1
|
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.
Collapse
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
| |
Collapse
|
2
|
Mo Z, Lin S, Chen W, He C. Protein Ligation and Labeling Enabled by a C-Terminal Tetracysteine Tag. Angew Chem Int Ed Engl 2022; 61:e202115377. [PMID: 35060269 DOI: 10.1002/anie.202115377] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Indexed: 01/01/2023]
Abstract
The hydrazinolysis of S-cyanylated peptide provides an alternative way to afford protein α-hydrazide, a key reagent used in native chemical ligation (NCL), without the aid of any inteins or enzymes. The currently used non-selective S-cyanylation, however, allows no other cysteine in the protein besides the one at the cleavage site. Herein, we report a regioselective S-cyanylation and hydrazinolysis strategy achieved via the fusion of a tetracysteine tag to the C-terminal of the protein of interest. We term it tetracysteine enabled protein ligation (TCEPL). While highly selective, the strategy is applicable for proteins expressed as inclusion bodies, and this was showcased by the efficient semi-synthesis of an iron-sulfur protein rubredoxin and the catalytic and hinge domains of matrix metalloprotease-14 (MMP-14) containing 207 amino acid residues. Furthermore, the TCEPL strategy was exploited for protein C-terminal labeling with amino reagents bearing a variety of functional groups, demonstrating its versatility and generality.
Collapse
Affiliation(s)
- Zeyuan Mo
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, 510640, P. R. China
| | - Shaomin Lin
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, 510640, P. R. China
| | - Wentao Chen
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, 510640, P. R. China
| | - Chunmao He
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, 510640, P. R. China
| |
Collapse
|
3
|
Mo Z, Lin S, Chen W, He C. Protein Ligation and Labeling Enabled by a C‐Terminal Tetracysteine Tag. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202115377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Zeyuan Mo
- School of Chemistry and Chemical Engineering South China University of Technology Guangzhou 510640 P. R. China
| | - Shaomin Lin
- School of Chemistry and Chemical Engineering South China University of Technology Guangzhou 510640 P. R. China
| | - Wentao Chen
- School of Chemistry and Chemical Engineering South China University of Technology Guangzhou 510640 P. R. China
| | - Chunmao He
- School of Chemistry and Chemical Engineering South China University of Technology Guangzhou 510640 P. R. China
| |
Collapse
|
4
|
Pomorski A, Krężel A. Biarsenical fluorescent probes for multifunctional site-specific modification of proteins applicable in life sciences: an overview and future outlook. Metallomics 2021; 12:1179-1207. [PMID: 32658234 DOI: 10.1039/d0mt00093k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Fluorescent modification of proteins of interest (POI) in living cells is desired to study their behaviour and functions in their natural environment. In a perfect setting it should be easy to perform, inexpensive, efficient and site-selective. Although multiple chemical and biological methods have been developed, only a few of them are applicable for cellular studies thanks to their appropriate physical, chemical and biological characteristics. One such successful system is a tetracysteine tag/motif and its selective biarsenical binders (e.g. FlAsH and ReAsH). Since its discovery in 1998 by Tsien and co-workers, this method has been enhanced and revolutionized in terms of its efficiency, formed complex stability and breadth of application. Here, we overview the whole field of knowledge, while placing most emphasis on recent reports. We showcase the improvements of classical biarsenical probes with various optical properties as well as multifunctional molecules that add new characteristics to proteins. We also present the evolution of affinity tags and motifs of biarsenical probes demonstrating much more possibilities in cellular applications. We summarize protocols and reported observations so both beginners and advanced users of biarsenical probes can troubleshoot their experiments. We address the concerns regarding the safety of biarsenical probe application. We showcase examples in virology, studies on receptors or amyloid aggregation, where application of biarsenical probes allowed observations that previously were not possible. We provide a summary of current applications ranging from bioanalytical sciences to allosteric control of selected proteins. Finally, we present an outlook to encourage more researchers to use these magnificent probes.
