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Minoshima M, Reja SI, Hashimoto R, Iijima K, Kikuchi K. Hybrid Small-Molecule/Protein Fluorescent Probes. Chem Rev 2024; 124:6198-6270. [PMID: 38717865 DOI: 10.1021/acs.chemrev.3c00549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Hybrid small-molecule/protein fluorescent probes are powerful tools for visualizing protein localization and function in living cells. These hybrid probes are constructed by diverse site-specific chemical protein labeling approaches through chemical reactions to exogenous peptide/small protein tags, enzymatic post-translational modifications, bioorthogonal reactions for genetically incorporated unnatural amino acids, and ligand-directed chemical reactions. The hybrid small-molecule/protein fluorescent probes are employed for imaging protein trafficking, conformational changes, and bioanalytes surrounding proteins. In addition, fluorescent hybrid probes facilitate visualization of protein dynamics at the single-molecule level and the defined structure with super-resolution imaging. In this review, we discuss development and the bioimaging applications of fluorescent probes based on small-molecule/protein hybrids.
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Affiliation(s)
- Masafumi Minoshima
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Shahi Imam Reja
- Immunology Frontier Research Center, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Ryu Hashimoto
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Kohei Iijima
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Kazuya Kikuchi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
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2
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Bai Y, Zhang S, Dong H, Liu Y, Liu C, Zhang X. Advanced Techniques for Detecting Protein Misfolding and Aggregation in Cellular Environments. Chem Rev 2023; 123:12254-12311. [PMID: 37874548 DOI: 10.1021/acs.chemrev.3c00494] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Protein misfolding and aggregation, a key contributor to the progression of numerous neurodegenerative diseases, results in functional deficiencies and the creation of harmful intermediates. Detailed visualization of this misfolding process is of paramount importance for improving our understanding of disease mechanisms and for the development of potential therapeutic strategies. While in vitro studies using purified proteins have been instrumental in delivering significant insights into protein misfolding, the behavior of these proteins in the complex milieu of living cells often diverges significantly from such simplified environments. Biomedical imaging performed in cell provides cellular-level information with high physiological and pathological relevance, often surpassing the depth of information attainable through in vitro methods. This review highlights a variety of methodologies used to scrutinize protein misfolding within biological systems. This includes optical-based methods, strategies leaning on mass spectrometry, in-cell nuclear magnetic resonance, and cryo-electron microscopy. Recent advancements in these techniques have notably deepened our understanding of protein misfolding processes and the features of the resulting misfolded species within living cells. The progression in these fields promises to catalyze further breakthroughs in our comprehension of neurodegenerative disease mechanisms and potential therapeutic interventions.
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Affiliation(s)
- Yulong Bai
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang Province, China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Shengnan Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Hui Dong
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
- University of the Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Xin Zhang
- Department of Chemistry, 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
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3
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Xia Q, Wan W, Jin W, Huang Y, Sun R, Wang M, Jing B, Peng C, Dong X, Zhang R, Gao Z, Liu Y. Solvatochromic Cellular Stress Sensors Reveal the Compactness Heterogeneity and Dynamics of Aggregated Proteome. ACS Sens 2022; 7:1919-1925. [PMID: 35776067 DOI: 10.1021/acssensors.2c00566] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Deterioration of protein homeostasis (proteostasis) often induces aberrant proteome aggregation. Visualization and dissection of the stressed proteome are of particular interest given their association with numerous degenerative diseases. Recent progress in chemical cellular stress sensors allows for direct visualization of aggregated proteome. Beyond its localization and morphology, the physicochemical nature and the dynamics of the aggregated proteome have been challenging to explore. Herein, we developed a series of solvatochromic fluorene-based D-π-A probes that can selectively and noncovalently bind to a misfolded and aggregated proteome and report on their compactness heterogeneity upon cellular stresses. We achieved this goal by variation of the heterocyclic acceptors to modulate their solvatochromism and binding affinity to amorphous aggregated proteins. The optimized sensor P6 was capable of sensing the polarity differences among different aggregated proteins via its fluorescence emission wavelength. In live cells, P6 revealed the cellular compactness heterogeneity in the aggregated proteome upon cellular stresses. Given the combinative solvatochromic and noncovalent properties, our probe can reversibly monitor the dynamic changes in the aggregated proteome compactness upon stress and after stress recovery, suggesting its potential applications in search of therapeutics to counteract disease-causing proteome stresses.
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Affiliation(s)
- Qiuxuan Xia
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Wang Wan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Wenhan Jin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Yanan Huang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Rui Sun
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Mengdie Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Biao Jing
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.,The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China
| | - Congcong Peng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.,The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China
| | - Xuepeng Dong
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China
| | - Rixin Zhang
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China
| | - Zhenming Gao
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian, 116023, China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
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4
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Dudanova I. Biosensors for Studying Neuronal Proteostasis. Front Mol Neurosci 2022; 15:829365. [PMID: 35345600 PMCID: PMC8957107 DOI: 10.3389/fnmol.2022.829365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 01/31/2022] [Indexed: 01/18/2023] Open
Abstract
Cellular health depends on the integrity and functionality of the proteome. Each cell is equipped with a protein quality control machinery that maintains protein homeostasis (proteostasis) by helping proteins adopt and keep their native structure, and ensuring the degradation of damaged proteins. Postmitotic cells such as neurons are especially vulnerable to disturbances of proteostasis. Defects of protein quality control occur in aging and have been linked to several disorders, including neurodegenerative diseases. However, the exact nature and time course of such disturbances in the context of brain diseases remain poorly understood. Sensors that allow visualization and quantitative analysis of proteostasis capacity in neurons are essential for gaining a better understanding of disease mechanisms and for testing potential therapies. Here, I provide an overview of available biosensors for assessing the functionality of the neuronal proteostasis network, point out the advantages and limitations of different sensors, and outline their potential for biological discoveries and translational applications.
