1
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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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Potential applications of BPFP1 in Bcl-2 protein quantification, carcinoma cell visualization, cell sorting and early cancer diagnosis. Eur J Med Chem 2021; 224:113725. [PMID: 34375882 DOI: 10.1016/j.ejmech.2021.113725] [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] [Received: 12/29/2020] [Revised: 07/03/2021] [Accepted: 07/26/2021] [Indexed: 12/24/2022]
Abstract
Overexpression of the Bcl-2 protein has emerged as a hallmark of carcinoma cells and can be employed as a biochemical biomarker of these cells. Therefore, some Bcl-2 protein fluorescence probes (BPFPs) were designed for Bcl-2 protein quantification and carcinoma cells labeling. The high Bcl-2 protein binding affinity (Ki < 1 nM) and selectivity (over 50,000-fold Bcl-2 protein selectivity against Mcl-1 protein) of BPFP1 endow it with the ability to detect trace amounts of Bcl-2 protein. After being incubated with a range of concentrations of Bcl-2 protein, BPFP1 exhibited the desired fluorescence properties and its fluorescence intensity is proportional to Bcl-2 protein concentration. Therefore, BPFP1 provides a convenient approach for Bcl-2 protein quantification and we could determine the concentration of Bcl-2 protein based on the BPFP1's fluorescence intensity. Subsequent studies revealed that BPFP1 can fluorescently label carcinoma cells by binding to overexpressed Bcl-2 protein in living cells, and can distinguish carcinoma cells (HL-60 cells and ACHN cells) from normal-tissue cells (HUVECs) according to the different Bcl-2 protein expression levels between carcinoma cells and normal tissue cells. In the present study, BPFP1 represents a new tool for Bcl-2 protein quantification, carcinoma cell visualization and cell sorting. Moreover, BPFP1 can be used in the future for early cancer diagnosis by detecting carcinoma cells in patient tissues.
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3
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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: 55] [Impact Index Per Article: 13.8] [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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4
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Thiel Z, Nguyen J, Rivera‐Fuentes P. Genetically Encoded Activators of Small Molecules for Imaging and Drug Delivery. Angew Chem Int Ed Engl 2020; 59:7669-7677. [PMID: 31898373 PMCID: PMC7318188 DOI: 10.1002/anie.201915521] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Indexed: 12/30/2022]
Abstract
Chemical biologists have developed many tools based on genetically encoded macromolecules and small, synthetic compounds. The two different approaches are extremely useful, but they have inherent limitations. In this Minireview, we highlight examples of strategies that combine both concepts to tackle challenging problems in chemical biology. We discuss applications in imaging, with a focus on super-resolved techniques, and in probe and drug delivery. We propose future directions in this field, hoping to inspire chemical biologists to develop new combinations of synthetic and genetically encoded probes.
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Affiliation(s)
- Zacharias Thiel
- Institute of Chemical Sciences and EngineeringEPF LausanneCH C2 425, Station 61015LausanneSwitzerland
- Laboratory of Organic ChemistryETH ZurichVladimir-Prelog-Weg 38093ZurichSwitzerland
| | - Jade Nguyen
- Institute of Chemical Sciences and EngineeringEPF LausanneCH C2 425, Station 61015LausanneSwitzerland
- Laboratory of Organic ChemistryETH ZurichVladimir-Prelog-Weg 38093ZurichSwitzerland
| | - Pablo Rivera‐Fuentes
- Institute of Chemical Sciences and EngineeringEPF LausanneCH C2 425, Station 61015LausanneSwitzerland
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5
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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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6
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Cristie-David AS, Chen J, Nowak DB, Bondy AL, Sun K, Park SI, Banaszak Holl MM, Su M, Marsh ENG. Coiled-Coil-Mediated Assembly of an Icosahedral Protein Cage with Extremely High Thermal and Chemical Stability. J Am Chem Soc 2019; 141:9207-9216. [PMID: 31117640 DOI: 10.1021/jacs.8b13604] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The organization of protein molecules into higher-order nanoscale architectures is ubiquitous in Nature and represents an important goal in synthetic biology. Furthermore, the stabilization of enzyme activity has many practical applications in biotechnology and medicine. Here we describe the symmetry-directed design of an extremely stable, enzymatically active, hollow protein cage of Mr ≈ 2.1 MDa with dimensions similar to those of a small icosahedral virus. The cage was constructed based on icosahedral symmetry by genetically fusing a trimeric protein (TriEst) to a small pentameric de novo-designed coiled