1
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Santos E, 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; 19:1725-1732. [PMID: 39046136 PMCID: PMC11334107 DOI: 10.1021/acschembio.4c00125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 07/05/2024] [Accepted: 07/15/2024] [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)
| | - 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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Guo Y, Zhang X. Unveiling intracellular phase separation: advances in optical imaging of biomolecular condensates. Trends Biochem Sci 2024:S0968-0004(24)00163-4. [PMID: 39034215 DOI: 10.1016/j.tibs.2024.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 06/20/2024] [Accepted: 06/25/2024] [Indexed: 07/23/2024]
Abstract
Intracellular biomolecular condensates, which form via phase separation, display a highly organized ultrastructure and complex properties. Recent advances in optical imaging techniques, including super-resolution microscopy and innovative microscopic methods that leverage the intrinsic properties of the molecules observed, have transcended the limitations of conventional microscopies. These advances facilitate the exploration of condensates at finer scales and in greater detail. The deployment of these emerging but sophisticated imaging tools allows for precise observations of the multiphasic organization and physicochemical properties of these condensates, shedding light on their functions in cellular processes. In this review, we highlight recent progress in methodological innovations and their profound implications for understanding the organization and dynamics of intracellular biomolecular condensates.
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Affiliation(s)
- Yinfeng Guo
- Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, Hangzhou 310030, PR China
| | - Xin Zhang
- Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, Hangzhou 310030, PR China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, PR China.
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3
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Li M, Chen Y, He W, Guo Z. Fluorescence and Lifetime Imaging of Endoplasmic Reticulum Polarity Change During Ferroptosis. Chemistry 2024; 30:e202401285. [PMID: 38628070 DOI: 10.1002/chem.202401285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Indexed: 05/28/2024]
Abstract
As a new form of regulated cell death, ferroptosis is closely related to various diseases. Tracing ferroptosis related biological behavior is helpful to better understand this process and its related biology. Considering that ferroptosis is featured with remarkable lipid peroxidation which can easily change the membranes' compositions and structures, it is potential to detect intracellular environmental changes for direct assessment of ferroptosis. In view of the close relationship between endoplasmic reticulum (ER) and ferroptosis, we designed an ER-targeted and polarity-sensitive fluorescent probe SBD-CH, which has superior photostability and can respond to polarity with high selectivity without the affection of viscosity. SBD-CH can monitor the trend of ER polarity during ferroptosis by confocal laser scanning microscopy (CLSM), and analyze the distribution of polarity in ferroptosis by fluorescence lifetime imaging microscopy (FLIM). During Erastin induced ferroptosis, the polarity of ER in HT-1080 cells increased and the polarity distribution in ER was more dispersed. Our work provides an effective strategy for evaluating the process of ferroptosis by monitoring the changes of ER polarity.
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Affiliation(s)
- Mingfeng Li
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, Jiangsu, PR China
| | - Yuncong Chen
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, Jiangsu, PR China
- Department of Cardiothoracic Surgery, Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, 210008, Jiangsu, PR China
- Nanchuang (Jiangsu) Institute of Chemistry and Health, Nanjing, 210000, Jiangsu, PR China
| | - Weijiang He
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, Jiangsu, PR China
- Nanchuang (Jiangsu) Institute of Chemistry and Health, Nanjing, 210000, Jiangsu, PR China
| | - Zijian Guo
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, Jiangsu, PR China
- Nanchuang (Jiangsu) Institute of Chemistry and Health, Nanjing, 210000, Jiangsu, PR China
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4
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Zhang D, Chen Z, Du Z, Bao B, Su N, Chen X, Ge Y, Lin Q, Yang L, Hua Y, Wang S, Hua X, Zuo F, Li N, Liu R, Jiang L, Bao C, Zhao Y, Loscalzo J, Yang Y, Zhu L. Design of a palette of SNAP-tag mimics of fluorescent proteins and their use as cell reporters. Cell Discov 2023; 9:56. [PMID: 37311750 DOI: 10.1038/s41421-023-00546-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 03/18/2023] [Indexed: 06/15/2023] Open
Abstract
Naturally occurring fluorescent proteins (FPs) are the most widely used tools for tracking cellular proteins and sensing cellular events. Here, we chemically evolved the self-labeling SNAP-tag into a palette of SNAP-tag mimics of fluorescent proteins (SmFPs) that possess bright, rapidly inducible fluorescence ranging from cyan to infrared. SmFPs are integral chemical-genetic entities based on the same fluorogenic principle as FPs, i.e., induction of fluorescence of non-emitting molecular rotors by conformational locking. We demonstrate the usefulness of these SmFPs in real-time tracking of protein expression, degradation, binding interactions, trafficking, and assembly, and show that these optimally designed SmFPs outperform FPs like GFP in many important ways. We further show that the fluorescence of circularly permuted SmFPs is sensitive to the conformational changes of their fusion partners, and that these fusion partners can be used for the development of single SmFP-based genetically encoded calcium sensors for live cell imaging.
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Affiliation(s)
- Dasheng Zhang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Zhengda Chen
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Zengmin Du
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Bingkun Bao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Ni Su
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Xianjun Chen
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China.
| | - Yihui Ge
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Qiuning Lin
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Lipeng Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Yujie Hua
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Shuo Wang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Xin Hua
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Fangting Zuo
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Ningfeng Li
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Renmei Liu
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Li Jiang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Chunyan Bao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yuzheng Zhao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Joseph Loscalzo
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yi Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China.
| | - Linyong Zhu
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China.
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.
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5
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Nishiura M, Hori Y, Umeno M, Kikuchi K. Visualization of multiple localizations of GLUT4 by fluorescent probes of PYP-tag with designed unnatural warhead. Chem Sci 2023; 14:5925-5935. [PMID: 37293637 PMCID: PMC10246691 DOI: 10.1039/d3sc00724c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/08/2023] [Indexed: 06/10/2023] Open
Abstract
Within a cell, multiple copies of the same protein coexist in different pathways and behave differently. Being able to individually analyze the constant actions of proteins in a cell is crucial to know the pathways through which they pass and which physiological functions they are deeply involved in. However, until now, it has been difficult to distinguish protein copies with distinct translocation properties by fluorescence labeling with different colors in living cells. In this study, we have created an unnatural ligand with an unprecedented protein-tag labeling property in living cells and overcome the above-mentioned problem. Of special interest is that some fluorescent probes with the ligand can selectively and efficiently label intracellular proteins without binding to cell-surface proteins, even if the proteins are present on the cell membrane. We also developed a cell-membrane impermeable fluorescent probe that selectively labels cell-surface proteins without labeling of intracellular proteins. These localization-selective properties enabled us to visually discriminate two kinetically distinct glucose transporter 4 (GLUT4) molecules that show different multiple subcellular localization and translocation dynamics in live cells. Taking advantage of the probes, we revealed that N-glycosylation of GLUT4 influences intracellular localization. Furthermore, we were able to visually distinguish active GLUT4 molecules that underwent membrane translocation at least twice within an hour from those that remained intracellularly, discovering previously unrecognized dynamic behaviors of GLUT4. This technology provides not only a valuable tool for study on multiple localization and dynamics of proteins but also important information on diseases caused by protein translocation dysfunction.