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Affiliation(s)
- Irina Dudanova
- Molecular Neurodegeneration Group, Max Planck Institute of Neurobiology, Martinsried, Germany
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5
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Ye S, Hsiung CH, Tang Y, Zhang X. Visualizing the Multistep Process of Protein Aggregation in Live Cells. Acc Chem Res 2022; 55:381-390. [PMID: 35040316 PMCID: PMC9098262 DOI: 10.1021/acs.accounts.1c00648] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Protein aggregation is a biological phenomenon in which aberrantly processed or mutant proteins misfold and assemble into a variety of insoluble aggregates. Decades of studies have delineated the structure, interaction, and activity of proteins in either their natively folded structures or insoluble aggregates such as amyloid fibrils. However, a variety of intermediate species exist between these two extreme states in the protein folding landscape. Herein, we collectively term these intermediate species as misfolded protein oligomers, including soluble oligomers and preamyloid oligomers that are formed by unfolded or misfolded proteins. While extensive tools have been developed to study folded proteins or amyloid fibrils, research to understand the properties and activities of misfolded protein oligomers has been limited by the lack of methods to detect and interrogate these species in live cells.In this Account, we describe our efforts in the development of chemical methods that allow for the characterization of the multistep protein aggregation process, in particular the misfolded protein oligomers, in living cells. As the start of this journey, we attempted to develop a fluorogenic method wherein the misfolded oligomers could turn on the fluorescence of chemical probes that are conjugated to the protein-of-interest (POI). To this end, we produced a series of destabilized HaloTag variants, formulating the primary component of the AgHalo sensor, which misfolds and aggregates when cells are subjected to stress. When AgHalo is covalently conjugated with a solvatochromic fluorophore, misfolding of the AgHalo conjugate would activate fluorescence, resulting in the observation of misfolded oligomers. Following this work, we extended the scope of detection from AgHalo to any protein-of-interest via the AggTag method, wherein the POIs are genetically fused to self-labeling protein tags (HaloTag or SNAP-tag). Focusing on the molecular rotor-based fluorophores, we applied the modulated fluorescent protein (FP) chromophore core as a prototype for the AggTag probes, to enable the fluorogenic detection of misfolded soluble oligomers of multiple proteins in live cells. Next, we further developed the AggTag method to distinguish insoluble aggregates from misfolded oligomers, using two classes of probes that activate different fluorescence emission toward these two conformations. To enable this goal, we applied physical organic chemistry and computational chemistry to discover a new category of triode-like fluorophores, wherein the π orbitals of either an electron density regulator or the donor-acceptor linkages are used to control the rotational barriers of fluorophores in the excited states. This mechanism allows us to rationally design molecular rotor-based fluorophores that have desired responses to viscosity, thus extending the application of the AggTag method.In summary, our work allows the direct monitoring of the misfolded protein oligomers and differentiation of insoluble aggregates from other conformations in live cells, thus enabling studies of many currently unanswered questions in protein aggregation. Future directions are to develop methods that enable quantitative analyses of the protein aggregation process. Further, new methods are needed to detect and to quantify the formation and maturation of protein or RNA condensates that form membraneless organelles.
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Affiliation(s)
- Songtao Ye
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States,Present address: School of Science and School of Life Sciences, Westlake University; Institute of Natural Sciences, Westlake Institute for Advanced Study; Westlake Laboratory of Life Sciences and Biomedicine; 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Chia-Heng Hsiung
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States,Present address: School of Science and School of Life Sciences, Westlake University; Institute of Natural Sciences, Westlake Institute for Advanced Study; Westlake Laboratory of Life Sciences and Biomedicine; 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Yuqi Tang
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States,Present address: School of Science and School of Life Sciences, Westlake University; Institute of Natural Sciences, Westlake Institute for Advanced Study; Westlake Laboratory of Life Sciences and Biomedicine; 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Xin Zhang
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States,Present address: School of Science and School of Life Sciences, Westlake University; Institute of Natural Sciences, Westlake Institute for Advanced Study; Westlake Laboratory of Life Sciences and Biomedicine; 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
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6
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Sabouri S, Liu M, Zhang S, Yao B, Soleimaninejad H, Baxter AA, Armendariz-Vidales G, Subedi P, Duan C, Lou X, Hogan CF, Heras B, Poon IKH, Hong Y. Construction of a Highly Sensitive Thiol-Reactive AIEgen-Peptide Conjugate for Monitoring Protein Unfolding and Aggregation in Cells. Adv Healthc Mater 2021; 10:e2101300. [PMID: 34655462 DOI: 10.1002/adhm.202101300] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 09/24/2021] [Indexed: 01/09/2023]
Abstract
Impairment of the protein quality control network leads to the accumulation of unfolded and aggregated proteins. Direct detection of unfolded protein accumulation in the cells may provide the possibility for early diagnosis of neurodegenerative diseases. Here a new platform based on a peptide-conjugated thiol-reactive aggregation-induced emission fluorogen (AIEgen), named MI-BTD-P (or D1), for labeling and tracking unfolded proteins in cells is reported. In vitro experiments with model proteins show that the non-fluorescent D1 only becomes highly fluorescent when reacted with the thiol group of free cysteine (Cys) residues on unfolded proteins but not glutathione or folded proteins with buried or surface exposed Cys. When the labeled unfolded proteins form aggregates, D1 fluorescence intensity is further increased, and fluorescence lifetime is prolonged. D1 is then used to measure unfolded protein loads in cells by flow cytometry and track the aggregate formation of the D1 labeled unfolded proteins using confocal microscopy. In combination with fluorescence lifetime imaging technique, the proteome at different folding statuses can be better differentiated, demonstrating the versatility of this new platform. The rational design of D1 demonstrates the outlook of incorporation of diverse functional groups to achieve maximal sensitivity and selectivity in biological samples.
