerland
- Laboratory of Organic ChemistryETH ZurichVladimir-Prelog-Weg 38093ZurichSwitzerland
| | - Pablo Rivera‐Fuentes
- Institute of Chemical Sciences and EngineeringEPF LausanneCH C2 425, Station 61015LausanneSwitzerland
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15
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Thiel Z, Nguyen J, Rivera‐Fuentes P. Genetically Encoded Activators of Small Molecules for Imaging and Drug Delivery. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Zacharias Thiel
- Institute of Chemical Sciences and Engineering EPF Lausanne CH C2 425, Station 6 1015 Lausanne Switzerland
- Laboratory of Organic Chemistry ETH Zurich Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Jade Nguyen
- Institute of Chemical Sciences and Engineering EPF Lausanne CH C2 425, Station 6 1015 Lausanne Switzerland
- Laboratory of Organic Chemistry ETH Zurich Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Pablo Rivera‐Fuentes
- Institute of Chemical Sciences and Engineering EPF Lausanne CH C2 425, Station 6 1015 Lausanne Switzerland
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16
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Kumar N, Hori Y, Nishiura M, Kikuchi K. Rapid no-wash labeling of PYP-tag proteins with reactive fluorogenic ligands affords stable fluorescent protein conjugates for long-term cell imaging studies. Chem Sci 2020; 11:3694-3701. [PMID: 34094058 PMCID: PMC8152630 DOI: 10.1039/d0sc00499e] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Covalent labeling systems that employ protein-tags or chemical probes to convert proteins into fluorescent conjugates are powerful tools for carrying out real time imaging and pulse-chase tracking studies that enable the spatiotemporal role of proteins in complex biological systems to be investigated. In this study, we have covalently modified a specific nucleophilic cysteine residue of the PYP-tag protein with weakly fluorescent α,β-unsaturated ketone (conjugate addition) and α-halomethyl ketone (SN2 reaction) acceptors to afford highly fluorescent PYP-tag-dimethylaminocoumarin (DMAC) conjugates, whose ligands are covalently bound to the PYP-protein through stable thioether linkers. A chloromethylketone derived DMAC-CMK reagent was found to afford the best kinetic and stability profile for labeling the PYP-tag in cellular systems, with in vitro studies demonstrating that PYP-DMAC-CMK conjugates exhibit excellent photostability and cellular stability profiles which enables them to be used for long-term protein imaging studies in cellular systems. The potential of using this no wash fluorescent labeling PYP-tag-DMAC system to visualise dividing cells undergoing mitosis and for imaging a PYP-tag fused telomere binding protein bound to chromatin in cell nuclei has been demonstrated.
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Affiliation(s)
- Naresh Kumar
- Graduate School of Engineering, Osaka University Suita Osaka 565-0871 Japan
| | - Yuichiro Hori
- Graduate School of Engineering, Osaka University Suita Osaka 565-0871 Japan
- Immunology Frontier Research Center, Osaka University Suita Osaka 565-0871 Japan
| | - Miyako Nishiura
- Graduate School of Engineering, Osaka University Suita Osaka 565-0871 Japan
| | - Kazuya Kikuchi
- Graduate School of Engineering, Osaka University Suita Osaka 565-0871 Japan
- Immunology Frontier Research Center, Osaka University Suita Osaka 565-0871 Japan
- Quantum Information and Quantum Biology Division, Osaka University Suita Osaka 565-0871 Japan
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17
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Abstract
Protein folding in the cell is mediated by an extensive network of >1,000 chaperones, quality control factors, and trafficking mechanisms collectively termed the proteostasis network. While the components and organization of this network are generally well established, our understanding of how protein-folding problems are identified, how the network components integrate to successfully address challenges, and what types of biophysical issues each proteostasis network component is capable of addressing remains immature. We describe a chemical biology-informed framework for studying cellular proteostasis that relies on selection of interesting protein-folding problems and precise researcher control of proteostasis network composition and activities. By combining these methods with multifaceted strategies to monitor protein folding, degradation, trafficking, and aggregation in cells, researchers continue to rapidly generate new insights into cellular proteostasis.
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Affiliation(s)
- Rebecca M Sebastian
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Matthew D Shoulders
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
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18
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Deal PE, Liu P, Al-Abdullatif SH, Muller VR, Shamardani K, Adesnik H, Miller EW. Covalently Tethered Rhodamine Voltage Reporters for High Speed Functional Imaging in Brain Tissue. J Am Chem Soc 2020; 142:614-622. [PMID: 31829585 PMCID: PMC6949409 DOI: 10.1021/jacs.9b12265] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Voltage-sensitive fluorophores enable the direct visualization of membrane potential changes in living systems. To pair the speed and sensitivity of chemically synthesized fluorescent indicators with cell-type specific genetic methods, we here develop Rhodamine-based Voltage Reporters (RhoVR) that can be covalently tethered to genetically encoded, self-labeling enzymes. These chemical-genetic hybrids feature a photoinduced electron transfer triggered RhoVR voltage-sensitive indicator coupled to a chloroalkane HaloTag ligand through a long, water-soluble polyethylene glycol linker (RhoVR-Halo). When applied to cells, RhoVR-Halo dyes selectively and covalently bind to surface-expressed HaloTag enzyme on genetically modified cells. RhoVR-Halo dyes maintain high voltage sensitivities-up to 34% ΔF/F per 100 mV-and fast response times typical of untargeted RhoVRs, while gaining the selectivity of genetically encodable voltage indicators. We show that RhoVR-Halos can record action potentials in single trials from cultured rat hippocampal neurons and can be used in concert with green-fluorescent Ca2+ indicators like GCaMP to provide simultaneous voltage and Ca2+ imaging. In a brain slice, RhoVR-Halos provide exquisite labeling of defined cells and can be imaged using epifluorescence, confocal, or two-photon microscopy. Using high-speed epifluorescence microscopy, RhoVR-Halos provide a read-out of action potentials from labeled cortical neurons in a rat brain slice, without the need for trial averaging. These results demonstrate the potential of hybrid chemical-genetic voltage indicators to combine the optical performance of small-molecule chromophores with the inherent selectivity of genetically encodable systems, permitting imaging modalities inaccessible to either technique individually.