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Affiliation(s)
- Miyako Nishiura
- Department of Applied Chemistry, Graduate School of Engineering, and Division of Applied Chemistry, Osaka University Suita Osaka 565-0871 Japan
| | - Yuichiro Hori
- Department of Chemistry, Faculty of Science, Kyushu University Fukuoka Fukuoka 819-0395 Japan
| | - Maho Umeno
- Department of Applied Chemistry, Graduate School of Engineering, and Division of Applied Chemistry, Osaka University Suita Osaka 565-0871 Japan
| | - Kazuya Kikuchi
- Department of Applied Chemistry, Graduate School of Engineering, and Division of Applied Chemistry, 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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6
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Jung KH, Sun J, Hsiung CH, Lance Lian X, Liu Y, Zhang X. Nuclear bodies protect phase separated proteins from degradation in stressed proteome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.19.537522. [PMID: 37131610 PMCID: PMC10153235 DOI: 10.1101/2023.04.19.537522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
RNA-binding proteins (RBPs) containing intrinsically disordered domains undergo liquid-liquid phase separation to form nuclear bodies under stress conditions. This process is also connected to the misfolding and aggregation of RBPs, which are associated with a series of neurodegenerative diseases. However, it remains elusive how folding states of RBPs changes upon the formation and maturation of nuclear bodies. Here, we describe SNAP-tag based imaging methods to visualize the folding states of RBPs in live cells via time-resolved quantitative microscopic analyses of their micropolarity and microviscosity. Using these imaging methods in conjunction with immunofluorescence imaging, we demonstrate that RBPs, represented by TDP-43, initially enters the PML nuclear bodies in its native state upon transient proteostasis stress, albeit it begins to misfolded during prolonged stress. Furthermore, we show that heat shock protein 70 co-enters the PML nuclear bodies to prevent the degradation of TDP-43 from the proteotoxic stress, thus revealing a previously unappreciated protective role of the PML nuclear bodies in the prevention of stress-induced degradation of TDP-43. In summary, our imaging methods described in the manuscript, for the first time, reveal the folding states of RBPs, which were previously challenging to study with conventional methods in nuclear bodies of live cells. This study uncovers the mechanistic correlations between the folding states of a protein and functions of nuclear bodies, in particular PML bodies. We envision that the imaging methods can be generally applied to elucidating the structural aspects of other proteins that exhibit granular structures under biological stimulus.
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Affiliation(s)
- Kwan Ho Jung
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The Huck Institute of Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, 16802, United States
| | - Jiarui Sun
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The Huck Institute of Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, 16802, United States
| | - Chia-Heng Hsiung
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The Huck Institute of Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, 16802, United States
- Present address: Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang Province, China; Westlake Laboratory of Life Sciences and Biomedicine; 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
- Department of Biomedical Engineering, The Huck Institute of Life Sciences, Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, 16802, United States
| | - Xiaojun Lance Lian
- Department of Biomedical Engineering, The Huck Institute of Life Sciences, Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, 16802, United States
| | - Yu Liu
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China
| | - Xin Zhang
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The Huck Institute of Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, 16802, United States
- Present address: Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang Province, China; Westlake Laboratory of Life Sciences and Biomedicine; 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
- Department of Biomedical Engineering, The Huck Institute of Life Sciences, Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, 16802, United States
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7
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Dreyer R, Pfukwa R, Barth S, Hunter R, Klumperman B. The Evolution of SNAP-Tag Labels. Biomacromolecules 2023; 24:517-530. [PMID: 36607253 DOI: 10.1021/acs.biomac.2c01238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The conjugation of proteins with synthetic molecules can be conducted in many different ways. In this Perspective, we focus on tag-based techniques and specifically on the SNAP-tag technology. The SNAP-tag technology makes use of a fusion protein between a protein of interest and an enzyme tag that enables the actual conjugation reaction. The SNAP-tag is based on the O6-alkylguanine-DNA alkyltransferase (AGT) enzyme and is optimized to react selectively with O6-benzylguanine (BG) substrates. BG-containing dye derivatives have frequently been used to introduce a fluorescent tag to a specific protein. We believe that the site-specific conjugation of polymers to proteins can significantly benefit from the SNAP-tag technology. Especially, polymers synthesized via reversible deactivation radical polymerization allow for the facile introduction of a BG end group to enable SNAP-tag conjugation.
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Affiliation(s)
- Rudolf Dreyer
- Stellenbosch University, Department of Chemistry and Polymer Science, Private Bag X1, Matieland 7602, South Africa
| | - Rueben Pfukwa
- Stellenbosch University, Department of Chemistry and Polymer Science, Private Bag X1, Matieland 7602, South Africa
| | - Stefan Barth
- Medical Biotechnology and Immunotherapy Research Unit, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory 7935, South Africa.,South African Research Chair in Cancer Biotechnology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Observatory 7935, South Africa
| | - Roger Hunter
- Department of Chemistry, Faculty of Science, University of Cape Town, Rondebosch 7701, South Africa
| | - Bert Klumperman
- Stellenbosch University, Department of Chemistry and Polymer Science, Private Bag X1, Matieland 7602, South Africa
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8
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Choosing the Probe for Single-Molecule Fluorescence Microscopy. Int J Mol Sci 2022; 23:ijms232314949. [PMID: 36499276 PMCID: PMC9735909 DOI: 10.3390/ijms232314949] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/18/2022] [Accepted: 11/24/2022] [Indexed: 12/03/2022] Open
Abstract
Probe choice in single-molecule microscopy requires deeper evaluations than those adopted for less sensitive fluorescence microscopy studies. Indeed, fluorophore characteristics can alter or hide subtle phenomena observable at the single-molecule level, wasting the potential of the sophisticated instrumentation and algorithms developed for advanced single-molecule applications. There are different reasons for this, linked, e.g., to fluorophore aspecific interactions, brightness, photostability, blinking, and emission and excitation spectra. In particular, these spectra and the excitation source are interdependent, and the latter affects the autofluorescence of sample substrate, medium, and/or biological specimen. Here, we review these and other critical points for fluorophore selection in single-molecule microscopy. We also describe the possible kinds of fluorophores and the microscopy techniques based on single-molecule fluorescence. We explain the importance and impact of the various issues in fluorophore choice, and discuss how this can become more effective and decisive for increasingly demanding experiments in single- and multiple-color applications.