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Affiliation(s)
- Soheila Sabouri
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Mengjie Liu
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Shouxiang Zhang
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Bicheng Yao
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Hamid Soleimaninejad
- Biological Optical Microscopy Platform (BOMP), The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Amy A Baxter
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Georgina Armendariz-Vidales
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Pramod Subedi
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Chong Duan
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 4300078, China
| | - Xiaoding Lou
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 4300078, China
| | - Conor F Hogan
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Begoña Heras
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Ivan K H Poon
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Yuning Hong
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, 3086, Australia
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7
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Shen D, Bai Y, Liu Y. Chemical Biology Toolbox to Visualize Protein Aggregation in Live Cells. Chembiochem 2021; 23:e202100443. [PMID: 34613660 DOI: 10.1002/cbic.202100443] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/05/2021] [Indexed: 11/09/2022]
Abstract
Protein misfolding and aggregation is a complex biochemical process and has been associated with numerous human degenerative diseases. Developing novel chemical and biological tools and approaches to visualize aggregated proteins in live cells is in high demand for mechanistic studies, diagnostics, and therapeutics. In this review, we summarize the recent developments in the chemical biology toolbox applied to protein aggregation studies in live cells. These methods exploited fluorescent protein tags, fluorescent chemical tags, and small-molecule probes to visualize the protein-aggregation process, detect proteome stresses, and quantify the protein homeostasis network capacity. Inspired by these seminal works, we have generalized design principles for the development of new detection methods and probes in the future that will illuminate this important biological process.
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Affiliation(s)
- Di Shen
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, P. R. China
| | - Yulong Bai
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, P. R. China
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8
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Yang S, Zhan Y, Shou W, Chen L, Lin Z, Guo L. 1,2,4-Triaminobenzene as a Fluorescent Probe for Intracellular pH Imaging and Point-of-Care Ammonia Sensing. ACS APPLIED BIO MATERIALS 2021; 4:6065-6072. [PMID: 35006915 DOI: 10.1021/acsabm.1c00404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
As one of the health indicators, intracellular pH plays important roles in many processes of cell functions. Abnormal pH changes would result in the occurrence of inflammation, cancer, and other diseases. Thus, it is of significant importance to develop effective techniques for sensitive detection of pH changes for the clinical diagnosis of various diseases related to cells. In this paper, 1,2,4-triaminobenzene hydrochloride was explored as an organic molecular fluorescent probe for sensitive and selective detection of intracellular pH changes for the first time. Due to the protonation and deprotonation of amino groups of the probe, its fluorescent intensity at 599 nm or the ratio of absorbance at 505 and 442 nm has a good linear relationship with pH values in the range of 5.0-7.0. Benefiting from the excellent physical and chemical properties of 1,2,4-triaminobenzene hydrochloride, the fluorescent probe has good water solubility, low toxicity, high photostability, great reversibility, good cell penetration, fast response speed, and so on. As a proof-of-concept demonstration, the proposed probe is employed for the fluorescence imaging of cells and mouse tissue sections with satisfactory performance in pH differentiation. Additionally, the probe was successfully employed to prepare test strips as a kind of point-of-care testing device to detect ammonia, which showed great potential in practical applications.
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Affiliation(s)
- Shuangting Yang
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian Province 350116, China.,College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, Zhejiang Province, China
| | - Yuanjin Zhan
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian Province 350116, China
| | - Wen Shou
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian Province 350116, China.,College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, Zhejiang Province, China
| | - Lifen Chen
- College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, Zhejiang Province, China
| | - Zhenyu Lin
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian Province 350116, China
| | - Longhua Guo
- College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, Zhejiang Province, China
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9
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Wan W, Jin W, Huang Y, Xia Q, Bai Y, Lyu H, Liu D, Dong X, Li W, Liu Y. Monitoring the Dynamics of Proteome Aggregation in Live Cells Using a Solubilized and Noncovalent Analogue of Fluorescent Protein Chromophores. Anal Chem 2020; 93:1717-1724. [PMID: 33382253 DOI: 10.1021/acs.analchem.0c04309] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Wang Wan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Wenhan Jin
- Department of Biotechnology, Dalian Medical University, No. 9 Lvshun South Road West, Dalian 116044, China
| | - Yanan Huang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Qiuxuan Xia
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yulong Bai
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haochen Lyu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Dongning Liu
- Department of Biotechnology, Dalian Medical University, No. 9 Lvshun South Road West, Dalian 116044, China
| | - Xuepeng Dong
- Department of Biotechnology, Dalian Medical University, No. 9 Lvshun South Road West, Dalian 116044, China
| | - Weiling Li
- Department of Biotechnology, Dalian Medical University, No. 9 Lvshun South Road West, Dalian 116044, China
- Liaoning Key Laboratory of Hematopoietic Stem Cell Transplantation and Translational Medicine, Second Hospital of Dalian Medical University, Dalian 116027, China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
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10
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Houser J, Kozmon S, Mishra D, Hammerová Z, Wimmerová M, Koča J. The CH-π Interaction in Protein-Carbohydrate Binding: Bioinformatics and In Vitro Quantification. Chemistry 2020; 26:10769-10780. [PMID: 32208534 DOI: 10.1002/chem.202000593] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 03/18/2020] [Indexed: 12/16/2022]
Abstract
The molecular recognition of carbohydrates by proteins plays a key role in many biological processes including immune response, pathogen entry into a cell, and cell-cell adhesion (e.g., in cancer metastasis). Carbohydrates interact with proteins mainly through hydrogen bonding, metal-ion-mediated interaction, and non-polar dispersion interactions. The role of dispersion-driven CH-π interactions (stacking) in protein-carbohydrate recognition has been underestimated for a long time considering the polar interactions to be the main forces for saccharide interactions. However, over the last few years it turns out that non-polar interactions are equally important. In this study, we analyzed the CH-π interactions employing bioinformatics (data mining, structural analysis), several experimental (isothermal titration calorimetry (ITC), X-ray crystallography), and computational techniques. The Protein Data Bank (PDB) has been used as a source of structural data. The PDB contains over 12 000 protein complexes with carbohydrates. Stacking interactions are very frequently present in such complexes (about 39 % of identified structures). The calculations and the ITC measurement results suggest that the CH-π stacking contribution to the overall binding energy ranges from 4 up to 8 kcal mol-1 . All the results show that the stacking CH-π interactions in protein-carbohydrate complexes can be considered to be a driving force of the binding in such complexes.