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Affiliation(s)
- Parker E. Deal
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Pei Liu
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Sarah H. Al-Abdullatif
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Vikram R. Muller
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Kiarash Shamardani
- Department of Molecular & Cell Biology, University of California, Berkeley, California 94720, United States
- Helen Wills Neuroscience Institute. University of California, Berkeley, California 94720, United States
| | - Hillel Adesnik
- Department of Molecular & Cell Biology, University of California, Berkeley, California 94720, United States
- Helen Wills Neuroscience Institute. University of California, Berkeley, California 94720, United States
| | - Evan W. Miller
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Department of Molecular & Cell Biology, University of California, Berkeley, California 94720, United States
- Helen Wills Neuroscience Institute. University of California, Berkeley, California 94720, United States
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19
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Gao J, Hori Y, Takeuchi O, Kikuchi K. Live-Cell Imaging of Protein Degradation Utilizing Designed Protein-Tag Mutant and Fluorescent Probe with Turn-Off Switch. Bioconjug Chem 2019; 31:577-583. [DOI: 10.1021/acs.bioconjchem.9b00696] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
| | | | - Osamu Takeuchi
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
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20
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Lopez Quezada L, Li K, McDonald SL, Nguyen Q, Perkowski AJ, Pharr CW, Gold B, Roberts J, McAulay K, Saito K, Somersan Karakaya S, Javidnia PE, Porras de Francisco E, Amieva MM, Dı́az SP, Mendoza Losana A, Zimmerman M, Liang HPH, Zhang J, Dartois V, Sans S, Lagrange S, Goullieux L, Roubert C, Nathan C, Aubé J. Dual-Pharmacophore Pyrithione-Containing Cephalosporins Kill Both Replicating and Nonreplicating Mycobacterium tuberculosis. ACS Infect Dis 2019; 5:1433-1445. [PMID: 31184461 DOI: 10.1021/acsinfecdis.9b00112] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The historical view of β-lactams as ineffective antimycobacterials has given way to growing interest in the activity of this class against Mycobacterium tuberculosis (Mtb) in the presence of a β-lactamase inhibitor. However, most antimycobacterial β-lactams kill Mtb only or best when the bacilli are replicating. Here, a screen of 1904 β-lactams led to the identification of cephalosporins substituted with a pyrithione moiety at C3' that are active against Mtb under both replicating and nonreplicating conditions, neither activity requiring a β-lactamase inhibitor. Studies showed that activity against nonreplicating Mtb required the in situ release of the pyrithione, independent of the known class A β-lactamase, BlaC. In contrast, replicating Mtb could be killed both by released pyrithione and by the parent β-lactam. Thus, the antimycobacterial activity of pyrithione-containing cephalosporins arises from two mechanisms that kill mycobacteria in different metabolic states.
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Affiliation(s)
- Landys Lopez Quezada
- Department of Microbiology and Immunology, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Kelin Li
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, 125 Mason Farm Road, Chapel Hill, North Carolina 27599, United States
| | - Stacey L. McDonald
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, 125 Mason Farm Road, Chapel Hill, North Carolina 27599, United States
| | - Quyen Nguyen
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, 125 Mason Farm Road, Chapel Hill, North Carolina 27599, United States
| | - Andrew J. Perkowski
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, 125 Mason Farm Road, Chapel Hill, North Carolina 27599, United States
| | - Cameron W. Pharr
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, 125 Mason Farm Road, Chapel Hill, North Carolina 27599, United States
| | - Ben Gold
- Department of Microbiology and Immunology, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Julia Roberts
- Department of Microbiology and Immunology, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Kathrine McAulay
- Center for Global Health, Weill Cornell Medicine, 402 East 67th Street, New York, New York 10065, United States
- Les Centres GHESKIO, 33, Boulevard Harry Truman, Port-au-Prince, Haiti
| | - Kohta Saito
- Department of Medicine, Weill Cornell Medical College, New York, New York 10065, United States
| | - Selin Somersan Karakaya
- Department of Medicine, Weill Cornell Medical College, New York, New York 10065, United States
| | - Prisca Elis Javidnia
- Department of Medicine, Weill Cornell Medical College, New York, New York 10065, United States
| | - Esther Porras de Francisco
- Diseases of the Developing World (DDW), Tres Cantos Medicine Development Campus, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Manuel Marin Amieva
- Diseases of the Developing World (DDW), Tres Cantos Medicine Development Campus, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Sara Palomo Dı́az
- Diseases of the Developing World (DDW), Tres Cantos Medicine Development Campus, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Alfonso Mendoza Losana
- Diseases of the Developing World (DDW), Tres Cantos Medicine Development Campus, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Matthew Zimmerman
- Public Health Research Institute, New Jersey Medical School, Rutgers, the State University of New Jersey, 225 Warren Street, Newark, New Jersey 07013, United States
| | - Hsin-Pin Ho Liang
- Public Health Research Institute, New Jersey Medical School, Rutgers, the State University of New Jersey, 225 Warren Street, Newark, New Jersey 07013, United States
| | - Jun Zhang
- Department of Microbiology and Immunology, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Veronique Dartois
- Public Health Research Institute, New Jersey Medical School, Rutgers, the State University of New Jersey, 225 Warren Street, Newark, New Jersey 07013, United States
| | - Stéphanie Sans
- Evotec ID (Lyon), SAS, 1541, Avenue Marcel Merieux, Marcy l’Etoile 69280, France
| | - Sophie Lagrange
- Evotec ID (Lyon), SAS, 1541, Avenue Marcel Merieux, Marcy l’Etoile 69280, France
| | - Laurent Goullieux
- Evotec ID (Lyon), SAS, 1541, Avenue Marcel Merieux, Marcy l’Etoile 69280, France
| | - Christine Roubert
- Evotec ID (Lyon), SAS, 1541, Avenue Marcel Merieux, Marcy l’Etoile 69280, France
| | - Carl Nathan
- Department of Microbiology and Immunology, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Jeffrey Aubé
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, 125 Mason Farm Road, Chapel Hill, North Carolina 27599, United States
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21
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Li B, Zhou X, Yang P, Zhu L, Zhong Y, Cai Z, Jiang B, Cai X, Liu J, Jiang X. Photoactivatable Fluorogenic Labeling via Turn-On "Click-Like" Nitroso-Diene Bioorthogonal Reaction. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1802039. [PMID: 31380178 PMCID: PMC6662066 DOI: 10.1002/advs.201802039] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 03/27/2019] [Indexed: 06/10/2023]
Abstract
Fluorogenic labeling enables imaging cellular molecules of interest with minimal background. This process is accompanied with the notable increase of the quantum yield of fluorophore, thus minimizing the background signals from unactivated profluorophores. Herein, the development of a highly efficient and bioorthogonal nitroso-based Diels-Alder fluorogenic reaction is presented and its usefulness is validated as effective and controllable in fluorescent probes and live-cell labeling strategies for dynamic cellular imaging. It is demonstrated that nitroso-based cycloaddition is an efficient fluorogenic labeling tool through experiments of further UV-activatable fluorescent labeling on proteins and live cells. The ability of tuning the fluorescence of labeled proteins by UV-irradiation enables selective activation of proteins of interest in a particular cell compartment at a given time point, while leaving the remaining labeled molecules untouched.