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9
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Jiang C, Huang H, Kang X, Yang L, Xi Z, Sun H, Pluth MD, Yi L. NBD-based synthetic probes for sensing small molecules and proteins: design, sensing mechanisms and biological applications. Chem Soc Rev 2021; 50:7436-7495. [PMID: 34075930 PMCID: PMC8763210 DOI: 10.1039/d0cs01096k] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Compounds with a nitrobenzoxadiazole (NBD) skeleton exhibit prominent useful properties including environmental sensitivity, high reactivity toward amines and biothiols (including H2S) accompanied by distinct colorimetric and fluorescent changes, fluorescence-quenching ability, and small size, all of which facilitate biomolecular sensing and self-assembly. Amines are important biological nucleophiles, and the unique activity of NBD ethers with amines has allowed for site-specific protein labelling and for the detection of enzyme activities. Both H2S and biothiols are involved in a wide range of physiological processes in mammals, and misregulation of these small molecules is associated with numerous diseases including cancers. In this review, we focus on NBD-based synthetic probes as advanced chemical tools for biomolecular sensing. Specifically, we discuss the sensing mechanisms and selectivity of the probes, the design strategies for multi-reactable multi-quenching probes, and the associated biological applications of these important constructs. We also highlight self-assembled NBD-based probes and outline future directions for NBD-based chemosensors. We hope that this comprehensive review will facilitate the development of future probes for investigating and understanding different biological processes and aid the development of potential theranostic agents.
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Affiliation(s)
- Chenyang Jiang
- State Key Laboratory of Organic-Inorganic Composites and Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology (BUCT), Beijing 100029, China.
| | - Haojie Huang
- State Key Laboratory of Organic-Inorganic Composites and Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology (BUCT), Beijing 100029, China.
| | - Xueying Kang
- State Key Laboratory of Organic-Inorganic Composites and Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology (BUCT), Beijing 100029, China.
| | - Liu Yang
- Department of Chemistry and Center of Super-Diamond and Advanced Films (COSDAF), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China.
| | - Zhen Xi
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, National Pesticide Engineering Research Center, Collaborative Innovation Center of Chemical Science and Engineering, Nankai University, Tianjin 300071, China.
| | - Hongyan Sun
- Department of Chemistry and Center of Super-Diamond and Advanced Films (COSDAF), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China. and Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, China
| | - Michael D Pluth
- Department of Chemistry and Biochemistry, Materials Science Institute, Knight Campus for Accelerating Scientific Impact, Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA.
| | - Long Yi
- State Key Laboratory of Organic-Inorganic Composites and Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology (BUCT), Beijing 100029, China.
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10
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An assembly-regulated SNAP-tag fluorogenic probe for long-term super-resolution imaging of mitochondrial dynamics. Biosens Bioelectron 2021; 176:112886. [PMID: 33421760 DOI: 10.1016/j.bios.2020.112886] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/27/2020] [Accepted: 12/08/2020] [Indexed: 12/17/2022]
Abstract
Super-resolution fluorescence microscopy has emerged as a powerful tool for studying mitochondrial dynamics in living cells. However, the lack of photostable and chemstable probe makes long-term super-resolution imaging of mitochondria still a challenging work. Herein, we reported a 4-azetidinyl-naphthliamide derived SNAP-tag probe AN-BG exhibiting excellent fluorogenicity and photostability for long-term super-resolution imaging of mitochondrial dynamics. The azetidinyl group and naphthalimide fluorophore are in a flat conformation which can effectively suppress twisted intramolecular charge transfer and then effectively improve the brightness and photostability. This planarized molecular structure is conducive to the formation of fluorescence-quenched J-aggregates, and the protein labeling process will depolymerize the probes and restore fluorescence. Fluorescent labeling mitochondrial inner membrane proteins via SNAP tags overcomes the shortcomings that variations in mitochondrial inner membrane potential will release probes attached to mitochondria by electrostatic interactions. Therefore, AN-BG realized the stable labeling of mitochondria and the long-term imaging of mitochondrial dynamics under super-resolution microscopy.
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11
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Macias‐Contreras M, Zhu L. The Collective Power of Genetically Encoded Protein/Peptide Tags and Bioorthogonal Chemistry in Biological Fluorescence Imaging. CHEMPHOTOCHEM 2020. [DOI: 10.1002/cptc.202000215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Miguel Macias‐Contreras
- Department of Chemistry and Biochemistry Florida State University 95 Chieftan Way Tallahassee FL 32306-4390 USA
| | - Lei Zhu
- Department of Chemistry and Biochemistry Florida State University 95 Chieftan Way Tallahassee FL 32306-4390 USA
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12
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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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13
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Santos EM, Berbasova T, Wang W, Salmani RE, Sheng W, Vasileiou C, Geiger JH, Borhan B. Engineering of a Red Fluorogenic Protein/Merocyanine Complex for Live-Cell Imaging. Chembiochem 2020; 21:723-729. [PMID: 31482666 PMCID: PMC7379159 DOI: 10.1002/cbic.201900428] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Indexed: 12/25/2022]
Abstract
A reengineered human cellular retinol binding protein II (hCRBPII), a 15-kDa protein belonging to the intracellular lipid binding protein (iLBP) family, generates a highly fluorescent red pigment through the covalent linkage of a merocyanine aldehyde to an active site lysine residue. The complex exhibits "turn-on" fluorescence, due to a weakly fluorescent aldehyde that "lights up" with subsequent formation of a strongly fluorescent merocyanine dye within the binding pocket of the protein. Cellular penetration of merocyanine is rapid, and fluorophore maturation is nearly instantaneous. The hCRBPII/merocyanine complex displays high quantum yield, low cytotoxicity, specificity in labeling organelles, and compatibility in both cancer cell lines and yeast cells. The hCRBPII/merocyanine tag is brighter than most common red fluorescent proteins.
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Affiliation(s)
- Elizabeth M. Santos
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824 USA
| | - Tetyana Berbasova
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824 USA
| | - Wenjing Wang
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824 USA
| | | | - Wei Sheng
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824 USA
| | - Chrysoula Vasileiou
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824 USA
| | - James H. Geiger
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824 USA
| | - Babak Borhan
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824 USA
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14
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Wilson DL, Kool ET. Ultrafast Oxime Formation Enables Efficient Fluorescence Light-up Measurement of DNA Base Excision. J Am Chem Soc 2019; 141:19379-19388. [PMID: 31774658 DOI: 10.1021/jacs.9b09812] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
DNA glycosylases constitute a biologically and biomedically important group of DNA repair enzymes responsible for initiating base excision repair (BER). Measuring their activities can be useful for studying the mechanisms DNA damage and repair and for practical applications in cancer diagnosis and drug screening. Previous fluorescence methods for assaying DNA glycosylases are often complex and/or limited in scope to a single enzyme type. Here we report a universal base excision reporter (UBER) fluorescence probe design that implements an unprecedentedly rapid oxime reaction (>150 M-1 s-1) with high specificity for the abasic (AP) site of DNA. The molecular rotor design achieves a robust >250-500-fold increase in fluorescence upon reaction with AP sites in DNA. By using the fluorescence reporter in concert with specific DNA lesion-containing substrates, the UBER probe can be used in a coupled assay in principle with any DNA glycosylase. We demonstrate the utility of the UBER probe by assaying five different glycosylases in real time as well as profiling glycosylase activity in cell lysates. We anticipate that the UBER probe will be of considerable utility to researchers studying DNA repair biology owing to its high level of generalizability, ease of use, and compatibility with biologically derived samples.