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Affiliation(s)
- Josef Houser
- Central European Institute of Technology, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 61137, Brno, Czech Republic
| | - Stanislav Kozmon
- Central European Institute of Technology, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic.,Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 84538, Bratislava, Slovak Republic
| | - Deepti Mishra
- Central European Institute of Technology, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Zuzana Hammerová
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 61137, Brno, Czech Republic
| | - Michaela Wimmerová
- Central European Institute of Technology, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 61137, Brno, Czech Republic.,Department of Biochemistry, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Jaroslav Koča
- Central European Institute of Technology, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 61137, Brno, Czech Republic
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11
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Thiel Z, Nguyen J, Rivera‐Fuentes P. Genetically Encoded Activators of Small Molecules for Imaging and Drug Delivery. Angew Chem Int Ed Engl 2020; 59:7669-7677. [PMID: 31898373 PMCID: PMC7318188 DOI: 10.1002/anie.201915521] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Indexed: 12/30/2022]
Abstract
Chemical biologists have developed many tools based on genetically encoded macromolecules and small, synthetic compounds. The two different approaches are extremely useful, but they have inherent limitations. In this Minireview, we highlight examples of strategies that combine both concepts to tackle challenging problems in chemical biology. We discuss applications in imaging, with a focus on super-resolved techniques, and in probe and drug delivery. We propose future directions in this field, hoping to inspire chemical biologists to develop new combinations of synthetic and genetically encoded probes.
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Affiliation(s)
- Zacharias Thiel
- Institute of Chemical Sciences and EngineeringEPF LausanneCH C2 425, Station 61015LausanneSwitzerland
- Laboratory of Organic ChemistryETH ZurichVladimir-Prelog-Weg 38093ZurichSwitzerland
| | - Jade Nguyen
- Institute of Chemical Sciences and EngineeringEPF LausanneCH C2 425, Station 61015LausanneSwitzerland
- Laboratory of Organic ChemistryETH ZurichVladimir-Prelog-Weg 38093ZurichSwitzerland
| | - Pablo Rivera‐Fuentes
- Institute of Chemical Sciences and EngineeringEPF LausanneCH C2 425, Station 61015LausanneSwitzerland
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12
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Thiel Z, Nguyen J, Rivera‐Fuentes P. Genetically Encoded Activators of Small Molecules for Imaging and Drug Delivery. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Zacharias Thiel
- Institute of Chemical Sciences and Engineering EPF Lausanne CH C2 425, Station 6 1015 Lausanne Switzerland
- Laboratory of Organic Chemistry ETH Zurich Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Jade Nguyen
- Institute of Chemical Sciences and Engineering EPF Lausanne CH C2 425, Station 6 1015 Lausanne Switzerland
- Laboratory of Organic Chemistry ETH Zurich Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Pablo Rivera‐Fuentes
- Institute of Chemical Sciences and Engineering EPF Lausanne CH C2 425, Station 6 1015 Lausanne Switzerland
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13
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Nakayama A, Otani A, Inokuma T, Tsuji D, Mukaiyama H, Nakayama A, Itoh K, Otaka A, Tanino K, Namba K. Development of a 1,3a,6a-triazapentalene derivative as a compact and thiol-specific fluorescent labeling reagent. Commun Chem 2020; 3:6. [PMID: 36703318 PMCID: PMC9812263 DOI: 10.1038/s42004-019-0250-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 12/11/2019] [Indexed: 01/29/2023] Open
Abstract
For the fluorescence imaging of biologically active small compounds, the development of compact fluorophores that do not perturb bioactivity is required. Here we report a compact derivative of fluorescent 1,3a,6a-triazapentalenes, 2-isobutenylcarbonyl-1,3a,6a-triazapentalene (TAP-VK1), as a fluorescent labeling reagent. The reaction of TAP-VK1 with various aliphatic thiols proceeds smoothly to afford the corresponding 1,4-adducts in high yields, and nucleophiles other than thiols do not react. After the addition of thiol groups in dichloromethane, the emission maximum of TAP-VK1 shifts to a shorter wavelength and the fluorescence intensity is substantially increased. The utility of TAP-VK1 as a compact fluorescent labeling reagent is clearly demonstrated by the labeling of Captopril, which is a small molecular drug for hypertension. The successful imaging of Captopril, one of the most compact drugs, in this study demonstrates the usefulness of compact fluorophores for mechanistic studies.