coil domain, separated by a flexible oligo-glycine linker sequence. Screening a small library of designs in which the linker length varied from 2 to 12 residues identified a construct containing 8 glycine residues (Ico8) that formed well-defined cages. Characterization by dynamic light scattering, negative stain, and cryo-EM and by atomic force and IR-photoinduced force microscopy established that Ico8 assembles into a flexible hollow cage comprising 20 copies of the esterase trimer, 60 protein subunits in total, with overall icosahedral geometry. Notably, the cages formed by Ico8 proved to be extremely stable toward thermal and chemical denaturation: whereas TriEst was unfolded by heating ( Tm ≈ 75 °C) or denatured by 1.5 M guanidine hydrochloride, the Ico8 cages remained folded even at 120 °C or in 8 M guanidine hydrochloride. The increased stability of the cages is a new property that emerges from the higher-order structure of the protein cage, rather than being intrinsic to the components from which it is constructed.
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Affiliation(s)
- Ajitha S Cristie-David
- Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Junjie Chen
- Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Derek B Nowak
- Molecular Vista Inc , Via Del Oro Suite 110 , San Jose , California 95119 , United States
| | - Amy L Bondy
- Life Sciences Institute , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Kai Sun
- Michigan Center for Materials Characterization , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Sung I Park
- Molecular Vista Inc , Via Del Oro Suite 110 , San Jose , California 95119 , United States
| | - Mark M Banaszak Holl
- Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Min Su
- Life Sciences Institute , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - E Neil G Marsh
- Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States.,Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
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7
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Liu T, Dong G, Xu F, Han B, Fang H, Huang Y, Zhou Y, Du L, Li M. Discovery of Turn-On Fluorescent Probes for Detecting Bcl-2 Protein. Anal Chem 2019; 91:5722-5728. [DOI: 10.1021/acs.analchem.8b05853] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Tingting Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (MOE), School of Pharmacy, Shandong University, Jinan, Shandong 250012, China
| | - Gaopan Dong
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (MOE), School of Pharmacy, Shandong University, Jinan, Shandong 250012, China
| | - Feng Xu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (MOE), School of Pharmacy, Shandong University, Jinan, Shandong 250012, China
| | - Bo Han
- Department of Pathology, School of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Hao Fang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (MOE), School of Pharmacy, Shandong University, Jinan, Shandong 250012, China
| | - Yun Huang
- Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, Texas 77030, United States
| | - Yubin Zhou
- Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, Texas 77030, United States
| | - Lupei Du
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (MOE), School of Pharmacy, Shandong University, Jinan, Shandong 250012, China
| | - Minyong Li
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (MOE), School of Pharmacy, Shandong University, Jinan, Shandong 250012, China
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong 250100, China
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8
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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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9
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Lechner H, Ferruz N, Höcker B. Strategies for designing non-natural enzymes and binders. Curr Opin Chem Biol 2018; 47:67-76. [PMID: 30248579 DOI: 10.1016/j.cbpa.2018.07.022] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 07/16/2018] [Accepted: 07/17/2018] [Indexed: 12/20/2022]
Abstract
The design of tailor-made enzymes is a major goal in biochemical research that can result in wide-range applications and will lead to a better understanding of how proteins fold and function. In this review we highlight recent advances in enzyme and small molecule binder design. A focus is placed on novel strategies for the design of scaffolds, developments in computational methods, and recent applications of these techniques on receptors, sensors, and enzymes. Further, the integration of computational and experimental methodologies is discussed. The outlined examples of designed enzymes and binders for various purposes highlight the importance of this topic and underline the need for tailor-made proteins.
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Affiliation(s)
- Horst Lechner
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Noelia Ferruz
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Birte Höcker
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany.