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Affiliation(s)
- David L Wilson
- Department of Chemistry, Stanford Cancer Institute and ChEM-H Institute , Stanford University , Stanford , California 94305 , United States
| | - Eric T Kool
- Department of Chemistry, Stanford Cancer Institute and ChEM-H Institute , Stanford University , Stanford , California 94305 , United States
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15
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Prole DL, Taylor CW. A genetically encoded toolkit of functionalized nanobodies against fluorescent proteins for visualizing and manipulating intracellular signalling. BMC Biol 2019; 17:41. [PMID: 31122229 PMCID: PMC6533734 DOI: 10.1186/s12915-019-0662-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 05/02/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Intrabodies enable targeting of proteins in live cells, but generating specific intrabodies against the thousands of proteins in a proteome poses a challenge. We leverage the widespread availability of fluorescently labelled proteins to visualize and manipulate intracellular signalling pathways in live cells by using nanobodies targeting fluorescent protein tags. RESULTS We generated a toolkit of plasmids encoding nanobodies against red and green fluorescent proteins (RFP and GFP variants), fused to functional modules. These include fluorescent sensors for visualization of Ca2+, H+ and ATP/ADP dynamics; oligomerising or heterodimerising modules that allow recruitment or sequestration of proteins and identification of membrane contact sites between organelles; SNAP tags that allow labelling with fluorescent dyes and targeted chromophore-assisted light inactivation; and nanobodies targeted to lumenal sub-compartments of the secretory pathway. We also developed two methods for crosslinking tagged proteins: a dimeric nanobody, and RFP-targeting and GFP-targeting nanobodies fused to complementary hetero-dimerizing domains. We show various applications of the toolkit and demonstrate, for example, that IP3 receptors deliver Ca2+ to the outer membrane of only a subset of mitochondria and that only one or two sites on a mitochondrion form membrane contacts with the plasma membrane. CONCLUSIONS This toolkit greatly expands the utility of intrabodies and will enable a range of approaches for studying and manipulating cell signalling in live cells.
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Affiliation(s)
- David L Prole
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK.
| | - Colin W Taylor
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK.
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16
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Uchiyama S, Yano K, Fukatsu E, de Silva AP. Precise Proton Mapping near Ionic Micellar Membranes with Fluorescent Photoinduced‐Electron‐Transfer Sensors. Chemistry 2019; 25:8522-8527. [DOI: 10.1002/chem.201806270] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 04/01/2019] [Indexed: 11/10/2022]
Affiliation(s)
- Seiichi Uchiyama
- Graduate School of Pharmaceutical SciencesThe University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo Japan
| | - Kayo Yano
- Graduate School of Pharmaceutical SciencesThe University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo Japan
| | - Eiko Fukatsu
- Graduate School of Pharmaceutical SciencesThe University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo Japan
| | - A. Prasanna de Silva
- School of Chemistry and Chemical EngineeringQueen's University Belfast BT9 5AG Northern Ireland
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17
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Norris SR, Warner CC, Lampkin BJ, Bouc P, VanVeller B. Synthesis and Spectral Properties of Push–Pull Dyes Based on Isobenzofuran Scaffolds. Org Lett 2019; 21:3817-3821. [DOI: 10.1021/acs.orglett.9b01260] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sean R. Norris
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Caroline C. Warner
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Bryan J. Lampkin
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Paige Bouc
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Brett VanVeller
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
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18
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Jung KH, Kim SF, Liu Y, Zhang X. A Fluorogenic
AggTag
Method Based on Halo‐ and SNAP‐Tags to Simultaneously Detect Aggregation of Two Proteins in Live Cells. Chembiochem 2019; 20:1078-1087. [DOI: 10.1002/cbic.201800782] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Kwan Ho Jung
- Department of ChemistryThe Pennsylvania State University University Park PA 16802 USA
| | - Sojung F. Kim
- Department of ChemistryThe Pennsylvania State University University Park PA 16802 USA
| | - Yu Liu
- Department of ChemistryThe Pennsylvania State University University Park PA 16802 USA
| | - Xin Zhang
- Department of ChemistryThe Pennsylvania State University University Park PA 16802 USA
- Department of Biochemistry and Molecular BiologyThe Pennsylvania State University University Park PA 16802 USA
- The Huck Institutes of the Life SciencesThe Pennsylvania State University University Park PA 16802 USA
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19
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Jung KH, Fares M, Grainger LS, Wolstenholme CH, Hou A, Liu Y, Zhang X. A SNAP-tag fluorogenic probe mimicking the chromophore of the red fluorescent protein Kaede. Org Biomol Chem 2019; 17:1906-1915. [PMID: 30265264 DOI: 10.1039/c8ob01483c] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Self-labelling protein tags with fluorogenic probes serve as great fluorescence imaging tools to understand key questions of protein dynamics and functions in living cells. In the present study, we report a SNAP-tag fluorogenic probe 4c mimicking the chromophore of the red fluorescent protein Kaede. The molecular rotor properties of 4c were utilized as a fluorogenic probe for SNAP-tag, such that conjugation with SNAPf protein leads to inhibition of twisted intramolecular charge transfer, triggering fluorogenecity. Upon conjugation with SNAPf, 4c exhibited approximately a 90-fold enhancement in fluorescence intensity with fast labelling kinetics (k2 = 15 000 M-1 s-1). Biochemical and spectroscopic studies confirmed that fluorescence requires formation of folded SNAPf·4c covalent conjugate between Cys 145 and 4c. Confocal microscopy and flow cytometry showed that 4c is capable of detecting SNAPf proteins or SNAPf fused with a protein of interest in living cells. This work provides a framework to develop the large family of FP chromophores into fluorogenic probes for self-labelling protein tags.