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Affiliation(s)
- Atsushi Nakayama
- grid.267335.60000 0001 1092 3579Department of Pharmaceutical Sciences, Tokushima University, 1-78-1 Shomachi, Tokushima, 770-8505 Japan ,grid.267335.60000 0001 1092 3579Research Cluster on “Innovative Chemical Sensing”, Tokushima University, 1-78-1 Shomachi, Tokushima, 770-8505 Japan
| | - Akira Otani
- grid.267335.60000 0001 1092 3579Department of Pharmaceutical Sciences, Tokushima University, 1-78-1 Shomachi, Tokushima, 770-8505 Japan
| | - Tsubasa Inokuma
- grid.267335.60000 0001 1092 3579Department of Pharmaceutical Sciences, Tokushima University, 1-78-1 Shomachi, Tokushima, 770-8505 Japan ,grid.267335.60000 0001 1092 3579Research Cluster on “Innovative Chemical Sensing”, Tokushima University, 1-78-1 Shomachi, Tokushima, 770-8505 Japan
| | - Daisuke Tsuji
- grid.267335.60000 0001 1092 3579Department of Pharmaceutical Sciences, Tokushima University, 1-78-1 Shomachi, Tokushima, 770-8505 Japan
| | - Haruka Mukaiyama
- grid.267335.60000 0001 1092 3579Department of Pharmaceutical Sciences, Tokushima University, 1-78-1 Shomachi, Tokushima, 770-8505 Japan
| | - Akira Nakayama
- grid.26999.3d0000 0001 2151 536XDepartment of Chemical System Engineering, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku Tokyo, 113-8656 Japan
| | - Kohji Itoh
- grid.267335.60000 0001 1092 3579Department of Pharmaceutical Sciences, Tokushima University, 1-78-1 Shomachi, Tokushima, 770-8505 Japan
| | - Akira Otaka
- grid.267335.60000 0001 1092 3579Department of Pharmaceutical Sciences, Tokushima University, 1-78-1 Shomachi, Tokushima, 770-8505 Japan
| | - Keiji Tanino
- grid.39158.360000 0001 2173 7691Department of Chemistry, Faculty of Science, Hokkaido University, Kita-ku Sapporo, 060-0810 Japan
| | - Kosuke Namba
- grid.267335.60000 0001 1092 3579Department of Pharmaceutical Sciences, Tokushima University, 1-78-1 Shomachi, Tokushima, 770-8505 Japan ,grid.267335.60000 0001 1092 3579Research Cluster on “Innovative Chemical Sensing”, Tokushima University, 1-78-1 Shomachi, Tokushima, 770-8505 Japan
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Zhang S, Liu M, Tan LYF, Hong Q, Pow ZL, Owyong TC, Ding S, Wong WWH, Hong Y. A Maleimide‐functionalized Tetraphenylethene for Measuring and Imaging Unfolded Proteins in Cells. Chem Asian J 2019; 14:904-909. [DOI: 10.1002/asia.201900150] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/14/2019] [Indexed: 12/30/2022]
Affiliation(s)
- Shouxiang Zhang
- Department of Chemistry and Physics La Trobe Institute for Molecular Science La Trobe University Melbourne VIC 3086 Australia
| | - Mengjie Liu
- Department of Chemistry and Physics La Trobe Institute for Molecular Science La Trobe University Melbourne VIC 3086 Australia
| | - Lewis Yi Fong Tan
- Department of Chemistry and Physics La Trobe Institute for Molecular Science La Trobe University Melbourne VIC 3086 Australia
| | - Quentin Hong
- ARC Centre of Excellence in Exciton Science, School of Chemistry Bio21 Institute The University of Melbourne Parkville VIC 3010 Australia
| | - Ze Liang Pow
- ARC Centre of Excellence in Exciton Science, School of Chemistry Bio21 Institute The University of Melbourne Parkville VIC 3010 Australia
| | - Tze Cin Owyong
- Department of Chemistry and Physics La Trobe Institute for Molecular Science La Trobe University Melbourne VIC 3086 Australia
- ARC Centre of Excellence in Exciton Science, School of Chemistry Bio21 Institute The University of Melbourne Parkville VIC 3010 Australia
| | - Siyang Ding
- Department of Chemistry and Physics La Trobe Institute for Molecular Science La Trobe University Melbourne VIC 3086 Australia
| | - Wallace W. H. Wong
- ARC Centre of Excellence in Exciton Science, School of Chemistry Bio21 Institute The University of Melbourne Parkville VIC 3010 Australia
| | - Yuning Hong
- Department of Chemistry and Physics La Trobe Institute for Molecular Science La Trobe University Melbourne VIC 3086 Australia
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An aptamer-based four-color fluorometic method for simultaneous determination and imaging of alpha-fetoprotein, vascular endothelial growth factor-165, carcinoembryonic antigen and human epidermal growth factor receptor 2 in living cells. Mikrochim Acta 2019; 186:204. [PMID: 30796534 DOI: 10.1007/s00604-019-3312-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 02/11/2019] [Indexed: 12/19/2022]
Abstract
The extraordinary fluorescence quenching capability of graphene oxide (GO) was coupled to the specific recognition capability of aptamers to design a four-color fluorescent nanoprobe for multiplexed detection and imaging of tumor-associated proteins in living cells. Specifically, alpha-fetoprotein (AFP), vascular endothelial growth factor-165 (VEGF165), carcinoembryonic antigen (CEA), and human epidermal growth factor receptor 2 (HER2) were detected. Due to strong π interaction, the fluorescence of labeled aptamers is quenched by GO. Four fluorophore-labeled aptamers that bind the tumor-associated proteins were adsorbed on GO to form the four-color nanoprobe with quenched fluorescence. The nanoprobes were internalized into cells via endocytosis, where the aptamer/GO nanoprobes bind the intracellular tumor-associated proteins. The aptamer-protein complexes thus formed detach from GO, and fluorescence recovers. Each analyte has its typical color (AFP: blue; VEGF165: green; CEA: yellow; HER2: red). As a result, simultaneous detection and imaging of multiple tumor-associated proteins in living cells were achieved. This nanoprobe has a fast response and is highly specific and biocompatible. The linear ranges for AFP, VEGF165, CEA, and HER2 are 0.8 nM-160 nM, 0.5 nM-100 nM, 1.0 nM-200 nM, and 1.2 nM-240 nM, respectively. Detection limits were 0.45 nM for AFP, 0.30 nM for VEGF165, 0.62 nM for CEA, and 0.96 nM for HER2. The probe allows for a fast distinction between tumor cells and normal cells via imaging. Graphical abstract Schematic presentation of the development of a four-color fluorometic method based on aptamer and graphene oxide for simultaneous detection and imaging of alpha-fetoprotein, vascular endothelial growth factor-165, carcinoembryonic antigen and human epidermal growth factor receptor 2 in living cells.
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Abstract
Fluorescent folding sensor is a powerful tool to detect proteome stresses, including heat, osmotic, oxidative, and drug induced stresses. Monitoring proteome stress using these sensors allows us to dissect the mechanism of cellular stress and find therapeutics that ameliorate stress related diseases. Here we present a HaloTag-based fluorogenic proteome stress sensor (AgHalo) to robustly detect and quantify proteome stresses in live cells. We describe how proteome stresses are monitored in both bacterial and mammalian live cells using fluorescence confocal microscope and fluorescence plate reader.