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10
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Edwardson TGW, Mori T, Hilvert D. Rational Engineering of a Designed Protein Cage for siRNA Delivery. J Am Chem Soc 2018; 140:10439-10442. [PMID: 30091604 DOI: 10.1021/jacs.8b06442] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Oligonucleotide therapeutics have transformative potential in modern medicine but are poor drug candidates in themselves unless fitted with compensatory carrier systems. We describe a simple approach to transform a designed porous protein cage into a nucleic acid delivery vehicle. By introducing arginine mutations to the lumenal surface, a positively supercharged capsule is created, which can encapsidate oligonucleotides in vitro with high binding affinity. We demonstrate that the siRNA-loaded cage is taken up by mammalian cells and releases its cargo to induce RNAi and knockdown gene expression. These general concepts could also be applied to alternative scaffold designs, expediting the development of artificial protein cages toward delivery applications.
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Affiliation(s)
| | - Takahiro Mori
- Laboratory of Organic Chemistry , ETH Zurich , 8093 Zurich , Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry , ETH Zurich , 8093 Zurich , Switzerland
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11
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Liu T, Gao Y, Zhang X, Wan Y, Du L, Fang H, Li M. Discovery of a Turn-On Fluorescent Probe for Myeloid Cell Leukemia-1 Protein. Anal Chem 2017; 89:11173-11177. [DOI: 10.1021/acs.analchem.7b01148] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Tingting Liu
- Department
of Medicinal Chemistry, Key Laboratory of Chemical Biology (MOE),
School of Pharmacy, Shandong University, Jinan, Shandong 250012, China
| | - Yuqi Gao
- Department
of Medicinal Chemistry, Key Laboratory of Chemical Biology (MOE),
School of Pharmacy, Shandong University, Jinan, Shandong 250012, China
| | - Xiaomeng Zhang
- Department
of Medicinal Chemistry, Key Laboratory of Chemical Biology (MOE),
School of Pharmacy, Shandong University, Jinan, Shandong 250012, China
| | - Yichao Wan
- Key
Laboratory of Theoretical Organic Chemistry and Functional Molecule
(MOE), College of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, Hunan 411201, China
| | - Lupei Du
- Department
of Medicinal Chemistry, Key Laboratory of Chemical Biology (MOE),
School of Pharmacy, Shandong University, Jinan, Shandong 250012, China
| | - Hao Fang
- Department
of Medicinal Chemistry, Key Laboratory of Chemical Biology (MOE),
School of Pharmacy, Shandong University, Jinan, Shandong 250012, China
| | - Minyong Li
- Department
of Medicinal Chemistry, Key Laboratory of Chemical Biology (MOE),
School of Pharmacy, Shandong University, Jinan, Shandong 250012, China
- State
Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong 250100, China
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12
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Otte KB, Maurer E, Kirtz M, Grabs D, Althoff E, Bartsch S, Vogel A, Nestl BM, Hauer B. Synthesis of Sebacic Acid Using a De Novo Designed Retro-Aldolase as a Key Catalyst. ChemCatChem 2017. [DOI: 10.1002/cctc.201601551] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Konrad B. Otte
- Institute of Technical Biochemistry; Universitaet Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Elena Maurer
- Institute of Technical Biochemistry; Universitaet Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Marko Kirtz
- Institute of Technical Biochemistry; Universitaet Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | | | | | | | - Andreas Vogel
- c-LEcta GmbH; Perlickstrasse 5 04103 Leipzig Germany
| | - Bettina M. Nestl
- Institute of Technical Biochemistry; Universitaet Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Bernhard Hauer
- Institute of Technical Biochemistry; Universitaet Stuttgart; Allmandring 31 70569 Stuttgart Germany
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13
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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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14
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Anderson CE, Shah KG, Yager P. Sensitive Protein Detection and Quantification in Paper-Based Microfluidics for the Point of Care. Methods Enzymol 2017; 589:383-411. [PMID: 28336071 DOI: 10.1016/bs.mie.2017.01.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The design of appropriate diagnostic assays for the point of care requires development of suitable biosensors, detection methods, and diagnostic platforms for sensitive, quantitative detection of biological analytes. Protein targets in particular are especially challenging to detect quantitatively and sensitively due to the lack of amplification strategies akin to nucleic acid amplification. However, recent advances in transducer and biosensor design, new detection labels, and paper-based microfluidics may realize the goal of sensitive, fast, portable, and low-cost protein detection. In this review, we discuss the biochemistry, optics, and engineering advances that may be leveraged to design such a sensitive protein diagnostic assay. The binding kinetics, mechanisms of binding in porous networks, and potential transducers are explained in detail. We discuss the relative merits of various optical detection strategies, potential detection labels, optical readout approaches, and image-processing techniques that are amenable to point-of-care use. To conclude, we present a systematic analysis of potential approaches to enhance the sensitivity of paper-based assays. The assay development framework presented here provides bioassay developers a strategy to methodically enhance the sensitivity and point-of-care suitability of protein diagnostics.