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Affiliation(s)
- Kwan Ho Jung
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
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20
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Fares M, Zhang X. Quantification of Cellular Proteostasis in Live Cells by Fluorogenic Assay Using the AgHalo Sensor. ACTA ACUST UNITED AC 2018; 11:e58. [PMID: 30489038 DOI: 10.1002/cpch.58] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Proper cellular proteostasis is essential to cellular fitness and viability. Exogenous stress conditions compromise proteostasis and cause aggregation of cellular proteins. We have developed a fluorogenic sensor (AgHalo) to quantify stress-induced proteostasis deficiency. The AgHalo sensor uses a destabilized HaloTag variant to represent aggregation-prone cellular proteins and is equipped with a series of fluorogenic probes that exhibit a fluorescence increase when the sensor forms either soluble oligomers or insoluble aggregates. Herein, we present protocols that describe how the AgHalo sensor can be employed to visualize and quantify proteome stress in live cells using a direct fluorescence read-out and visualization with a fluorescence microplate reader and a microscope. Additionally, protocols for using the AgHalo sensor in combination with fluorogenic probes and commercially available HaloTag probes to enable two-color imaging experiments are described. These protocols will enable use of the AgHalo sensor to visualize and quantify proteostasis in live cells, a task that is difficult to accomplish using previous, always-fluorescent methods. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Matthew Fares
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania
| | - Xin Zhang
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania.,The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania
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21
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Lee FH, Chew CY, Hwu JR, Tan KT. Biotinylated fluorescent probe for the specific and quantitative determination of blood glucose. J CHIN CHEM SOC-TAIP 2018. [DOI: 10.1002/jccs.201800293] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Fang-Hong Lee
- Department of Chemistry; National Tsing Hua University; Hsinchu Taiwan, Republic of China
| | - Chee Ying Chew
- Department of Chemistry; National Tsing Hua University; Hsinchu Taiwan, Republic of China
| | - Jih Ru Hwu
- Department of Chemistry; National Tsing Hua University; Hsinchu Taiwan, Republic of China
- Frontier Research Center on Fundamental and Applied Sciences of Matters; National Tsing Hua University; Hsinchu Taiwan, Republic of China
| | - Kui-Thong Tan
- Department of Chemistry; National Tsing Hua University; Hsinchu Taiwan, Republic of China
- Frontier Research Center on Fundamental and Applied Sciences of Matters; National Tsing Hua University; Hsinchu Taiwan, Republic of China
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22
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Chen HJ, Chew CY, Chang EH, Tu YW, Wei LY, Wu BH, Chen CH, Yang YT, Huang SC, Chen JK, Chen IC, Tan KT. S-Cis Diene Conformation: A New Bathochromic Shift Strategy for Near-Infrared Fluorescence Switchable Dye and the Imaging Applications. J Am Chem Soc 2018; 140:5224-5234. [DOI: 10.1021/jacs.8b01159] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
| | | | | | | | | | | | - Chien-Hung Chen
- Institute of Biomedical Engineering and Nanomedicine, National Health Research Institutes, Miaoli 35053, Taiwan (ROC)
| | - Ya-Ting Yang
- Institute of Biomedical Engineering and Nanomedicine, National Health Research Institutes, Miaoli 35053, Taiwan (ROC)
| | - Su-Chin Huang
- Institute of Biomedical Engineering and Nanomedicine, National Health Research Institutes, Miaoli 35053, Taiwan (ROC)
| | - Jen-Kun Chen
- Institute of Biomedical Engineering and Nanomedicine, National Health Research Institutes, Miaoli 35053, Taiwan (ROC)
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23
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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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24
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Zhang S, Chen G, Wang Y, Wang Q, Zhong Y, Yang XF, Li Z, Li H. Far-Red Fluorescent Probe for Imaging of Vicinal Dithiol-Containing Proteins in Living Cells Based on a pKa Shift Mechanism. Anal Chem 2018; 90:2946-2953. [DOI: 10.1021/acs.analchem.7b05429] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Shengrui Zhang
- Key
Laboratory of Synthetic and Natural Functional Molecule Chemistry
of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an, Shaanxi 710127, People’s Republic of China
- Shaanxi
Key Laboratory of Catalysis, School of Chemistry and Environment Science, Shaanxi University of Technology, Hanzhong, Shaanxi 723000, People’s Republic of China
| | - Guojun Chen
- Key
Laboratory of Synthetic and Natural Functional Molecule Chemistry
of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an, Shaanxi 710127, People’s Republic of China
| | - Yuanyuan Wang
- Key
Laboratory of Synthetic and Natural Functional Molecule Chemistry
of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an, Shaanxi 710127, People’s Republic of China
| | - Qin Wang
- Key
Laboratory of Synthetic and Natural Functional Molecule Chemistry
of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an, Shaanxi 710127, People’s Republic of China
- Shaanxi
Key Laboratory of Catalysis, School of Chemistry and Environment Science, Shaanxi University of Technology, Hanzhong, Shaanxi 723000, People’s Republic of China
| | - Yaogang Zhong
- College
of Life Sciences, Northwest University, Xi’an, Shaanxi 710069, People’s Republic of China
| | - Xiao-Feng Yang
- Key
Laboratory of Synthetic and Natural Functional Molecule Chemistry
of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an, Shaanxi 710127, People’s Republic of China
| | - Zheng Li
- College
of Life Sciences, Northwest University, Xi’an, Shaanxi 710069, People’s Republic of China
| | - Hua Li
- College
of Chemistry and Chemical Engineering, Xi’an Shiyou University, Xi’an, Shaanxi 710065, People’s Republic of China
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25
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Hong YR, Lam CH, Tan KT. Fluorogenic Protein Labeling Probes to Study the Morphological Interplay between PreLamin and Mature Lamin. Bioconjug Chem 2017; 28:2895-2902. [DOI: 10.1021/acs.bioconjchem.7b00611] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yi-Ru Hong
- 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)
| | - Chak Hin Lam
- 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)
| | - 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)
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26
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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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27
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Thooft AM, Cassaidy K, VanVeller B. A Small Push-Pull Fluorophore for Turn-on Fluorescence. J Org Chem 2017; 82:8842-8847. [PMID: 28714302 DOI: 10.1021/acs.joc.7b00939] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A new class of push-pull dyes is reported based on the structures of benzoxa- and benzothiadiazole heterocycles. This new class of dyes displays red-shifted wavelengths of emission and greater sensitivity to polarity and hydrogen bonding solvents relative to previously known derivatives.