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17
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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: 3] [Impact Index Per Article: 0.4] [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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18
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Manzoor O, Soleja N, Mohsin M. Nanoscale gizmos - the novel fluorescent probes for monitoring protein activity. Biochem Eng J 2018; 133:83-95. [PMID: 32518506 PMCID: PMC7270366 DOI: 10.1016/j.bej.2018.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 12/27/2017] [Accepted: 02/06/2018] [Indexed: 11/15/2022]
Abstract
Genetically-encoded FRET, organic dye, QD based sensors. Real-time monitoring of the respective metabolite level at sub cellular level. Spatio temporal resolution of the fluorophores by low intensity light. Monitoring of various metabolite levels in any cell type prokaryotic and eukaryotic as well. Functional analysis of the role of proteases in several diseases.
Nanobiotechnology has emerged inherently as an interdisciplinary field, with collaborations from researchers belonging to diverse backgrounds like molecular biology, materials science and organic chemistry. Till the current times, researchers have been able to design numerous types of nanoscale fluorescent tool kits for monitoring protein–protein interactions through real time cellular imagery in a fluorescence microscope. It is apparent that supplementing any protein of interest with a fluorescence habit traces its function and regulation within a cell. Our review therefore highlights the application of several fluorescent probes such as molecular organic dyes, quantum dots (QD) and fluorescent proteins (FPs) to determine activity state, expression and localization of proteins in live and fixed cells. The focus is on Fluorescence Resonance Energy Transfer (FRET) based nanosensors that have been developed by researchers to visualize and monitor protein dynamics and quantify metabolites of diverse nature. FRET based toolkits permit the resolution of ambiguities that arise due to the rotation of sensor molecules and flexibility of the probe. Achievements of live cell imaging and efficient spatiotemporal resolution however have been possible only with the advent of fluorescence microscopic technology, equipped with precisely sensitive automated softwares.
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19
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Liu Y, Zhang X. Heat Shock Protein Reports on Proteome Stress. Biotechnol J 2018; 13. [DOI: 10.1002/biot.201800039] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Yu Liu
- Department of Chemistry, 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 Institute of the Life Sciences, The Pennsylvania State University; University Park PA 16802 USA
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20
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Sharma R, Pramanik MM, Chandramouli B, Rastogi N, Kumar N. Understanding organellar protein folding capacities and assessing their pharmacological modulation by small molecules. Eur J Cell Biol 2018; 97:114-125. [DOI: 10.1016/j.ejcb.2018.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 12/22/2017] [Accepted: 01/06/2018] [Indexed: 02/08/2023] Open
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21
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Liu Y, Miao K, Li Y, Fares M, Chen S, Zhang X. A HaloTag-Based Multicolor Fluorogenic Sensor Visualizes and Quantifies Proteome Stress in Live Cells Using Solvatochromic and Molecular Rotor-Based Fluorophores. Biochemistry 2018; 57:4663-4674. [DOI: 10.1021/acs.biochem.8b00135] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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22
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A biosensor-based framework to measure latent proteostasis capacity. Nat Commun 2018; 9:287. [PMID: 29348634 PMCID: PMC5773518 DOI: 10.1038/s41467-017-02562-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 12/11/2017] [Indexed: 12/11/2022] Open
Abstract
The pool of quality control proteins (QC) that maintains protein-folding homeostasis (proteostasis) is dynamic but can become depleted in human disease. A challenge has been in quantitatively defining the depth of the QC pool. With a new biosensor, flow cytometry-based methods and mathematical modeling we measure the QC capacity to act as holdases and suppress biosensor aggregation. The biosensor system comprises a series of barnase kernels with differing folding stability that engage primarily with HSP70 and HSP90 family proteins. Conditions of proteostasis stimulation and stress alter QC holdase activity and aggregation rates. The method reveals the HSP70 chaperone cycle to be rate limited by HSP70 holdase activity under normal conditions, but this is overcome by increasing levels of the BAG1 nucleotide exchange factor to HSPA1A or activation of the heat shock gene cluster by HSF1 overexpression. This scheme opens new paths for biosensors of disease and proteostasis systems. A pool of quality control proteins (QC) maintains the protein-folding homeostasis in the cell, but its quantitative analysis is challenging. Here the authors develop a FRET sensor based on the protein barnase, able to quantify QC holdase activity and its ability to suppress protein aggregation.
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23
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Fares M, Li Y, Liu Y, Miao K, Gao Z, Zhai Y, Zhang X. A Molecular Rotor-Based Halo-Tag Ligand Enables a Fluorogenic Proteome Stress Sensor to Detect Protein Misfolding in Mildly Stressed Proteome. Bioconjug Chem 2018; 29:215-224. [DOI: 10.1021/acs.bioconjchem.7b00763] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Matthew Fares
- Department of Chemistry, ‡Department of Biochemistry and Molecular Biology, and §The Huck Institutes
of Life Sciences, The Pennsylvania State University, University
Park, Pennsylvania 16802, United States
| | - Yinghao Li
- Department of Chemistry, ‡Department of Biochemistry and Molecular Biology, and §The Huck Institutes
of Life Sciences, The Pennsylvania State University, University
Park, Pennsylvania 16802, United States
| | - Yu Liu
- Department of Chemistry, ‡Department of Biochemistry and Molecular Biology, and §The Huck Institutes
of Life Sciences, The Pennsylvania State University, University
Park, Pennsylvania 16802, United States
| | - Kun Miao
- Department of Chemistry, ‡Department of Biochemistry and Molecular Biology, and §The Huck Institutes
of Life Sciences, The Pennsylvania State University, University
Park, Pennsylvania 16802, United States
| | - Zi Gao
- Department of Chemistry, ‡Department of Biochemistry and Molecular Biology, and §The Huck Institutes
of Life Sciences, The Pennsylvania State University, University
Park, Pennsylvania 16802, United States
| | - Yufeng Zhai
- Department of Chemistry, ‡Department of Biochemistry and Molecular Biology, and §The Huck Institutes
of Life Sciences, The Pennsylvania State University, University
Park, Pennsylvania 16802, United States
| | - Xin Zhang
- Department of Chemistry, ‡Department of Biochemistry and Molecular Biology, and §The Huck Institutes
of Life Sciences, The Pennsylvania State University, University
Park, Pennsylvania 16802, United States
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Pan S, Jang SY, Liew SS, Fu J, Wang D, Lee JS, Yao SQ. A Vinyl Sulfone-Based Fluorogenic Probe Capable of Selective Labeling of PHGDH in Live Mammalian Cells. Angew Chem Int Ed Engl 2017; 57:579-583. [PMID: 29193627 DOI: 10.1002/anie.201710856] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Indexed: 11/05/2022]
Abstract
Chemical probes are powerful tools for interrogating small molecule-target interactions. With additional fluorescence Turn-ON functionality, such probes might enable direct measurements of target engagement in live mammalian cells. DNS-pE (and its terminal alkyne-containing version DNS-pE2) is the first small molecule that can selectively label endogenous 3-phosphoglycerate dehydrogenase (PHGDH) from various mammalian cells. Endowed with an electrophilic vinyl sulfone moiety that possesses fluorescence-quenching properties, DNS-pE/DNS-pE2 became highly fluorescent only upon irreversible covalent modification of PHGDH. With an inhibitory property (in vitro Ki =7.4 μm) comparable to that of known PHGDH inhibitors, our probes thus offer a promising approach to simultaneously image endogenous PHGDH activities and study its target engagement in live-cell settings.