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Affiliation(s)
- Bai Li
- Guangdong Key Laboratory of Chiral Molecule and Drug DiscoverySchool of Pharmaceutical SciencesSun Yat‐Sen UniversityGuangzhouGuangdong510006China
| | - Xian‐Hao Zhou
- Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghai201210China
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
- University of Chinese Academy of SciencesBeijing100049China
| | - Peng‐Yu Yang
- Guangdong Key Laboratory of Chiral Molecule and Drug DiscoverySchool of Pharmaceutical SciencesSun Yat‐Sen UniversityGuangzhouGuangdong510006China
| | - Liping Zhu
- Guangdong Key Laboratory of Chiral Molecule and Drug DiscoverySchool of Pharmaceutical SciencesSun Yat‐Sen UniversityGuangzhouGuangdong510006China
| | - Yuan Zhong
- Guangdong Key Laboratory of Chiral Molecule and Drug DiscoverySchool of Pharmaceutical SciencesSun Yat‐Sen UniversityGuangzhouGuangdong510006China
| | - Zhengjun Cai
- Guangdong Key Laboratory of Chiral Molecule and Drug DiscoverySchool of Pharmaceutical SciencesSun Yat‐Sen UniversityGuangzhouGuangdong510006China
| | - Biao Jiang
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
- University of Chinese Academy of SciencesBeijing100049China
| | - Xiaoqing Cai
- Guangdong Key Laboratory of Chiral Molecule and Drug DiscoverySchool of Pharmaceutical SciencesSun Yat‐Sen UniversityGuangzhouGuangdong510006China
| | - Jia Liu
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
| | - Xianxing Jiang
- Guangdong Key Laboratory of Chiral Molecule and Drug DiscoverySchool of Pharmaceutical SciencesSun Yat‐Sen UniversityGuangzhouGuangdong510006China
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22
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Reja SI, Minoshima M, Hori Y, Kikuchi K. Development of an effective protein-labeling system based on smart fluorogenic probes. J Biol Inorg Chem 2019; 24:443-455. [PMID: 31152238 DOI: 10.1007/s00775-019-01669-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 05/15/2019] [Indexed: 12/23/2022]
Abstract
Proteins are an important component of living systems and play a crucial role in various physiological functions. Fluorescence imaging of proteins is a powerful tool for monitoring protein dynamics. Fluorescent protein (FP)-based labeling methods are frequently used to monitor the movement and interaction of cellular proteins. However, alternative methods have also been developed that allow the use of synthetic fluorescent probes to target a protein of interest (POI). Synthetic fluorescent probes have various advantages over FP-based labeling methods. They are smaller in size than the fluorescent proteins, offer a wide variety of colors and have improved photochemical properties. There are various chemical recognition-based labeling techniques that can be used for labeling a POI with a synthetic probe. In this review, we focus on the development of protein-labeling systems, particularly the SNAP-tag, BL-tag, and PYP-tag systems, and understanding the fluorescence behavior of the fluorescently labeled target protein in these systems. We also discuss the smart fluorogenic probes for these protein-labeling systems and their applications. The fluorogenic protein labeling will be a useful tool to investigate complex biological phenomena in future work on cell biology.
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Affiliation(s)
- Shahi Imam Reja
- Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Masafumi Minoshima
- Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Yuichiro Hori
- Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan
- Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, 565-0871, Japan
| | - Kazuya Kikuchi
- Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan.
- Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, 565-0871, Japan.
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23
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Zhang D, Liu R, Bao C, Zhang C, Yang L, Deng L, Bao B, Yang J, Chen X, Lin Q, Yang Y, Zhu L. Development of Acrylamide-Based Rapid and Multicolor Fluorogenic Probes for High Signal-to-Noise Live Cell Imaging. Bioconjug Chem 2019; 30:184-191. [PMID: 30566325 DOI: 10.1021/acs.bioconjchem.8b00827] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein covalent labeling is dramatically useful for studying protein function in living cells and organisms. In this field, the chemical tag technique combined with fluorogenic probes has emerged as a powerful tool. Herein, a series of TMP tag fluorogenic probes have been developed to span the green to full blue spectral range. These probes feature an acrylamide unit that acts as a linker group to conjugate the fluorophore and the ligand as well as a quencher and a covalent reaction group. After the probes bind to eDHFR:L28C, the acrylamide unit specifically reacts with the thiol group of the L28C residue beside the ligand binding pocket, achieving protein-specific labeling without any liberation of leaving groups. With these probes, multicolor and specific protein labeling with a fast reaction rate ( t1/2 = 33 s) and dramatic fluorescence enhancement (4000-fold) were obtained. Furthermore, no-wash protein labeling in both living cells and zebrafish was successfully achieved. We expect it may provide a general and highly effective chemical tool for the study of protein function in living cells and organisms.
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Affiliation(s)
- Dasheng Zhang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China.,School of Chemistry and Molecular Engineering , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China
| | - Renmei Liu
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China.,School of Pharmacy , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China
| | - Chunyan Bao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China.,School of Chemistry and Molecular Engineering , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China
| | - Chenxia Zhang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China.,School of Pharmacy , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China
| | - Lipeng Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China.,School of Chemistry and Molecular Engineering , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China
| | - Lei Deng
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China.,School of Pharmacy , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China
| | - Bingkun Bao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China.,School of Chemistry and Molecular Engineering , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China
| | - Jing Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China.,School of Pharmacy , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China
| | - Xianjun Chen
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China.,School of Pharmacy , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China
| | - Qiuning Lin
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China.,School of Chemistry and Molecular Engineering , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China
| | - Yi Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China.,School of Pharmacy , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China
| | - Linyong Zhu
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China.,School of Chemistry and Molecular Engineering , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China
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24
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Kumar N, Hori Y, Kikuchi K. Live-Cell Imaging of DNA Methylation Based on Synthetic-Molecule/Protein Hybrid Probe. CHEM REC 2018; 18:1672-1680. [PMID: 29863802 DOI: 10.1002/tcr.201800039] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 05/18/2018] [Indexed: 12/15/2022]
Abstract
The epigenetic modification of DNA involves the conversion of cytosine to 5-methylcytosine, also known as DNA methylation. DNA methylation is important in modulating gene expression and thus, regulating genome and cellular functions. Recent studies have shown that aberrations in DNA methylation are associated with various epigenetic disorders or diseases including cancer. This stimulates great interest in the development of methods that can detect and visualize DNA methylation. For instance, fluorescent proteins (FPs) in conjugation with methyl-CpG-binding domain (MBD) have been employed for live-cell imaging of DNA methylation. However, the FP-based approach showed fluorescence signals for both the DNA-bound and -unbound states and thus differentiation between these states is difficult. Synthetic-molecule/protein hybrid probes can provide an alternative to overcome this restriction. In this article, we discuss the synthetic-molecule/protein hybrid probe that we developed recently for live-cell imaging of DNA methylation, which exhibited fluorescence enhancement only after binding to methylated DNA.
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Affiliation(s)
- Naresh Kumar
- Graduate School of Engineering, Osaka University Suita, Osaka, 565-0871, Japan
| | - Yuichiro Hori
- Graduate School of Engineering, Osaka University Suita, Osaka, 565-0871, Japan.,Immunology Fontier Research Center, Osaka University Suita, Osaka, 565-0871, Japan
| | - Kazuya Kikuchi
- Graduate School of Engineering, Osaka University Suita, Osaka, 565-0871, Japan.,Immunology Fontier Research Center, Osaka University Suita, Osaka, 565-0871, Japan
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25
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Lotze J, Wolf P, Reinhardt U, Seitz O, Mörl K, Beck-Sickinger AG. Time-Resolved Tracking of Separately Internalized Neuropeptide Y 2 Receptors by Two-Color Pulse-Chase. ACS Chem Biol 2018; 13:618-627. [PMID: 29268018 DOI: 10.1021/acschembio.7b00999] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Internalization and intracellular trafficking of G protein-coupled receptors (GPCR) plays an important role in the signal transduction. These processes are often highly dynamic and take place rapidly. In the past 10 years, it became obvious that internalized GPCRs are also capable of signaling via arrestin or heterotrimeric G proteins within the endosomal compartment. Real-time imaging of receptors in living cells can help to evaluate the temporal and spatial localization. We achieved a two-color pulse-chase labeling approach, which allowed the tracking of the human neuropeptide Y2 receptor (hY2R) in the same cell at different times. The ability to visualize the internalization pathway of two separately labeled and separately stimulated subsets of hY2R in a time-resolved manner revealed a rapid trafficking. Fusion of the two hY2R subsets was already observed 10 min after stimulation in the early endosomal compartment without subsequent separation of the fused receptor populations. The results demonstrate that the cells do not discriminate between receptors that were stimulated and internalized at different time points.