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Affiliation(s)
- Andrea Marie Thooft
- Department of Chemistry, Iowa State University , Ames, Iowa 50011, United States
| | - Kyle Cassaidy
- Department of Chemistry, Iowa State University , Ames, Iowa 50011, United States
| | - Brett VanVeller
- Department of Chemistry, Iowa State University , Ames, Iowa 50011, United States
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28
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Liu Y, Fares M, Dunham NP, Gao Z, Miao K, Jiang X, Bollinger SS, Boal AK, Zhang X. AgHalo: A Facile Fluorogenic Sensor to Detect Drug-Induced Proteome Stress. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702417] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Yu Liu
- Department of Chemistry; The Pennsylvania State University; University Park PA 16802 USA
| | - Matthew Fares
- Department of Chemistry; The Pennsylvania State University; University Park PA 16802 USA
| | - Noah P. Dunham
- Department of Biochemistry and Molecular Biology; The Pennsylvania State University; University Park PA 16802 USA
| | - Zi Gao
- Department of Biochemistry and Molecular Biology; The Pennsylvania State University; University Park PA 16802 USA
| | - Kun Miao
- Department of Chemistry; The Pennsylvania State University; University Park PA 16802 USA
| | - Xueyuan Jiang
- Department of Biochemistry and Molecular Biology; The Pennsylvania State University; University Park PA 16802 USA
| | - Samuel S. Bollinger
- Department of Chemistry; The Pennsylvania State University; University Park PA 16802 USA
| | - Amie K. Boal
- Department of Chemistry; The Pennsylvania State University; University Park PA 16802 USA
- Department of Biochemistry and Molecular Biology; The Pennsylvania State University; University Park PA 16802 USA
| | - Xin Zhang
- Department of Chemistry; The Pennsylvania State University; University Park PA 16802 USA
- Department of Biochemistry and Molecular Biology; The Pennsylvania State University; University Park PA 16802 USA
- The Huck Institutes of Life Sciences; The Pennsylvania State University; University Park PA 16802 USA
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29
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Liu Y, Fares M, Dunham NP, Gao Z, Miao K, Jiang X, Bollinger SS, Boal AK, Zhang X. AgHalo: A Facile Fluorogenic Sensor to Detect Drug-Induced Proteome Stress. Angew Chem Int Ed Engl 2017; 56:8672-8676. [PMID: 28557281 DOI: 10.1002/anie.201702417] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Indexed: 11/08/2022]
Abstract
Drug-induced proteome stress that involves protein aggregation may cause adverse effects and undermine the safety profile of a drug. Safety of drugs is regularly evaluated using cytotoxicity assays that measure cell death. However, these assays provide limited insights into the presence of proteome stress in live cells. A fluorogenic protein sensor is reported to detect drug-induced proteome stress prior to cell death. An aggregation prone Halo-tag mutant (AgHalo) was evolved to sense proteome stress through its aggregation. Detection of such conformational changes was enabled by a fluorogenic ligand that fluoresces upon AgHalo forming soluble aggregates. Using 5 common anticancer drugs, we exemplified detection of differential proteome stress before any cell death was observed. Thus, this sensor can be used to evaluate drug safety in a regime that the current cytotoxicity assays cannot cover and be generally applied to detect proteome stress induced by other toxins.
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Affiliation(s)
- Yu Liu
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Matthew Fares
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Noah P Dunham
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Zi Gao
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Kun Miao
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Xueyuan Jiang
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Samuel S Bollinger
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Amie K Boal
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Xin Zhang
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA.,The Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
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30
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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
![]()
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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31
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Clark SA, Singh V, Vega Mendoza D, Margolin W, Kool ET. Light-Up "Channel Dyes" for Haloalkane-Based Protein Labeling in Vitro and in Bacterial Cells. Bioconjug Chem 2016; 27:2839-2843. [PMID: 27998074 DOI: 10.1021/acs.bioconjchem.6b00613] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We describe a novel molecular strategy for engendering a strong light-up signal in fluorescence tagging of the genetically encoded HaloTag protein domain. We designed a set of haloalkane-derivatized dyes having twisted internal charge transfer (TICT) structures potentially narrow enough to partially fit into the enzyme's haloalkane-binding channel. Testing a range of short chain lengths revealed a number of active dyes, with seven carbons yielding optimum light-up signal. The dimethylaminostilbazolium chloroheptyl dye (1d) yields a 27-fold fluorescence emission enhancement (λex = 535 nm; Em(max) = 616 nm) upon reaction with the protein. The control compound with standard 12-atom linkage shows less efficient signaling, consistent with our channel-binding hypothesis. For emission further to the red, we also prepared a chloroheptyl naphthalene-based dye; compound 2 emits at 653 nm with strong fluorescence enhancement upon reaction with the HaloTag domain. The two dyes (1d, 2) were successfully tested in wash-free imaging of protein localization in bacteria, using a HaloTag fusion of the filamenting temperature-sensitive mutant Z (FtsZ) protein in Escherichia coli (E. coli). The new dye conjugates are inexpensive and easily synthesized enzyme substrates with low background and large Stokes shifts, offering substantial benefits over known fluorescent substrates for the HaloTag enzyme.
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Affiliation(s)
- Spencer A Clark
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Vijay Singh
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Daniel Vega Mendoza
- Department of Microbiology and Molecular Genetics, McGovern Medical School , Houston, Texas 77030, United States
| | - William Margolin
- Department of Microbiology and Molecular Genetics, McGovern Medical School , Houston, Texas 77030, United States
| | - Eric T Kool
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
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32
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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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33
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Zeng YS, Gao RC, Wu TW, Cho C, Tan KT. Fluorescent Probe Encapsulated in SNAP-Tag Protein Cavity To Eliminate Nonspecific Fluorescence and Increase Detection Sensitivity. Bioconjug Chem 2016; 27:1872-9. [DOI: 10.1021/acs.bioconjchem.6b00290] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Yan-Syun Zeng
- Department of Chemistry, and ‡Frontier Research Center on Fundamental
and Applied
Sciences of Matters, National Tsing Hua University, 101 Sec.
2, Kuang Fu Road, Hsinchu 30013, Taiwan, ROC
| | - Ruo-Cing Gao
- Department of Chemistry, and ‡Frontier Research Center on Fundamental
and Applied
Sciences of Matters, National Tsing Hua University, 101 Sec.
2, Kuang Fu Road, Hsinchu 30013, Taiwan, ROC
| | - Ting-Wei Wu
- Department of Chemistry, and ‡Frontier Research Center on Fundamental
and Applied
Sciences of Matters, National Tsing Hua University, 101 Sec.
2, Kuang Fu Road, Hsinchu 30013, Taiwan, ROC
| | - Chien Cho
- Department of Chemistry, and ‡Frontier Research Center on Fundamental
and Applied
Sciences of Matters, National Tsing Hua University, 101 Sec.
2, Kuang Fu Road, Hsinchu 30013, 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 Road, Hsinchu 30013, Taiwan, ROC
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34
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Montoya LA, Pluth MD. Organelle-Targeted H2S Probes Enable Visualization of the Subcellular Distribution of H2S Donors. Anal Chem 2016; 88:5769-74. [PMID: 27171507 DOI: 10.1021/acs.analchem.6b00087] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Hydrogen sulfide (H2S) is an essential biological signaling molecule in diverse biological regulatory pathways. To provide new chemical tools for H2S imaging, we report here a fluorescent H2S detection platform (HSN2-BG) that is compatible with subcellular localization SNAP-tag fusion protein methodologies and use appropriate fusion protein constructs to demonstrate mitochondrial and lysosomal localization. We also demonstrate the efficacy of this detection platform to image endogenous H2S in Chinese hamster ovary (CHO) cells and use the developed constructs to report on the subcellular H2S distributions provided by common H2S donor molecules AP39, ADT-OH, GYY4137, and diallyltrisulfide (DATS). The developed constructs provide a platform poised to provide new insights into the subcellular distribution of common H2S donors and a useful tool for investigating H2S biochemistry.