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Affiliation(s)
| | - Kamal G Shah
- University of Washington, Seattle, WA, United States
| | - Paul Yager
- University of Washington, Seattle, WA, United States.
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15
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Chen W, Dong J, Plate L, Mortenson DE, Brighty GJ, Li S, Liu Y, Galmozzi A, Lee PS, Hulce JJ, Cravatt BF, Saez E, Powers ET, Wilson IA, Sharpless KB, Kelly JW. Arylfluorosulfates Inactivate Intracellular Lipid Binding Protein(s) through Chemoselective SuFEx Reaction with a Binding Site Tyr Residue. J Am Chem Soc 2016; 138:7353-64. [PMID: 27191344 PMCID: PMC4909538 DOI: 10.1021/jacs.6b02960] [Citation(s) in RCA: 197] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Arylfluorosulfates have appeared only rarely in the literature and have not been explored as probes for covalent conjugation to proteins, possibly because they were assumed to possess high reactivity, as with other sulfur(VI) halides. However, we find that arylfluorosulfates become reactive only under certain circumstances, e.g., when fluoride displacement by a nucleophile is facilitated. Herein, we explore the reactivity of structurally simple arylfluorosulfates toward the proteome of human cells. We demonstrate that the protein reactivity of arylfluorosulfates is lower than that of the corresponding aryl sulfonyl fluorides, which are better characterized with regard to proteome reactivity. We discovered that simple hydrophobic arylfluorosulfates selectively react with a few members of the intracellular lipid binding protein (iLBP) family. A central function of iLBPs is to deliver small-molecule ligands to nuclear hormone receptors. Arylfluorosulfate probe 1 reacts with a conserved tyrosine residue in the ligand-binding site of a subset of iLBPs. Arylfluorosulfate probes 3 and 4, featuring a biphenyl core, very selectively and efficiently modify cellular retinoic acid binding protein 2 (CRABP2), both in vitro and in living cells. The X-ray crystal structure of the CRABP2-4 conjugate, when considered together with binding site mutagenesis experiments, provides insight into how CRABP2 might activate arylfluorosulfates toward site-specific reaction. Treatment of breast cancer cells with probe 4 attenuates nuclear hormone receptor activity mediated by retinoic acid, an endogenous client lipid of CRABP2. Our findings demonstrate that arylfluorosulfates can selectively target single iLBPs, making them useful for understanding iLBP function.