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Affiliation(s)
- Jonathan Lotze
- Institute of Biochemistry, Leipzig University, 04103 Leipzig, Germany
| | - Philipp Wolf
- Institute of Biochemistry, Leipzig University, 04103 Leipzig, Germany
| | - Ulrike Reinhardt
- Institute of Chemistry, Humboldt-University Berlin, 12489 Berlin, Germany
| | - Oliver Seitz
- Institute of Chemistry, Humboldt-University Berlin, 12489 Berlin, Germany
| | - Karin Mörl
- Institute of Biochemistry, Leipzig University, 04103 Leipzig, Germany
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26
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Leng S, Qiao Q, Miao L, Deng W, Cui J, Xu Z. A wash-free SNAP-tag fluorogenic probe based on the additive effects of quencher release and environmental sensitivity. Chem Commun (Camb) 2018; 53:6448-6451. [PMID: 28560360 DOI: 10.1039/c7cc01483j] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A 1,8-naphthalimide-derived fluorogenic probe was reported to label SNAP-tag fusion proteins in living cells. The probe can rapidly label a SNAP-tag and exhibit a fluorescence increase of 36-fold due to the additive effects of environment sensitivity of fluorophores and inhibition of photo-induced electron transfer from O6-benzylguanine to the fluorophore. The labeling of intracellular proteins has been successfully achieved without a wash-out procedure.
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Affiliation(s)
- Shuang Leng
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
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27
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Sato R, Kozuka J, Ueda M, Mishima R, Kumagai Y, Yoshimura A, Minoshima M, Mizukami S, Kikuchi K. Intracellular Protein-Labeling Probes for Multicolor Single-Molecule Imaging of Immune Receptor-Adaptor Molecular Dynamics. J Am Chem Soc 2017; 139:17397-17404. [PMID: 29119782 DOI: 10.1021/jacs.7b08262] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Single-molecule imaging (SMI) has been widely utilized to investigate biomolecular dynamics and protein-protein interactions in living cells. However, multicolor SMI of intracellular proteins is challenging because of high background signals and other limitations of current fluorescence labeling approaches. To achieve reproducible intracellular SMI, a labeling probe ensuring both efficient membrane permeability and minimal non-specific binding to cell components is essential. We developed near-infrared fluorescent probes for protein labeling that specifically bind to a mutant β-lactamase tag. By structural fine-tuning of cell permeability and minimized non-specific binding, SiRcB4 enabled multicolor SMI in combination with a HaloTag-based red-fluorescent probe. Upon addition of both chemical probes at sub-nanomolar concentrations, single-molecule imaging revealed the dynamics of TLR4 and its adaptor protein, TIRAP, which are involved in the innate immune system. Statistical analysis of the quantitative properties and time-lapse changes in dynamics revealed a protein-protein interaction in response to ligand stimulation.
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Affiliation(s)
- Ryota Sato
- Department of Material and Life Science, Graduate School of Engineering, Osaka University , Suita, Osaka 565-0871, Japan
| | - Jun Kozuka
- RIKEN Quantitative Biology , Suita, Osaka 565-0874, Japan
| | - Masahiro Ueda
- RIKEN Quantitative Biology , Suita, Osaka 565-0874, Japan
| | - Reiko Mishima
- Quantitative Immunology Research Unit, WPI-Immunology Frontier Research Center, Osaka University , Suita, Osaka 565-0871, Japan
| | - Yutaro Kumagai
- Quantitative Immunology Research Unit, WPI-Immunology Frontier Research Center, Osaka University , Suita, Osaka 565-0871, Japan
| | - Akimasa Yoshimura
- Department of Material and Life Science, Graduate School of Engineering, Osaka University , Suita, Osaka 565-0871, Japan
| | - Masafumi Minoshima
- Department of Material and Life Science, Graduate School of Engineering, Osaka University , Suita, Osaka 565-0871, Japan
| | - Shin Mizukami
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University , Sendai, Miyagi, 980-8577, Japan
| | - Kazuya Kikuchi
- Department of Material and Life Science, Graduate School of Engineering, Osaka University , Suita, Osaka 565-0871, Japan.,Chemical Imaging Techniques, WPI-Immunology Frontier Research Center, Osaka University , Suita, Osaka 565-0871, Japan
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28
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Leng S, Qiao QL, Gao Y, Miao L, Deng WG, Xu ZC. SNAP-tag fluorogenic probes for wash free protein labeling. CHINESE CHEM LETT 2017. [DOI: 10.1016/j.cclet.2017.03.034] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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29
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Gallo E, Jarvik JW. Breaking the color barrier - a multi-selective antibody reporter offers innovative strategies of fluorescence detection. J Cell Sci 2017; 130:2644-2653. [PMID: 28615413 DOI: 10.1242/jcs.202952] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 06/08/2017] [Indexed: 01/14/2023] Open
Abstract
A novel bi-partite fluorescence platform exploits the high affinity and selectivity of antibody scaffolds to capture and activate small-molecule fluorogens. In this report, we investigated the property of multi-selectivity activation by a single antibody against diverse cyanine family fluorogens. Our fluorescence screen identified three cell-impermeant fluorogens, each with unique emission spectra (blue, green and red) and nanomolar affinities. Most importantly, as a protein fusion tag to G-protein-coupled receptors, the antibody biosensor retained full activity - displaying bright fluorogen signals with minimal background on live cells. Because fluorogen-activating antibodies interact with their target ligands via non-covalent interactions, we were able to perform advanced multi-color detection strategies on live cells, previously difficult or impossible with conventional reporters. We found that by fine-tuning the concentrations of the different color fluorogen molecules in solution, a user may interchange the fluorescence signal (onset versus offset), execute real-time signal exchange via fluorogen competition, measure multi-channel fluorescence via co-labeling, and assess real-time cell surface receptor traffic via pulse-chase experiments. Thus, here we inform of an innovative reporter technology based on tri-color signal that allows user-defined fluorescence tuning in live-cell applications.