Collapse
Affiliation(s)
- Adam Pomorski
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland.
| | | |
Collapse
|
5
|
Ando T, Takamori Y, Yokoyama T, Yamamoto M, Kawakami T. Directed evolution of dibenzocyclooctyne-reactive peptide tags for protein labeling. Biochem Biophys Res Commun 2020; 534:27-33. [PMID: 33310184 DOI: 10.1016/j.bbrc.2020.12.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 12/03/2020] [Indexed: 01/02/2023]
Abstract
Protein labeling with a functional molecule is a technique widely used for protein research. The covalent reaction of self-labeling peptide tags with synthetic probe-modified small molecules enables tag-fused protein labeling with chemically diverse molecules, including fluorescent probes. We report the discovery, by in vitro directed evolution, of a novel 23-mer dibenzocyclooctyne (DBCO)-reactive peptide (DRP) tag using Systematic Evolution of Ligands by EXponential enrichment (SELEX) with a combination of a reconstituted cell-free translation system (PURE system) and cDNA display. The N- and C-terminal DRP truncations created a shorter 16-mer DBCO-reactive peptide (sDRP) tag without significant reactivity reduction. By fusing the sDRP tag to a model protein, we showed the chemical labeling and in-gel fluorescence imaging of the sDRP-fused protein using a fluorescent DBCO probe. Results showed that sDRP tag-mediated protein labeling has potential for use as a basic molecular tool in a variety of applications for protein research.
Collapse
Affiliation(s)
- Takehiro Ando
- Department of Life and Environmental Sciences, Integrated Graduate School of Medicine, Engineering, and Agricultural Sciences, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi, 400-8510, Japan
| | - Yukio Takamori
- Department of Life and Environmental Sciences, Integrated Graduate School of Medicine, Engineering, and Agricultural Sciences, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi, 400-8510, Japan
| | - Takumi Yokoyama
- Department of Life and Environmental Sciences, Integrated Graduate School of Medicine, Engineering, and Agricultural Sciences, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi, 400-8510, Japan
| | - Mizuki Yamamoto
- Department of Integrated Applied Life Science, Integrated Graduate School of Medicine, Engineering, and Agricultural Sciences, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi, 400-8510, Japan
| | - Takashi Kawakami
- Faculty of Life and Environmental Sciences, Graduate Faculty of Interdisciplinary Research, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi, 400-8510, Japan; JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan.
| |
Collapse
|
6
|
Pokhrel R, Tang T, Holub JM. Monitoring ligand-mediated helix 12 transitions within the human estrogen receptor α using bipartite tetracysteine display. Org Biomol Chem 2020; 18:6063-6071. [PMID: 32724950 DOI: 10.1039/d0ob01234c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Estrogen receptor α ligand-binding domains (ERα-LBD) expressing tetracysteine motifs bind FlAsH-EDT2 upon transition of helix 12 (H12) to a folded state. Changes in fluorescence intensity allowed surveillance of ligand-mediated H12 transitions and facilitated the determination of FlAsH association rates (kon) and apparent equilibrium dissociation constants (Kapp) to ERα-LBDs in the presence of estrogenic ligands.
Collapse
Affiliation(s)
- Ranju Pokhrel
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701, USA
| | | | | |
Collapse
|
7
|
Mari E, Bousmah Y, Boutin C, Léonce E, Milanole G, Brotin T, Berthault P, Erard M. Bimodal Detection of Proteins by 129 Xe NMR and Fluorescence Spectroscopy. Chembiochem 2019; 20:1450-1457. [PMID: 30650230 DOI: 10.1002/cbic.201800802] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Indexed: 11/10/2022]
Abstract
A full understanding of biological phenomena involves sensitive and noninvasive detection. Herein, we report the optimization of a probe for intracellular proteins that combines the advantages of fluorescence and hyperpolarized 129 Xe NMR spectroscopy detection. The fluorescence detection part is composed of six residues containing a tetracysteine tag (-CCXXCC-) genetically incorporated into the protein of interest and of a small organic molecule, CrAsH. CrAsH becomes fluorescent if it binds to the tetracysteine tag. The part of the biosensor that enables detection by means of 129 Xe NMR spectroscopy, which is linked to the CrAsH moiety by a spacer, is based on a cryptophane core that is fully suited to reversibly host xenon. Three different peptides, containing the tetracysteine tag and four organic biosensors of different stereochemistry, are benchmarked to propose the best couple that is fully suited for the in vitro detection of proteins.