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Affiliation(s)
- Leticia A Montoya
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, Materials Science Institute. University of Oregon , Eugene, Oregon 97403, United States
| | - Michael D Pluth
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, Materials Science Institute. University of Oregon , Eugene, Oregon 97403, United States
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35
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Lai WY, Tan KT. Environment-sensitive Fluorescent Turn-on Chemical Probe for the Specific Detection of O-Methylguanine-DNA Methyltransferase (MGMT) in Living Cells. J CHIN CHEM SOC-TAIP 2016. [DOI: 10.1002/jccs.201600015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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36
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Jiang T, Wang W, Wu X, Wu W, Bai H, Ma Z, Shen Y, Yang K, Li M. Discovery of New Substrates forLuxABBacterial Bioluminescence. Chem Biol Drug Des 2016; 88:197-208. [DOI: 10.1111/cbdd.12747] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Revised: 11/26/2015] [Accepted: 02/08/2016] [Indexed: 01/04/2023]
Affiliation(s)
- Tianyu Jiang
- Department of Medicinal Chemistry; Key Laboratory of Chemical Biology (MOE); School of Pharmaceutical Sciences; Shandong University; Jinan Shandong 250012 China
| | - Weishan Wang
- State Key Laboratory of Microbial Resources; Institute of Microbiology; Chinese Academy of Sciences; Beijing 100190 China
| | - Xingkang Wu
- Department of Natural Products; Key Laboratory of Chemical Biology (MOE); School of Pharmaceutical Sciences; Shandong University; Jinan Shandong 250012 China
| | - Wenxiao Wu
- Department of Medicinal Chemistry; Key Laboratory of Chemical Biology (MOE); School of Pharmaceutical Sciences; Shandong University; Jinan Shandong 250012 China
| | - Haixiu Bai
- Department of Medicinal Chemistry; Key Laboratory of Chemical Biology (MOE); School of Pharmaceutical Sciences; Shandong University; Jinan Shandong 250012 China
| | - Zhao Ma
- Department of Medicinal Chemistry; Key Laboratory of Chemical Biology (MOE); School of Pharmaceutical Sciences; Shandong University; Jinan Shandong 250012 China
| | - Yuemao Shen
- Department of Natural Products; Key Laboratory of Chemical Biology (MOE); School of Pharmaceutical Sciences; Shandong University; Jinan Shandong 250012 China
| | - Keqian Yang
- State Key Laboratory of Microbial Resources; Institute of Microbiology; Chinese Academy of Sciences; Beijing 100190 China
| | - Minyong Li
- Department of Medicinal Chemistry; Key Laboratory of Chemical Biology (MOE); School of Pharmaceutical Sciences; Shandong University; Jinan Shandong 250012 China
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37
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Sun Q, Sun D, Song L, Chen Z, Chen Z, Zhang W, Qian J. Highly Selective Fluorescent Turn-On Probe for Protein Thiols in Biotin Receptor-Positive Cancer Cells. Anal Chem 2016; 88:3400-5. [DOI: 10.1021/acs.analchem.6b00178] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Qian Sun
- Shanghai Key Laboratory of Functional Materials
Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Deheng Sun
- School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Lun Song
- Shanghai Key Laboratory of Functional Materials
Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Zhuo Chen
- School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
| | - Zhaoyang Chen
- Shanghai Key Laboratory of Functional Materials
Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Weibing Zhang
- Shanghai Key Laboratory of Functional Materials
Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Junhong Qian
- Shanghai Key Laboratory of Functional Materials
Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, China
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38
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Imaging and manipulating proteins in live cells through covalent labeling. Nat Chem Biol 2015; 11:917-23. [PMID: 26575238 DOI: 10.1038/nchembio.1959] [Citation(s) in RCA: 156] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 10/14/2015] [Indexed: 12/19/2022]
Abstract
The past 20 years have witnessed the advent of numerous technologies to specifically and covalently label proteins in cellulo and in vivo with synthetic probes. These technologies range from self-labeling proteins tags to non-natural amino acids, and the question is no longer how we can specifically label a given protein but rather with what additional functionality we wish to equip it. In addition, progress in fields such as super-resolution microscopy and genome editing have either provided additional motivation to label proteins with advanced synthetic probes or removed some of the difficulties of conducting such experiments. By focusing on two particular applications, live-cell imaging and the generation of reversible protein switches, we outline the opportunities and challenges of the field and how the synergy between synthetic chemistry and protein engineering will make it possible to conduct experiments that are not feasible with conventional approaches.
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39
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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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40
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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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41
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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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42
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Zhang M, Chakraborty SK, Sampath P, Rojas JJ, Hou W, Saurabh S, Thorne SH, Bruchez MP, Waggoner AS. Fluoromodule-based reporter/probes designed for in vivo fluorescence imaging. J Clin Invest 2015; 125:3915-27. [PMID: 26348895 DOI: 10.1172/jci81086] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 07/30/2015] [Indexed: 12/26/2022] Open
Abstract
Optical imaging of whole, living animals has proven to be a powerful tool in multiple areas of preclinical research and has allowed noninvasive monitoring of immune responses, tumor and pathogen growth, and treatment responses in longitudinal studies. However, fluorescence-based studies in animals are challenging because tissue absorbs and autofluoresces strongly in the visible light spectrum. These optical properties drive development and use of fluorescent labels that absorb and emit at longer wavelengths. Here, we present a far-red absorbing fluoromodule-based reporter/probe system and show that this system can be used for imaging in living mice. The probe we developed is a fluorogenic dye called SC1 that is dark in solution but highly fluorescent when bound to its cognate reporter, Mars1. The reporter/probe complex, or fluoromodule, produced peak emission near 730 nm. Mars1 was able to bind a variety of structurally similar probes that differ in color and membrane permeability. We demonstrated that a tool kit of multiple probes can be used to label extracellular and intracellular reporter-tagged receptor pools with 2 colors. Imaging studies may benefit from this far-red excited reporter/probe system, which features tight coupling between probe fluorescence and reporter binding and offers the option of using an expandable family of fluorogenic probes with a single reporter gene.