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Affiliation(s)
- Wentao Chen
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jiajia Dong
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Lars Plate
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - David E. Mortenson
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Gabriel J. Brighty
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Suhua Li
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yu Liu
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrea Galmozzi
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Peter S. Lee
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jonathan J. Hulce
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Benjamin F. Cravatt
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Enrique Saez
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Evan T. Powers
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian A. Wilson
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - K. Barry Sharpless
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jeffery W. Kelly
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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16
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Qian Y, Schürmann M, Janning P, Hedberg C, Waldmann H. Activity-Based Proteome Profiling Probes Based on Woodward's Reagent K with Distinct Target Selectivity. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602666] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yong Qian
- Max Planck Institute of Molecular Physiology; Otto-Hahn-Strasse 11 Dortmund Germany
| | - Marc Schürmann
- Max Planck Institute of Molecular Physiology; Otto-Hahn-Strasse 11 Dortmund Germany
| | - Petra Janning
- Max Planck Institute of Molecular Physiology; Otto-Hahn-Strasse 11 Dortmund Germany
| | - Christian Hedberg
- Department of Chemistry, Chemical Biology Centre (KBC); Umeå University; 90187 Umeå Sweden
| | - Herbert Waldmann
- Max Planck Institute of Molecular Physiology; Otto-Hahn-Strasse 11 Dortmund Germany
- Technical University Dortmund; Department of Chemistry and Chemical Biology; Otto-Hahn-Strasse 6 Dortmund Germany
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17
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Qian Y, Schürmann M, Janning P, Hedberg C, Waldmann H. Activity-Based Proteome Profiling Probes Based on Woodward's Reagent K with Distinct Target Selectivity. Angew Chem Int Ed Engl 2016; 55:7766-71. [DOI: 10.1002/anie.201602666] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Yong Qian
- Max Planck Institute of Molecular Physiology; Otto-Hahn-Strasse 11 Dortmund Germany
| | - Marc Schürmann
- Max Planck Institute of Molecular Physiology; Otto-Hahn-Strasse 11 Dortmund Germany
| | - Petra Janning
- Max Planck Institute of Molecular Physiology; Otto-Hahn-Strasse 11 Dortmund Germany
| | - Christian Hedberg
- Department of Chemistry, Chemical Biology Centre (KBC); Umeå University; 90187 Umeå Sweden
| | - Herbert Waldmann
- Max Planck Institute of Molecular Physiology; Otto-Hahn-Strasse 11 Dortmund Germany
- Technical University Dortmund; Department of Chemistry and Chemical Biology; Otto-Hahn-Strasse 6 Dortmund Germany
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18
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Liu Y, Zhang X, Chen W, Tan YL, Kelly JW. Fluorescence Turn-On Folding Sensor To Monitor Proteome Stress in Live Cells. J Am Chem Soc 2015; 137:11303-11. [PMID: 26305239 PMCID: PMC4755273 DOI: 10.1021/jacs.5b04366] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Proteome misfolding and/or aggregation, caused by a thermal perturbation or a related stress, transiently challenges the cellular protein homeostasis (proteostasis) network capacity of cells by consuming chaperone/chaperonin pathway and degradation pathway capacity. Developing protein client-based probes to quantify the cellular proteostasis network capacity in real time is highly desirable. Herein we introduce a small-molecule-regulated fluorescent protein folding sensor based on a thermo-labile mutant of the de novo designed retroaldolase (RA) enzyme. Since RA enzyme activity is not present in any cell, the protein folding sensor is bioorthogonal. The fluorogenic small molecule was designed to become fluorescent when it binds to and covalently reacts with folded and functional RA. Thus, in the first experimental paradigm, cellular proteostasis network capacity and its dynamics are reflected by RA-small molecule conjugate fluorescence, which correlates with the amount of folded and functional RA present, provided that pharmacologic chaperoning is minimized. In the second experimental scenario, the RA-fluorogenic probe conjugate is pre-formed in a cell by simply adding the fluorogenic probe to the cell culture media. Unreacted probe is then washed away before a proteome misfolding stress is applied in a pulse-chase-type experiment. Insufficient proteostasis network capacity is reflected by aggregate formation of the fluorescent RA-fluorogenic probe conjugate. Removal of the stress results in apparent RA-fluorogenic probe conjugate re-folding, mediated in part by the heat-shock response transcriptional program augmenting cytosolic proteostasis network capacity, and in part by time-dependent RA-fluorogenic probe conjugate degradation by cellular proteolysis.
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Affiliation(s)
- Yu Liu
- Department of Chemistry, ‡Department of Molecular and Experimental Medicine, and §The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Xin Zhang
- Department of Chemistry, ‡Department of Molecular and Experimental Medicine, and §The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Wentao Chen
- Department of Chemistry, ‡Department of Molecular and Experimental Medicine, and §The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Yun Lei Tan
- Department of Chemistry, ‡Department of Molecular and Experimental Medicine, and §The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Jeffery W Kelly
- Department of Chemistry, ‡Department of Molecular and Experimental Medicine, and §The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States
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