Collapse
Affiliation(s)
- Emilie Mari
- NIMBE, CEA, CNRS, Université de Paris Saclay, CEA Saclay, 91191, Gif-sur-Yvette, France
- Laboratoire de Chimie Physique, CNRS, Université Paris-Sud, Université Paris-Saclay, Batiment 349, 91405, Orsay, France
| | - Yasmina Bousmah
- Laboratoire de Chimie Physique, CNRS, Université Paris-Sud, Université Paris-Saclay, Batiment 349, 91405, Orsay, France
| | - Céline Boutin
- NIMBE, CEA, CNRS, Université de Paris Saclay, CEA Saclay, 91191, Gif-sur-Yvette, France
| | - Estelle Léonce
- NIMBE, CEA, CNRS, Université de Paris Saclay, CEA Saclay, 91191, Gif-sur-Yvette, France
| | - Gaelle Milanole
- SCBM, Université Paris-Saclay, CEA Saclay, 91191, Gif-sur-Yvette, France
| | - Thierry Brotin
- Université Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5182, Université Lyon 1, Laboratoire de Chimie, 46 allée d'Italie, 69364, Lyon, France
| | - Patrick Berthault
- NIMBE, CEA, CNRS, Université de Paris Saclay, CEA Saclay, 91191, Gif-sur-Yvette, France
| | - Marie Erard
- Laboratoire de Chimie Physique, CNRS, Université Paris-Sud, Université Paris-Saclay, Batiment 349, 91405, Orsay, France
| |
Collapse
|
8
|
Fernandes DD, Bamrah J, Kailasam S, Gomes GNW, Li Y, Wieden HJ, Gradinaru CC. Characterization of Fluorescein Arsenical Hairpin (FlAsH) as a Probe for Single-Molecule Fluorescence Spectroscopy. Sci Rep 2017; 7:13063. [PMID: 29026195 PMCID: PMC5638890 DOI: 10.1038/s41598-017-13427-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 09/21/2017] [Indexed: 01/27/2023] Open
Abstract
In recent years, new labelling strategies have been developed that involve the genetic insertion of small amino-acid sequences for specific attachment of small organic fluorophores. Here, we focus on the tetracysteine FCM motif (FLNCCPGCCMEP), which binds to fluorescein arsenical hairpin (FlAsH), and the ybbR motif (TVLDSLEFIASKLA) which binds fluorophores conjugated to Coenzyme A (CoA) via a phosphoryl transfer reaction. We designed a peptide containing both motifs for orthogonal labelling with FlAsH and Alexa647 (AF647). Molecular dynamics simulations showed that both motifs remain solvent-accessible for labelling reactions. Fluorescence spectra, correlation spectroscopy and anisotropy decay were used to characterize labelling and to obtain photophysical parameters of free and peptide-bound FlAsH. The data demonstrates that FlAsH is a viable probe for single-molecule studies. Single-molecule imaging confirmed dual labeling of the peptide with FlAsH and AF647. Multiparameter single-molecule Förster Resonance Energy Transfer (smFRET) measurements were performed on freely diffusing peptides in solution. The smFRET histogram showed different peaks corresponding to different backbone and dye orientations, in agreement with the molecular dynamics simulations. The tandem of fluorophores and the labelling strategy described here are a promising alternative to bulky fusion fluorescent proteins for smFRET and single-molecule tracking studies of membrane proteins.
Collapse
Affiliation(s)
- Dennis D Fernandes
- Department of Physics, University of Toronto, Toronto, Ontario, M5S 1A7, Canada.
- Department of Chemical & Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, L5L 1C6, Canada.
| | - Jasbir Bamrah
- Department of Chemical & Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, L5L 1C6, Canada
| | - Senthilkumar Kailasam
- Alberta RNA Research & Training Institute, Department of Chemistry & Biochemistry, University of Lethbridge, Lethbridge, Alberta, T1K 3M4, Canada
| | - Gregory-Neal W Gomes
- Department of Physics, University of Toronto, Toronto, Ontario, M5S 1A7, Canada
- Department of Chemical & Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, L5L 1C6, Canada
| | - Yuchong Li
- Department of Physics, University of Toronto, Toronto, Ontario, M5S 1A7, Canada
- Department of Chemical & Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, L5L 1C6, Canada
| | - Hans-Joachim Wieden
- Alberta RNA Research & Training Institute, Department of Chemistry & Biochemistry, University of Lethbridge, Lethbridge, Alberta, T1K 3M4, Canada
| | - Claudiu C Gradinaru
- Department of Physics, University of Toronto, Toronto, Ontario, M5S 1A7, Canada.