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Affiliation(s)
- Eugenio Gallo
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Jonathan W Jarvik
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA.,Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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30
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Zhang R, Sun Y, Tian M, Zhang G, Feng R, Li X, Guo L, Yu X, Sun JZ, He X. Phospholipid-Biomimetic Fluorescent Mitochondrial Probe with Ultrahigh Selectivity Enables In Situ and High-Fidelity Tissue Imaging. Anal Chem 2017; 89:6575-6582. [DOI: 10.1021/acs.analchem.7b00710] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Ruoyao Zhang
- Center
of Bio and Micro/Nano Functional Materials, State Key Laboratory of
Crystal Materials, Shandong University, Jinan 250100, People’s Republic of China
| | - Yuming Sun
- School
of Information Science and Engineering, Shandong University, Jinan 250100, People’s Republic of China
| | - Minggang Tian
- Center
of Bio and Micro/Nano Functional Materials, State Key Laboratory of
Crystal Materials, Shandong University, Jinan 250100, People’s Republic of China
| | - Ge Zhang
- Center
of Bio and Micro/Nano Functional Materials, State Key Laboratory of
Crystal Materials, Shandong University, Jinan 250100, People’s Republic of China
| | - Ruiqing Feng
- Center
of Bio and Micro/Nano Functional Materials, State Key Laboratory of
Crystal Materials, Shandong University, Jinan 250100, People’s Republic of China
| | - Xuechen Li
- Center
of Bio and Micro/Nano Functional Materials, State Key Laboratory of
Crystal Materials, Shandong University, Jinan 250100, People’s Republic of China
| | - Lifang Guo
- Center
of Bio and Micro/Nano Functional Materials, State Key Laboratory of
Crystal Materials, Shandong University, Jinan 250100, People’s Republic of China
| | - Xiaoqiang Yu
- Center
of Bio and Micro/Nano Functional Materials, State Key Laboratory of
Crystal Materials, Shandong University, Jinan 250100, People’s Republic of China
| | - Jing Zhi Sun
- MoE
Key Laboratory of Macromolecule Synthesis and Functionalization, Department
of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, People’s Republic of China
| | - Xiuquan He
- Department
of Anatomy, Shandong University School of Medicine, Jinan 250012, People’s Republic of China
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31
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Liu Y, Miao K, Dunham NP, Liu H, Fares M, Boal AK, Li X, Zhang X. The Cation-π Interaction Enables a Halo-Tag Fluorogenic Probe for Fast No-Wash Live Cell Imaging and Gel-Free Protein Quantification. Biochemistry 2017; 56:1585-1595. [PMID: 28221782 PMCID: PMC5362743 DOI: 10.1021/acs.biochem.7b00056] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
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The design of fluorogenic
probes for a Halo tag is highly desirable
but challenging. Previous work achieved this goal by controlling the
chemical switch of spirolactones upon the covalent conjugation between
the Halo tag and probes or by incorporating a “channel dye”
into the substrate binding tunnel of the Halo tag. In this work, we
have developed a novel class of Halo-tag fluorogenic probes that are
derived from solvatochromic fluorophores. The optimal probe, harboring
a benzothiadiazole scaffold, exhibits a 1000-fold fluorescence enhancement
upon reaction with the Halo tag. Structural, computational, and biochemical
studies reveal that the benzene ring of a tryptophan residue engages
in a cation−π interaction with the dimethylamino electron-donating
group of the benzothiadiazole fluorophore in its excited state. We
further demonstrate using noncanonical fluorinated tryptophan that
the cation−π interaction directly contributes to the
fluorogenicity of the benzothiadiazole fluorophore. Mechanistically,
this interaction could contribute to the fluorogenicity by promoting
the excited-state charge separation and inhibiting the twisting motion
of the dimethylamino group, both leading to an enhanced fluorogenicity.
Finally, we demonstrate the utility of the probe in no-wash direct
imaging of Halo-tagged proteins in live cells. In addition, the fluorogenic
nature of the probe enables a gel-free quantification of fusion proteins
expressed in mammalian cells, an application that was not possible
with previously nonfluorogenic Halo-tag probes. The unique mechanism
revealed by this work suggests that incorporation of an excited-state
cation−π interaction could be a feasible strategy for
enhancing the optical performance of fluorophores and fluorogenic
sensors.
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Affiliation(s)
| | | | | | - Hongbin Liu
- Department of Chemistry, University of Washington , Seattle, Washington 98105, United States
| | | | | | - Xiaosong Li
- Department of Chemistry, University of Washington , Seattle, Washington 98105, United States
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32
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Targetable fluorescent sensors for advanced cell function analysis. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2017. [DOI: 10.1016/j.jphotochemrev.2017.01.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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33
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Braner M, Wieneke R, Tampé R. Nanomolar affinity protein trans-splicing monitored in real-time by fluorophore–quencher pairs. Chem Commun (Camb) 2017; 53:545-548. [DOI: 10.1039/c6cc08862g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We combined high-affinity protein trans-splicing with fluorophore/quencher pairs for online detection of covalent N-terminal ‘traceless’ protein labeling at nanomolar concentrations under physiological conditions in cellular environment.
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Affiliation(s)
- M. Braner
- Institute of Biochemistry, Biocenter
- Goethe University Frankfurt
- 60438 Frankfurt a.M
- Germany
| | - R. Wieneke
- Institute of Biochemistry, Biocenter
- Goethe University Frankfurt
- 60438 Frankfurt a.M
- Germany
| | - R. Tampé
- Institute of Biochemistry, Biocenter
- Goethe University Frankfurt
- 60438 Frankfurt a.M
- Germany
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34
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Mizukami S, Kikuchi K. [Visualization and Functional Regulation of Live Cell Proteins Based on Labeling Probe Design]. YAKUGAKU ZASSHI 2016; 136:21-7. [PMID: 26725663 DOI: 10.1248/yakushi.15-00225-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
There are several approaches to understanding the physiological roles of biomolecules: (1) by observing the localization or activities of biomolecules (based on microscopic imaging experiments with fluorescent proteins or fluorescent probes) and (2) by investigating the cellular response via activation or suppression of functions of the target molecule (by using inhibitors, antagonists, siRNAs, etc.). In this context, protein-labeling technology serves as a powerful tool that can be used in various experiments, such as for fluorescence imaging of target proteins. Recently, we developed a protein-labeling technology that uses a mutant β-lactamase (a bacterial hydrolase) as the tag protein. In this protein-labeling technology, also referred to as the BL-tag technology, various β-lactam compounds were used as specific ligands that were covalently labeled to the tag. One major advantage of this labeling technology is that various functions can be carried out by suitably designing both the functional moieties such as the fluorophore and the β-lactam ligand structure. In this review, we briefly introduce the BL-tag technology and describe our future outlook for this technology, such as in fluorescence imaging of biomolecules and functional regulation of cellular proteins in living cells.
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Affiliation(s)
- Shin Mizukami
- Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University
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35
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Fluorogenic probes reveal a role of GLUT4 N-glycosylation in intracellular trafficking. Nat Chem Biol 2016; 12:853-9. [PMID: 27547921 DOI: 10.1038/nchembio.2156] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 06/03/2016] [Indexed: 02/04/2023]
Abstract
Glucose transporter 4 (GLUT4) is an N-glycosylated protein that maintains glucose homeostasis by regulating the protein translocation. To date, it has been unclear whether the N-glycan of GLUT4 contributes to its intracellular trafficking. Here, to clarify the role of the N-glycan, we developed fluorogenic probes that label cytoplasmic and plasma-membrane proteins for multicolor imaging of GLUT4 translocation. One of the probes, which is cell impermeant, selectively detected exocytosed GLUT4. Using this probe, we verified the 'log' of the trafficking, in which N-glycan-deficient GLUT4 was transiently translocated to the cell membrane upon insulin stimulation and was rapidly internalized without retention on the cell membrane. The results strongly suggest that the N-glycan functions in the retention of GLUT4 on the cell membrane. This study showed the utility of the fluorogenic probes and indicated that this imaging tool will be applicable for research on various membrane proteins that show dynamic changes in localization.