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Affiliation(s)
- Sijun Pan
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore
| | - Se-Young Jang
- Molecular Recognition Research Center, Bio-Med Program of KIST-School UST, Korea Institute of Science & Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, 136791, Korea
| | - Si Si Liew
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore
| | - Jiaqi Fu
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore
| | - Danyang Wang
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore
| | - Jun-Seok Lee
- Molecular Recognition Research Center, Bio-Med Program of KIST-School UST, Korea Institute of Science & Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, 136791, Korea
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore
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25
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Pan S, Jang SY, Liew SS, Fu J, Wang D, Lee JS, Yao SQ. A Vinyl Sulfone-Based Fluorogenic Probe Capable of Selective Labeling of PHGDH in Live Mammalian Cells. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201710856] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Sijun Pan
- Department of Chemistry; National University of Singapore; 3 Science Drive 3 Singapore 117543 Singapore
| | - Se-Young Jang
- Molecular Recognition Research Center; Bio-Med Program of KIST-School UST; Korea Institute of Science & Technology; Hwarangno 14-gil 5 Seongbuk-gu Seoul 136-791 136791 Korea
| | - Si Si Liew
- Department of Chemistry; National University of Singapore; 3 Science Drive 3 Singapore 117543 Singapore
| | - Jiaqi Fu
- Department of Chemistry; National University of Singapore; 3 Science Drive 3 Singapore 117543 Singapore
| | - Danyang Wang
- Department of Chemistry; National University of Singapore; 3 Science Drive 3 Singapore 117543 Singapore
| | - Jun-Seok Lee
- Molecular Recognition Research Center; Bio-Med Program of KIST-School UST; Korea Institute of Science & Technology; Hwarangno 14-gil 5 Seongbuk-gu Seoul 136-791 136791 Korea
| | - Shao Q. Yao
- Department of Chemistry; National University of Singapore; 3 Science Drive 3 Singapore 117543 Singapore
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26
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A thiol probe for measuring unfolded protein load and proteostasis in cells. Nat Commun 2017; 8:474. [PMID: 28883394 PMCID: PMC5589734 DOI: 10.1038/s41467-017-00203-5] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 06/12/2017] [Indexed: 12/13/2022] Open
Abstract
When proteostasis becomes unbalanced, unfolded proteins can accumulate and aggregate. Here we report that the dye, tetraphenylethene maleimide (TPE-MI) can be used to measure cellular unfolded protein load. TPE-MI fluorescence is activated upon labelling free cysteine thiols, normally buried in the core of globular proteins that are exposed upon unfolding. Crucially TPE-MI does not become fluorescent when conjugated to soluble glutathione. We find that TPE-MI fluorescence is enhanced upon reaction with cellular proteomes under conditions promoting accumulation of unfolded proteins. TPE-MI reactivity can be used to track which proteins expose more cysteine residues under stress through proteomic analysis. We show that TPE-MI can report imbalances in proteostasis in induced pluripotent stem cell models of Huntington disease, as well as cells transfected with mutant Huntington exon 1 before the formation of visible aggregates. TPE-MI also detects protein damage following dihydroartemisinin treatment of the malaria parasites Plasmodium falciparum. TPE-MI therefore holds promise as a tool to probe proteostasis mechanisms in disease. Proteostasis is maintained through a number of molecular mechanisms, some of which function to protect the folded state of proteins. Here the authors demonstrate the use of TPE-MI in a fluorigenic dye assay for the quantitation of unfolded proteins that can be used to assess proteostasis on a cellular or proteome scale.
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27
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Ding G, Lu Y, Su J, Qin X, Luo Z, Gao F, Chen L, Li H. Two intensified fluorescence colors' switching achieved by branched dye nanoaggregates. NANOSCALE 2017; 9:11158-11169. [PMID: 28749494 DOI: 10.1039/c7nr02169k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In this study, a variety of branched target dyes containing double internal proton transfer segments were synthesized. For comparison, some linear analogs including a single internal proton transfer part were synthesized. The corresponding reference molecules lacking proton transfer segments were also prepared. The properties and aggregation modes of these dye aggregates were investigated on the basis of scanning electron microscopy images, transmission electron microscopy images, dynamic light scattering, X-ray diffraction, UV/visible absorption spectra and fluorescence emission spectra. The results showed that molecular aggregates with the morphologies of nano-scaled rounded or cubic particles of the target branched dyes could be yielded in mixed organic solvent/H2O solution. A remarkable emission enhancement and fluorescence switching process (from bright yellow to luminous pure blue) under 365 nm lamp irradiation was observed for these target branched dye nanoaggregates. However, no aggregates of the reference branched dyes free of hydroxyl groups were formed and no obvious spectral variations were found. In contrast, all the studied linear dyes yielded molecular nanoaggregates in mixed organic solvent/H2O solution, and only intensified single normal blue fluorescence emission was presented. This study provided real examples of some branched organic dye aggregates which were capable of displaying naked-eye enhanced fluorescence color switching under an UV lamp.