- Department of Chemical & Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, L5L 1C6, Canada.
| |
Collapse
|
9
|
Bohl C, Pomorski A, Seemann S, Knospe AM, Zheng C, Krężel A, Rolfs A, Lukas J. Fluorescent probes for selective protein labeling in lysosomes: a case of α-galactosidase A. FASEB J 2017; 31:5258-5267. [PMID: 28821638 DOI: 10.1096/fj.201700058rrrr] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 07/31/2017] [Indexed: 12/13/2022]
Abstract
Fluorescence-based live-cell imaging (LCI) of lysosomal glycosidases is often hampered by unfavorable pH and redox conditions that reduce fluorescence output. Moreover, most lysosomal glycosidases are low-mass soluble proteins that do not allow for bulky fluorescent protein fusions. We selected α-galactosidase A (GALA) as a model lysosomal glycosidase involved in Anderson-Fabry disease (AFD) for the current LCI approach. Examination of the subcellular localization of AFD-causing mutants can reveal the mechanism underlying cellular trafficking deficits. To minimize genetic GALA modification, we employed a biarsenical labeling protocol with tetracysteine (TC-tag) detection. We tested the efficiency of halogen-substituted biarsenical probes to interact with C-terminally TC-tagged GALA peptide at pH 4.5 in vitro and identified F2FlAsH-EDT2 as a superior detection reagent for GALA. This probe provides improved signal/noise ratio in labeled COS-7 cells transiently expressing TC-tagged GALA. The investigated fluorescence-based LCI technology of TC-tagged lysosomal protein using an improved biarsenical probe can be used to identify novel compounds that promote proper trafficking of mutant GALA to lysosomal compartments and rescue the mutant phenotype.-Bohl, C., Pomorski, A., Seemann, S., Knospe, A.-M., Zheng, C., Krężel, A., Rolfs, A., Lukas, J. Fluorescent probes for selective protein labeling in lysosomes: a case of α-galactosidase A.
Collapse
Affiliation(s)
- Cornelius Bohl
- Albrecht-Kossel-Institute for Neuroregeneration, Rostock University Medical Center, Rostock, Mecklenburg-Vorpommern, Germany; and
| | - Adam Pomorski
- Department of Chemical Biology, Faculty of Biotechnology, University of Wroclaw, Wrocław, Poland
| | - Susanne Seemann
- Albrecht-Kossel-Institute for Neuroregeneration, Rostock University Medical Center, Rostock, Mecklenburg-Vorpommern, Germany; and
| | - Anne-Marie Knospe
- Albrecht-Kossel-Institute for Neuroregeneration, Rostock University Medical Center, Rostock, Mecklenburg-Vorpommern, Germany; and
| | - Chaonan Zheng
- Albrecht-Kossel-Institute for Neuroregeneration, Rostock University Medical Center, Rostock, Mecklenburg-Vorpommern, Germany; and
| | - Artur Krężel
- Department of Chemical Biology, Faculty of Biotechnology, University of Wroclaw, Wrocław, Poland
| | - Arndt Rolfs
- Albrecht-Kossel-Institute for Neuroregeneration, Rostock University Medical Center, Rostock, Mecklenburg-Vorpommern, Germany; and
| | - Jan Lukas
- Albrecht-Kossel-Institute for Neuroregeneration, Rostock University Medical Center, Rostock, Mecklenburg-Vorpommern, Germany; and
| |
Collapse
|
10
|
DIVERSE System: De Novo Creation of Peptide Tags for Non-enzymatic Covalent Labeling by In Vitro Evolution for Protein Imaging Inside Living Cells. ACTA ACUST UNITED AC 2016; 22:1671-9. [PMID: 26687484 DOI: 10.1016/j.chembiol.2015.10.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 10/10/2015] [Accepted: 10/15/2015] [Indexed: 10/22/2022]
Abstract
Polypeptide-tag/small-molecule pairs for specific cellular protein labeling are useful for visualizing cellular proteins and controlling their activity. Here, we report the development of an in vitro evolution-based (poly)peptide tag identification system named the DIVERSE (Directed In Vitro Evolution of Reactive peptide tags via Sequential Enrichment) system. In this system, an extremely diverse (10(14)) library of peptide tags, displayed by covalent attachment to their encoding cDNAs, is continuously prepared from the DNA library in a one-pot approach. Using this system, we demonstrated de novo creation of non-enzymatically covalent-labeling peptide tags for a synthetic small-molecule target from a random peptide library. Protein labeling with these tags was applicable to N- and C-terminal fusions, multiple different proteins and fluorophores, and intracellular labeling. The DIVERSE system can be used not only for the de novo creation of polypeptide tags but also sequence optimization of existing polypeptide tags from extremely diverse libraries.