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36
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DIVERSE System: De Novo Creation of Peptide Tags for Non-enzymatic Covalent Labeling by In Vitro Evolution for Protein Imaging Inside Living Cells. ACTA ACUST UNITED AC 2016; 22:1671-9. [PMID: 26687484 DOI: 10.1016/j.chembiol.2015.10.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 10/10/2015] [Accepted: 10/15/2015] [Indexed: 10/22/2022]
Abstract
Polypeptide-tag/small-molecule pairs for specific cellular protein labeling are useful for visualizing cellular proteins and controlling their activity. Here, we report the development of an in vitro evolution-based (poly)peptide tag identification system named the DIVERSE (Directed In Vitro Evolution of Reactive peptide tags via Sequential Enrichment) system. In this system, an extremely diverse (10(14)) library of peptide tags, displayed by covalent attachment to their encoding cDNAs, is continuously prepared from the DNA library in a one-pot approach. Using this system, we demonstrated de novo creation of non-enzymatically covalent-labeling peptide tags for a synthetic small-molecule target from a random peptide library. Protein labeling with these tags was applicable to N- and C-terminal fusions, multiple different proteins and fluorophores, and intracellular labeling. The DIVERSE system can be used not only for the de novo creation of polypeptide tags but also sequence optimization of existing polypeptide tags from extremely diverse libraries.
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37
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Baranczak A, Connelly S, Liu Y, Choi S, Grimster NP, Powers ET, Wilson IA, Kelly JW. Fluorogenic small molecules requiring reaction with a specific protein to create a fluorescent conjugate for biological imaging--what we know and what we need to learn. Biopolymers 2016; 101:484-95. [PMID: 24105107 DOI: 10.1002/bip.22407] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 09/03/2013] [Indexed: 01/03/2023]
Abstract
We seek fluorogenic small molecules that generate a fluorescent conjugate signal if and only if they react with a given protein-of-interest (i.e., small molecules for which noncovalent binding to the protein-of-interest is insufficient to generate fluorescence). Consequently, it is the new chemical entity afforded by the generally irreversible reaction between the small molecule and the protein-of-interest that enables the energy of an electron occupying the lowest unoccupied molecular orbital (LUMO) of the chromophore to be given off as a photon instead of being dissipated by nonradiative mechanisms in complex biological environments. This category of fluorogenic small molecules is created by starting with environmentally sensitive fluorophores that are modified by an essential functional group that efficiently quenches the fluorescence until a chemoselective reaction between that functional group and the protein-of-interest occurs, yielding the fluorescent conjugate. Fluorogenic small molecules are envisioned to be useful for a wide variety of applications, including live cell imaging without the requirement for washing steps and pulse-chase kinetic analyses of protein synthesis, trafficking, degradation, etc.
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Affiliation(s)
- Aleksandra Baranczak
- Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037; Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, 92037
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38
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Abstract
Over the years, there have been remarkable efforts in the development of selective protein labeling strategies. In this review, we deliver a comprehensive overview of the currently available bioorthogonal and chemoselective reactions. The ability to introduce bioorthogonal handles to proteins is essential to carry out bioorthogonal reactions for protein labeling in living systems. We therefore summarize the techniques that allow for site-specific "installation" of bioorthogonal handles into proteins. We also highlight the biological applications that have been achieved by selective chemical labeling of proteins.
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Affiliation(s)
- Xi Chen
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
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39
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Jung D, Sato K, Min K, Shigenaga A, Jung J, Otaka A, Kwon Y. Photo-triggered fluorescent labelling of recombinant proteins in live cells. Chem Commun (Camb) 2016; 51:9670-3. [PMID: 25977944 DOI: 10.1039/c5cc01067e] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A method to photo-chemically trigger fluorescent labelling of proteins in live cells is developed. The approach is based on photo-caged split-intein mediated conditional protein trans-splicing reaction and enabled background-free fluorescent labelling of target proteins with the necessary spatiotemporal control.
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Affiliation(s)
- Deokho Jung
- Department of Biomedical Engineering, Dongguk University-Seoul, Pildong 3-ga, Seoul, Korea.
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40
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Nishida Y, Ueda M, Hayashi M, Takeda N, Miyata O. Dimethylzinc-Mediated Chlorolactamization of Homoallylic Amines with Chloroform. European J Org Chem 2015. [DOI: 10.1002/ejoc.201501241] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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41
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Pham HH, Szent-Gyorgyi C, Brotherton WL, Schmidt BF, Zanotti KJ, Waggoner AS, Armitage BA. Bichromophoric dyes for wavelength shifting of dye-protein fluoromodules. Org Biomol Chem 2015; 13:3699-710. [PMID: 25679477 DOI: 10.1039/c4ob02522a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Dye-protein fluoromodules consist of fluorogenic dyes and single chain antibody fragments that form brightly fluorescent noncovalent complexes. This report describes two new bichromophoric dyes that extend the range of wavelengths of excitation or emission of existing fluoromodules. In one case, a fluorogenic thiazole orange (TO) was attached to an energy acceptor dye, Cy5. Upon binding to a protein that recognizes TO, red emission due to efficient energy transfer from TO to Cy5 replaces the green emission observed for monochromophoric TO bound to the same protein. Separately, TO was attached to a coumarin that serves as an energy donor. The same green emission is observed for coumarin-TO and TO bound to a protein, but efficient energy transfer allows violet excitation of coumarin-TO, versus longer wavelength, blue excitation of monochromophoric TO. Both bichromophores exhibit low nanomolar KD values for their respective proteins, >95% energy transfer efficiency and high fluorescence quantum yields.
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Affiliation(s)
- Ha H Pham
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
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42
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Hori Y, Hirayama S, Sato M, Kikuchi K. Redesign of a Fluorogenic Labeling System To Improve Surface Charge, Brightness, and Binding Kinetics for Imaging the Functional Localization of Bromodomains. Angew Chem Int Ed Engl 2015; 54:14368-71. [DOI: 10.1002/anie.201506935] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Yuichiro Hori
- Graduate School of Engineering, Osaka University, Osaka 565‐0871 (Japan)
- IFReC, Osaka University, Osaka 565‐0871 (Japan)
- JST, PRESTO, Osaka 565‐0871 (Japan)
| | - Shinya Hirayama
- Graduate School of Engineering, Osaka University, Osaka 565‐0871 (Japan)
| | - Motoki Sato
- Graduate School of Engineering, Osaka University, Osaka 565‐0871 (Japan)
| | - Kazuya Kikuchi
- Graduate School of Engineering, Osaka University, Osaka 565‐0871 (Japan)
- IFReC, Osaka University, Osaka 565‐0871 (Japan)
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43
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Hori Y, Hirayama S, Sato M, Kikuchi K. Redesign of a Fluorogenic Labeling System To Improve Surface Charge, Brightness, and Binding Kinetics for Imaging the Functional Localization of Bromodomains. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201506935] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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44
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Kamikawa Y, Hori Y, Yamashita K, Jin L, Hirayama S, Standley DM, Kikuchi K. Design of a protein tag and fluorogenic probe with modular structure for live-cell imaging of intracellular proteins. Chem Sci 2015; 7:308-314. [PMID: 29861984 PMCID: PMC5952543 DOI: 10.1039/c5sc02351c] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 09/28/2015] [Indexed: 01/17/2023] Open
Abstract
Conditional fluorescence imaging is a powerful technique for precise spatiotemporal analysis of proteins in live cells upon administration of a synthetic probe. To be applicable to various biological phenomena, probes must be membrane-permeable, have a high signal-to-noise ratio, and work quickly. To date, few probes meet all of these requirements. Here, we designed a fluorogenic probe (AcFCANB) that could label intracellular proteins fused to the photoactive yellow protein (PYP) tag in live cells within 30 min and used it to image heterochromatin protein 1 localization in nuclei. AcFCANB is based on a modular platform consisting of fluorophore, ligand and quencher. We accelerated the labeling reaction by strategic mutations of charged residues on the surface of PYP. A simple model based on molecular dynamics simulations quantitatively reproduced the cooperative effect of multiple mutations on labeling rate.