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Affiliation(s)
- Ge Ding
- College of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 400044, China.
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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: 1.4] [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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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: 77] [Impact Index Per Article: 9.6] [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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Radwan M, Wood RJ, Sui X, Hatters DM. When proteostasis goes bad: Protein aggregation in the cell. IUBMB Life 2017; 69:49-54. [PMID: 28066979 DOI: 10.1002/iub.1597] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 12/09/2016] [Indexed: 12/12/2022]
Abstract
Protein aggregation is a hallmark of the major neurodegenerative diseases including Alzheimer's, Parkinson's, Huntington's and motor neuron and is a symptom of a breakdown in the management of proteome foldedness. Indeed, it is remarkable that under normal conditions cells can keep their proteome in a highly crowded and confined space without uncontrollable aggregation. Proteins pose a particular challenge relative to other classes of biomolecules because upon synthesis they must typically follow a complex folding pathway to reach their functional conformation (native state). Non-native conformations, including the unfolded nascent chain, are highly prone to aberrant interactions, leading to aggregation. Here we review recent advances in knowledge of proteostasis, approaches to monitor proteostasis and the impact that protein aggregation has on biology. We also include discussion of the outstanding challenges. © 2017 IUBMB Life, 69(2):49-54, 2017.
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Affiliation(s)
- Mona Radwan
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 30 Flemington Road, Melbourne, Victoria, Australia
| | - Rebecca J Wood
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 30 Flemington Road, Melbourne, Victoria, Australia
| | - Xiaojing Sui
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 30 Flemington Road, Melbourne, Victoria, Australia
| | - Danny M Hatters
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 30 Flemington Road, Melbourne, Victoria, Australia
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Yang S, You M, Yang L, Zhang F, Wang Q, He P. A recyclable electrochemical sensing platform for breast cancer diagnosis based on homogeneous DNA hybridization and host-guest interaction between cucurbit [7]uril and ferrocene-nanosphere with signal amplification. J Electroanal Chem (Lausanne) 2016. [DOI: 10.1016/j.jelechem.2016.11.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Kusano S, Hayashida O. Development of Tetraphenylethylene-appended Tetraazacyclophanes: Evaluation of Aggregation-induced Emission Property and Application for Biomolecular Sensing. CHEM LETT 2016. [DOI: 10.1246/cl.160528] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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33
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Li LL, Li K, Liu YH, Xu HR, Yu XQ. Red emission fluorescent probes for visualization of monoamine oxidase in living cells. Sci Rep 2016; 6:31217. [PMID: 27499031 PMCID: PMC4976310 DOI: 10.1038/srep31217] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 07/14/2016] [Indexed: 12/20/2022] Open
Abstract
Here we report two novel red emission fluorescent probes for the highly sensitive and selective detection of monoamine oxidase (MAO) with large Stokes shift (227 nm). Both of the probes possess solid state fluorescence and can accomplish the identification of MAO on test papers. The probe MAO-Red-1 exhibited a detection limit down to 1.2 μg mL−1 towards MAO-B. Moreover, the cleavage product was unequivocally conformedby HPLC and LCMS and the result was in accordance with the proposed oxidative deamination mechanism. The excellent photostability of MAO-Red-1 was proved both in vitro and in vivo through fluorescent kinetic experiment and laser exposure experiment of confocal microscopy, respectively. Intracellular experiments also confirmed the low cytotoxity and exceptional cell imaging abilities of MAO-Red-1. It was validated both in HeLa and HepG2 cells that MAO-Red-1 was capable of reporting MAO activity through the variation of fluorescence intensity.
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Affiliation(s)
- Ling-Ling Li
- Key Laboratory of Green Chemistry and Technology, Ministry of Education,College of Chemistry, Sichuan University, No. 29, Wangjiang Road, Chengdu, 610064, P. R. China
| | - Kun Li
- Key Laboratory of Green Chemistry and Technology, Ministry of Education,College of Chemistry, Sichuan University, No. 29, Wangjiang Road, Chengdu, 610064, P. R. China
| | - Yan-Hong Liu
- Key Laboratory of Green Chemistry and Technology, Ministry of Education,College of Chemistry, Sichuan University, No. 29, Wangjiang Road, Chengdu, 610064, P. R. China
| | - Hao-Ran Xu
- Key Laboratory of Green Chemistry and Technology, Ministry of Education,College of Chemistry, Sichuan University, No. 29, Wangjiang Road, Chengdu, 610064, P. R. China
| | - Xiao-Qi Yu
- Key Laboratory of Green Chemistry and Technology, Ministry of Education,College of Chemistry, Sichuan University, No. 29, Wangjiang Road, Chengdu, 610064, P. R. China
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34
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Kaushik S, Cuervo AM. Proteostasis and aging. Nat Med 2016; 21:1406-15. [PMID: 26646497 DOI: 10.1038/nm.4001] [Citation(s) in RCA: 587] [Impact Index Per Article: 65.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Accepted: 11/02/2015] [Indexed: 12/12/2022]
Abstract
Accumulation of intracellular damage is an almost universal hallmark of aging. An improved understanding of the systems that contribute to cellular protein quality control has shed light on the reasons for the increased vulnerability of the proteome to stress in aging cells. Maintenance of protein homeostasis, or proteostasis, is attained through precisely coordinated systems that rapidly correct unwanted proteomic changes. Here we focus on recent developments that highlight the multidimensional nature of the proteostasis networks, which allow for coordinated protein homeostasis intracellularly, in between cells and even across organs, as well as on how they affect common age-associated diseases when they malfunction in aging.
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Affiliation(s)
- Susmita Kaushik
- Department of Developmental and Molecular Biology, Institute for Aging Studies, Albert Einstein College of Medicine, New York, New York, USA
| | - Ana Maria Cuervo
- Department of Developmental and Molecular Biology, Institute for Aging Studies, Albert Einstein College of Medicine, New York, New York, USA
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