Collapse
|
11
|
Walker AS, Rablen PX, Schepartz A. Rotamer-Restricted Fluorogenicity of the Bis-Arsenical ReAsH. J Am Chem Soc 2016; 138:7143-50. [PMID: 27163487 PMCID: PMC5381806 DOI: 10.1021/jacs.6b03422] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fluorogenic dyes such as FlAsH and ReAsH are used widely to localize, monitor, and characterize proteins and their assemblies in live cells. These bis-arsenical dyes can become fluorescent when bound to a protein containing four proximal Cys thiols-a tetracysteine (Cys4) motif. Yet the mechanism by which bis-arsenicals become fluorescent upon binding a Cys4 motif is unknown, and this nescience limits more widespread application of this tool. Here we probe the origins of ReAsH fluorogenicity using both computation and experiment. Our results support a model in which ReAsH fluorescence depends on the relative orientation of the aryl chromophore and the appended arsenic chelate: the fluorescence is rotamer-restricted. Our results do not support a model in which fluorogenicity arises from the relief of ring strain. The calculations identify those As-aryl rotamers that support fluorescence and those that do not and correlate well with prior experiments. The rotamer-restricted model we propose is supported further by biophysical studies: the excited-state fluorescence lifetime of a complex between ReAsH and a protein bearing a high-affinity Cys4 motif is longer than that of ReAsH-EDT2, and the fluorescence intensity of ReAsH-EDT2 increases in solvents of increasing viscosity. By providing a higher resolution view of the structural basis for fluorogenicity, these results provide a clear strategy for the design of more selective bis-arsenicals and better-optimized protein targets, with a concomitant improvement in the ability to characterize previously invisible protein conformational changes and assemblies in live cells.
Collapse
Affiliation(s)
- Allison S. Walker
- Department of Chemistry, Yale University, 225 Prospect St., New Haven CT 06520
| | - Paul X. Rablen
- Department of Chemistry & Biochemistry, Swarthmore College, 500 College Ave., Swarthmore, PA 19081
| | - Alanna Schepartz
- Department of Chemistry, Yale University, 225 Prospect St., New Haven CT 06520
- Department of Molecular, Cellular, and Developmental Biology, Yale University, 225 Prospect St., New Haven CT 06520
| |
Collapse
|
12
|
Martynov VI, Pakhomov AA, Popova NV, Deyev IE, Petrenko AG. Synthetic Fluorophores for Visualizing Biomolecules in Living Systems. Acta Naturae 2016; 8:33-46. [PMID: 28050265 PMCID: PMC5199205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The last decade has witnessed significant advance in the imaging of living systems using fluorescent markers. This progress has been primarily associated with the discovery of different spectral variants of fluorescent proteins. However, the fluorescent protein technology has its own limitations and, in some cases, the use of low-molecular-weight fluorophores is preferable. In this review, we describe the arsenal of synthetic fluorescent tools that are currently in researchers' hands and span virtually the entire spectrum, from the UV to visible and, further, to the near-infrared region. An overview of recent advances in site-directed introduction of synthetic fluorophores into target cellular objects is provided. Application of these fluorescent probes to the solution of a wide range of biological problems, in particular, to the determination of local ion concentrations and pH in living systems, is discussed.