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Affiliation(s)
| | - Yuichiro Hori
- Graduate School of Engineering , Osaka University , Osaka 565-0871 , Japan . .,IFReC , Osaka University , Osaka 565-0871 , Japan.,JST , PRESTO , Osaka 565-0871 , Japan
| | | | - Lin Jin
- IFReC , Osaka University , Osaka 565-0871 , Japan
| | - Shinya Hirayama
- Graduate School of Engineering , Osaka University , Osaka 565-0871 , Japan .
| | | | - Kazuya Kikuchi
- Graduate School of Engineering , Osaka University , Osaka 565-0871 , Japan . .,IFReC , Osaka University , Osaka 565-0871 , Japan
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45
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Liu Y, Zhang X, Chen W, Tan YL, Kelly JW. Fluorescence Turn-On Folding Sensor To Monitor Proteome Stress in Live Cells. J Am Chem Soc 2015; 137:11303-11. [PMID: 26305239 PMCID: PMC4755273 DOI: 10.1021/jacs.5b04366] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Proteome misfolding and/or aggregation, caused by a thermal perturbation or a related stress, transiently challenges the cellular protein homeostasis (proteostasis) network capacity of cells by consuming chaperone/chaperonin pathway and degradation pathway capacity. Developing protein client-based probes to quantify the cellular proteostasis network capacity in real time is highly desirable. Herein we introduce a small-molecule-regulated fluorescent protein folding sensor based on a thermo-labile mutant of the de novo designed retroaldolase (RA) enzyme. Since RA enzyme activity is not present in any cell, the protein folding sensor is bioorthogonal. The fluorogenic small molecule was designed to become fluorescent when it binds to and covalently reacts with folded and functional RA. Thus, in the first experimental paradigm, cellular proteostasis network capacity and its dynamics are reflected by RA-small molecule conjugate fluorescence, which correlates with the amount of folded and functional RA present, provided that pharmacologic chaperoning is minimized. In the second experimental scenario, the RA-fluorogenic probe conjugate is pre-formed in a cell by simply adding the fluorogenic probe to the cell culture media. Unreacted probe is then washed away before a proteome misfolding stress is applied in a pulse-chase-type experiment. Insufficient proteostasis network capacity is reflected by aggregate formation of the fluorescent RA-fluorogenic probe conjugate. Removal of the stress results in apparent RA-fluorogenic probe conjugate re-folding, mediated in part by the heat-shock response transcriptional program augmenting cytosolic proteostasis network capacity, and in part by time-dependent RA-fluorogenic probe conjugate degradation by cellular proteolysis.
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Affiliation(s)
- Yu Liu
- Department of Chemistry, ‡Department of Molecular and Experimental Medicine, and §The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Xin Zhang
- Department of Chemistry, ‡Department of Molecular and Experimental Medicine, and §The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Wentao Chen
- Department of Chemistry, ‡Department of Molecular and Experimental Medicine, and §The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Yun Lei Tan
- Department of Chemistry, ‡Department of Molecular and Experimental Medicine, and §The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Jeffery W Kelly
- Department of Chemistry, ‡Department of Molecular and Experimental Medicine, and §The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States
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46
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Telmer CA, Verma R, Teng H, Andreko S, Law L, Bruchez MP. Rapid, specific, no-wash, far-red fluorogen activation in subcellular compartments by targeted fluorogen activating proteins. ACS Chem Biol 2015; 10:1239-46. [PMID: 25650487 PMCID: PMC4867890 DOI: 10.1021/cb500957k] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
Live cell imaging
requires bright photostable dyes that can target
intracellular organelles and proteins with high specificity in a no-wash
protocol. Organic dyes possess the desired photochemical properties
and can be covalently linked to various protein tags. The currently
available fluorogenic dyes are in the green/yellow range where there
is high cellular autofluorescence and the near-infrared (NIR) dyes
need to be washed out. Protein-mediated activation of far-red fluorogenic
dyes has the potential to address these challenges because the cell-permeant
dye is small and nonfluorescent until bound to its activating protein,
and this binding is rapid. In this study, three single chain variable
fragment (scFv)-derived fluorogen activating proteins (FAPs), which
activate far-red emitting fluorogens, were evaluated for targeting,
brightness, and photostability in the cytosol, nucleus, mitochondria,
peroxisomes, and endoplasmic reticulum with a cell-permeant malachite
green analog in cultured mammalian cells. Efficient labeling was achieved
within 20–30 min for each protein upon the addition of nM concentrations
of dye, producing a signal that colocalized significantly with a linked
mCerulean3 (mCer3) fluorescent protein and organelle specific dyes
but showed divergent photostability and brightness properties dependent
on the FAP. These FAPs and the ester of malachite green dye (MGe)
can be used as specific, rapid, and wash-free labels for intracellular
sites in live cells with far-red excitation and emission properties,
useful in a variety of multicolor experiments.
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Affiliation(s)
- Cheryl A. Telmer
- Molecular Biosensor and Imaging
Center, Carnegie Mellon University, Mellon Institute, 4400 Fifth
Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Richa Verma
- Molecular Biosensor and Imaging
Center, Carnegie Mellon University, Mellon Institute, 4400 Fifth
Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Haibing Teng
- Molecular Biosensor and Imaging
Center, Carnegie Mellon University, Mellon Institute, 4400 Fifth
Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Susan Andreko
- Molecular Biosensor and Imaging
Center, Carnegie Mellon University, Mellon Institute, 4400 Fifth
Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Leann Law
- Molecular Biosensor and Imaging
Center, Carnegie Mellon University, Mellon Institute, 4400 Fifth
Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Marcel P. Bruchez
- Molecular Biosensor and Imaging
Center, Carnegie Mellon University, Mellon Institute, 4400 Fifth
Avenue, Pittsburgh, Pennsylvania 15213, United States
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47
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Liu TK, Hsieh PY, Zhuang YD, Hsia CY, Huang CL, Lai HP, Lin HS, Chen IC, Hsu HY, Tan KT. A rapid SNAP-tag fluorogenic probe based on an environment-sensitive fluorophore for no-wash live cell imaging. ACS Chem Biol 2014; 9:2359-65. [PMID: 25105835 DOI: 10.1021/cb500502n] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
One major limitation of labeling proteins with synthetic fluorophores is the high fluorescence background, which necessitates extensive washing steps to remove unreacted fluorophores. In this paper, we describe a novel fluorogenic probe based on an environment-sensitive fluorophore for labeling with SNAP-tag proteins. The probe exhibits dramatic fluorescence turn-on of 280-fold upon being labeled to SNAP-tag. The major advantages of our fluorogenic probe are the dramatic fluorescence turn-on, ease of synthesis, high selectivity, and rapid labeling with SNAP-tag. No-wash labeling of both intracellular and cell surface proteins was successfully achieved in living cells, and the localization of these proteins was specifically visualized.
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Affiliation(s)
- Tao-Kai Liu
- Department of Chemistry and ‡Frontier Research Center on Fundamental
and Applied
Sciences of Matters, National Tsing Hua University, 101 Sec.