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43
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Hou TC, Wu YY, Chiang PY, Tan KT. Near-infrared fluorescence activation probes based on disassembly-induced emission cyanine dye. Chem Sci 2015; 6:4643-4649. [PMID: 28717479 PMCID: PMC5500852 DOI: 10.1039/c5sc01330e] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 05/22/2015] [Indexed: 02/02/2023] Open
Abstract
Currently most of the fluorogenic probes are designed for the detection of enzymes which work by converting the non-fluorescence substrate into the fluorescence product via an enzymatic reaction. On the other hand, the design of fluorogenic probes for non-enzymatic proteins remains a great challenge. Herein, we report a general strategy to create near-IR fluorogenic probes, where a small molecule ligand is conjugated to a novel γ-phenyl-substituted Cy5 fluorophore, for the selective detection of proteins through a non-enzymatic process. Detail mechanistic studies reveal that the probes self-assemble to form fluorescence-quenched J-type aggregate. In the presence of target analyte, bright fluorescence in the near-IR region is emitted through the recognition-induced disassembly of the probe aggregate. This Cy5 fluorophore is a unique self-assembly/disassembly dye as it gives remarkable fluorescence enhancement. Based on the same design, three different fluorogenic probes were constructed and one of them was applied for the no-wash imaging of tumor cells for the detection of hypoxia-induced cancer-specific biomarker, transmembrane-type carbonic anhydrase IX.
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Affiliation(s)
- Tai-Cheng Hou
- Department of Chemistry , National Tsing Hua University , 101 Sec. 2, Kuang Fu Rd , Hsinchu 30013 , Taiwan , Republic of china . ; Tel: +886-3-5715131
| | - Ying-Yi Wu
- Department of Chemistry , National Tsing Hua University , 101 Sec. 2, Kuang Fu Rd , Hsinchu 30013 , Taiwan , Republic of china . ; Tel: +886-3-5715131
| | - Po-Yi Chiang
- Department of Chemistry , National Tsing Hua University , 101 Sec. 2, Kuang Fu Rd , Hsinchu 30013 , Taiwan , Republic of china . ; Tel: +886-3-5715131
| | - Kui-Thong Tan
- Department of Chemistry , National Tsing Hua University , 101 Sec. 2, Kuang Fu Rd , Hsinchu 30013 , Taiwan , Republic of china . ; Tel: +886-3-5715131
- Frontier Research Center on Fundamental and Applied Sciences of Matters , National Tsing Hua University , 101 Sec. 2, Kuang Fu Rd , Hsinchu 30013 , Taiwan , Republic of china
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44
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Chen Y, Tsao K, Keillor JW. Fluorogenic protein labelling: a review of photophysical quench mechanisms and principles of fluorogen design. CAN J CHEM 2015. [DOI: 10.1139/cjc-2014-0405] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Fluorescent labelling of specific proteins in complex biological systems remains an important challenge in chemical biology. One promising approach comprises the use of small molecules designed to react specifically with a targeted protein of interest and to increase in fluorescent intensity following this reaction. This kind of fluorogenic reaction generally derives from fluorescence quenching in the unreacted probe that is abrogated over the course of the reaction. Herein, we review the mechanistic principles of three major photophysical quenching mechanisms involving Förster resonance energy transfer (FRET), through-bond energy transfer (TBET), and photoinduced electron transfer (PeT). We then present design principles for novel fluorogenic probes based on an understanding of these quench mechanisms, with emphasis on the emerging utility of density functional theory (DFT) calculations in the design process.
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Affiliation(s)
- Yingche Chen
- Department of Chemistry, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N 6N5, Canada
- Department of Chemistry, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N 6N5, Canada
| | - Kelvin Tsao
- Department of Chemistry, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N 6N5, Canada
- Department of Chemistry, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N 6N5, Canada
| | - Jeffrey W. Keillor
- Department of Chemistry, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N 6N5, Canada
- Department of Chemistry, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N 6N5, Canada
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45
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Yapici I, Lee KSS, Berbasova T, Nosrati M, Jia X, Vasileiou C, Wang W, Santos EM, Geiger JH, Borhan B. "Turn-on" protein fluorescence: in situ formation of cyanine dyes. J Am Chem Soc 2015; 137:1073-80. [PMID: 25534273 PMCID: PMC4311949 DOI: 10.1021/ja506376j] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Protein reengineering of cellular retinoic acid binding protein II (CRABPII) has yielded a genetically addressable system, capable of binding a profluorophoric chromophore that results in fluorescent protein/chromophore complexes. These complexes exhibit far-red emission, with high quantum efficiencies and brightness and also exhibit excellent pH stability spanning the range of 2-11. In the course of this study, it became evident that single mutations of L121E and R59W were most effective in improving the fluorescent characteristics of CRABPII mutants as well as the kinetics of complex formation. The readily crystallizable nature of these proteins was invaluable to provide clues for the observed spectroscopic behavior that results from single mutation of key residues.
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Affiliation(s)
- Ipek Yapici
- Department of Chemistry, Michigan State University , East Lansing, Michigan 48824, United States
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46
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Song K, Awata J, Tritschler D, Bower R, Witman GB, Porter ME, Nicastro D. In situ localization of N and C termini of subunits of the flagellar nexin-dynein regulatory complex (N-DRC) using SNAP tag and cryo-electron tomography. J Biol Chem 2015; 290:5341-53. [PMID: 25564608 DOI: 10.1074/jbc.m114.626556] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cryo-electron tomography (cryo-ET) has reached nanoscale resolution for in situ three-dimensional imaging of macromolecular complexes and organelles. Yet its current resolution is not sufficient to precisely localize or identify most proteins in situ; for example, the location and arrangement of components of the nexin-dynein regulatory complex (N-DRC), a key regulator of ciliary/flagellar motility that is conserved from algae to humans, have remained elusive despite many cryo-ET studies of cilia and flagella. Here, we developed an in situ localization method that combines cryo-ET/subtomogram averaging with the clonable SNAP tag, a widely used cell biological probe to visualize fusion proteins by fluorescence microscopy. Using this hybrid approach, we precisely determined the locations of the N and C termini of DRC3 and the C terminus of DRC4 within the three-dimensional structure of the N-DRC in Chlamydomonas flagella. Our data demonstrate that fusion of SNAP with target proteins allowed for protein localization with high efficiency and fidelity using SNAP-linked gold nanoparticles, without disrupting the native assembly, structure, or function of the flagella. After cryo-ET and subtomogram averaging, we localized DRC3 to the L1 projection of the nexin linker, which interacts directly with a dynein motor, whereas DRC4 was observed to stretch along the N-DRC base plate to the nexin linker. Application of the technique developed here to the N-DRC revealed new insights into the organization and regulatory mechanism of this complex, and provides a valuable tool for the structural dissection of macromolecular complexes in situ.
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Affiliation(s)
- Kangkang Song
- From the Biology Department, Brandeis University, Waltham, Massachusetts 02454
| | - Junya Awata
- the Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, and
| | - Douglas Tritschler
- the Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455
| | - Raqual Bower
- the Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455
| | - George B Witman
- the Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, and
| | - Mary E Porter
- the Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455
| | - Daniela Nicastro
- From the Biology Department, Brandeis University, Waltham, Massachusetts 02454,
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