2, Kuang-Fu Rd., Hsinchu 30013, Taiwan (ROC)
- Department of Applied Chemistry and Institute of Molecular Science and ∥Center for Interdisciplinary
Science (CIS), National Chiao-Tung University, No.1001 Ta-Hsueh Road, Hsinchu 30010, Taiwan (ROC)
| | - Pei-Ying Hsieh
- Department of Chemistry and ‡Frontier Research Center on Fundamental
and Applied
Sciences of Matters, National Tsing Hua University, 101 Sec.
2, Kuang-Fu Rd., Hsinchu 30013, Taiwan (ROC)
- Department of Applied Chemistry and Institute of Molecular Science and ∥Center for Interdisciplinary
Science (CIS), National Chiao-Tung University, No.1001 Ta-Hsueh Road, Hsinchu 30010, Taiwan (ROC)
| | - Yu-De Zhuang
- Department of Chemistry and ‡Frontier Research Center on Fundamental
and Applied
Sciences of Matters, National Tsing Hua University, 101 Sec.
2, Kuang-Fu Rd., Hsinchu 30013, Taiwan (ROC)
- Department of Applied Chemistry and Institute of Molecular Science and ∥Center for Interdisciplinary
Science (CIS), National Chiao-Tung University, No.1001 Ta-Hsueh Road, Hsinchu 30010, Taiwan (ROC)
| | - Chi-Yang Hsia
- Department of Chemistry and ‡Frontier Research Center on Fundamental
and Applied
Sciences of Matters, National Tsing Hua University, 101 Sec.
2, Kuang-Fu Rd., Hsinchu 30013, Taiwan (ROC)
- Department of Applied Chemistry and Institute of Molecular Science and ∥Center for Interdisciplinary
Science (CIS), National Chiao-Tung University, No.1001 Ta-Hsueh Road, Hsinchu 30010, Taiwan (ROC)
| | - Chi-Ling Huang
- Department of Chemistry and ‡Frontier Research Center on Fundamental
and Applied
Sciences of Matters, National Tsing Hua University, 101 Sec.
2, Kuang-Fu Rd., Hsinchu 30013, Taiwan (ROC)
- Department of Applied Chemistry and Institute of Molecular Science and ∥Center for Interdisciplinary
Science (CIS), National Chiao-Tung University, No.1001 Ta-Hsueh Road, Hsinchu 30010, Taiwan (ROC)
| | - Hsiu-Ping Lai
- Department of Chemistry and ‡Frontier Research Center on Fundamental
and Applied
Sciences of Matters, National Tsing Hua University, 101 Sec.
2, Kuang-Fu Rd., Hsinchu 30013, Taiwan (ROC)
- Department of Applied Chemistry and Institute of Molecular Science and ∥Center for Interdisciplinary
Science (CIS), National Chiao-Tung University, No.1001 Ta-Hsueh Road, Hsinchu 30010, Taiwan (ROC)
| | - Hung-Sheung Lin
- Department of Chemistry and ‡Frontier Research Center on Fundamental
and Applied
Sciences of Matters, National Tsing Hua University, 101 Sec.
2, Kuang-Fu Rd., Hsinchu 30013, Taiwan (ROC)
- Department of Applied Chemistry and Institute of Molecular Science and ∥Center for Interdisciplinary
Science (CIS), National Chiao-Tung University, No.1001 Ta-Hsueh Road, Hsinchu 30010, Taiwan (ROC)
| | - I-Chia Chen
- Department of Chemistry and ‡Frontier Research Center on Fundamental
and Applied
Sciences of Matters, National Tsing Hua University, 101 Sec.
2, Kuang-Fu Rd., Hsinchu 30013, Taiwan (ROC)
- Department of Applied Chemistry and Institute of Molecular Science and ∥Center for Interdisciplinary
Science (CIS), National Chiao-Tung University, No.1001 Ta-Hsueh Road, Hsinchu 30010, Taiwan (ROC)
| | - Hsin-Yun Hsu
- Department of Chemistry and ‡Frontier Research Center on Fundamental
and Applied
Sciences of Matters, National Tsing Hua University, 101 Sec.
2, Kuang-Fu Rd., Hsinchu 30013, Taiwan (ROC)
- Department of Applied Chemistry and Institute of Molecular Science and ∥Center for Interdisciplinary
Science (CIS), National Chiao-Tung University, No.1001 Ta-Hsueh Road, Hsinchu 30010, Taiwan (ROC)
| | - Kui-Thong Tan
- Department of Chemistry and ‡Frontier Research Center on Fundamental
and Applied
Sciences of Matters, National Tsing Hua University, 101 Sec.
2, Kuang-Fu Rd., Hsinchu 30013, Taiwan (ROC)
- Department of Applied Chemistry and Institute of Molecular Science and ∥Center for Interdisciplinary
Science (CIS), National Chiao-Tung University, No.1001 Ta-Hsueh Road, Hsinchu 30010, Taiwan (ROC)
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48
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Applications of flow cytometry to characterize bacterial physiological responses. BIOMED RESEARCH INTERNATIONAL 2014; 2014:461941. [PMID: 25276788 PMCID: PMC4174974 DOI: 10.1155/2014/461941] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 08/13/2014] [Accepted: 08/13/2014] [Indexed: 12/30/2022]
Abstract
Although reports of flow cytometry (FCM) applied to bacterial analysis are increasing, studies of FCM related to human cells still vastly outnumber other reports. However, current advances in FCM combined with a new generation of cellular reporter probes have made this technique suitable for analyzing physiological responses in bacteria. We review how FCM has been applied to characterize distinct physiological conditions in bacteria including responses to antibiotics and other cytotoxic chemicals and physical factors, pathogen-host interactions, cell differentiation during biofilm formation, and the mechanisms governing development pathways such as sporulation. Since FCM is suitable for performing studies at the single-cell level, we describe how this powerful technique has yielded invaluable information about the heterogeneous distribution of differently and even specialized responding cells and how it may help to provide insights about how cell interaction takes place in complex structures, such as those that prevail in bacterial biofilms.
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49
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LDAI-Based Chemical Labeling of Intact Membrane Proteins and Its Pulse-Chase Analysis under Live Cell Conditions. ACTA ACUST UNITED AC 2014; 21:1013-22. [DOI: 10.1016/j.chembiol.2014.07.013] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 07/11/2014] [Accepted: 07/30/2014] [Indexed: 11/21/2022]
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50
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Photoclick chemistry: a fluorogenic light-triggered in vivo ligation reaction. Curr Opin Chem Biol 2014; 21:89-95. [PMID: 25022432 DOI: 10.1016/j.cbpa.2014.05.024] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 05/17/2014] [Accepted: 05/28/2014] [Indexed: 12/11/2022]
Abstract
The ability to use chemical reactivity to monitor and control biomolecular processes with a spatial and temporal precision motivated the development of light-triggered in vivo chemistries. To this end, the photoinduced tetrazole-alkene cycloaddition, also termed 'photoclick chemistry' offers a very rapid chemical ligation platform for the manipulation of biomolecules and matrices in vivo. Here we outline the recent developments in the optimization of this chemistry, ranging from the search for substrates that offer two-photon photoactivatability, superior reaction kinetics, and/or genetic encodability, to the study of the reaction mechanism. The applications of the photoclick chemistry in protein labeling in vitro and in vivo as well as in preparing 'smart' hydrogels for 3D cell culture are highlighted.
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