Collapse
Affiliation(s)
- V. I. Martynov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St., 16/10, Moscow, 117997, Russia
| | - A. A. Pakhomov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St., 16/10, Moscow, 117997, Russia
| | - N. V. Popova
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St., 16/10, Moscow, 117997, Russia
| | - I. E. Deyev
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St., 16/10, Moscow, 117997, Russia
| | - A. G. Petrenko
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St., 16/10, Moscow, 117997, Russia
| |
Collapse
|
13
|
Stumpf AD, Hoffmann C. Optical probes based on G protein-coupled receptors - added work or added value? Br J Pharmacol 2015; 173:255-66. [PMID: 26562218 DOI: 10.1111/bph.13382] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 09/22/2015] [Accepted: 10/26/2015] [Indexed: 12/22/2022] Open
Abstract
In 2003, the first report was published that presented proof of principle for a novel class of FRET biosensors for use in living cells. This novel sensor class was built on the base of GPCRs, which represent an integral transmembrane receptor family passing the membrane seven times and are thus also called the 7TM receptor family. As an estimated number of 30% of all marketed drugs exert their effects by modulating GPCR function, these initial reports promised the gain of novel insights into receptor function. Such FRET sensors have slowly, but progressively, made their way into the standard toolbox for GPCR research as several groups are now reporting on the generation and use of these sensors. By now, FRET sensors have been reported for 18 different GPCRs, and more are expected to be added. These particular receptor sensors have been used to investigate receptor dynamics in living cells to evaluate ligand binding and ligand efficacy in real time, to study voltage and mechanosensitivity of GPCRs or to study the influence of receptor polymorphisms on receptor function in real-time. In this review we will describe the different design principles of these GPCR-based sensors and will summarize their current biological applications in living cells.
Collapse
Affiliation(s)
- A D Stumpf
- Bio-Imaging Center, Rudolf-Virchow-Zentrum für Experimentelle Medizin, University of Würzburg, Würzburg, Germany.,Department of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany
| | - C Hoffmann
- Bio-Imaging Center, Rudolf-Virchow-Zentrum für Experimentelle Medizin, University of Würzburg, Würzburg, Germany.,Department of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany
| |
Collapse
|
14
|
Friedrich U, Datta S, Schubert T, Plössl K, Schneider M, Grassmann F, Fuchshofer R, Tiefenbach KJ, Längst G, Weber BHF. Synonymous variants in HTRA1 implicated in AMD susceptibility impair its capacity to regulate TGF-β signaling. Hum Mol Genet 2015; 24:6361-73. [PMID: 26310622 DOI: 10.1093/hmg/ddv346] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 08/19/2015] [Indexed: 12/16/2023] Open
Abstract
High-temperature requirement A1 (HTRA1) is a secreted serine protease reported to play a role in the development of several cancers and neurodegenerative diseases. Still, the mechanism underlying the disease processes largely remains undetermined. In age-related macular degeneration (AMD), a common cause of vision impairment and blindness in industrialized societies, two synonymous polymorphisms (rs1049331:C>T, and rs2293870:G>T) in exon 1 of the HTRA1 gene were associated with a high risk to develop disease. Here, we show that the two polymorphisms result in a protein with altered thermophoretic properties upon heat-induced unfolding, trypsin accessibility and secretion behavior, suggesting unique structural features of the AMD-risk-associated HTRA1 protein. Applying MicroScale Thermophoresis and protease digestion analysis, we demonstrate direct binding and proteolysis of transforming growth factor β1 (TGF-β1) by normal HTRA1 but not the AMD-risk-associated isoform. As a consequence, both HTRA1 isoforms strongly differed in their ability to control TGF-β mediated signaling, as revealed by reporter assays targeting the TGF-β1-induced serpin peptidase inhibitor (SERPINE1, alias PAI-1) promoter. In addition, structurally altered HTRA1 led to an impaired autocrine TGF-β signaling in microglia, as measured by a strong down-regulation of downstream effectors of the TGF-β cascade such as phosphorylated SMAD2 and PAI-1 expression. Taken together, our findings demonstrate the effects of two synonymous HTRA1 variants on protein structure and protein interaction with TGF-β1. As a consequence, this leads to an impairment of TGF-β signaling and microglial regulation. Functional implications of the altered properties on AMD pathogenesis remain to be clarified.
Collapse
Affiliation(s)
- Ulrike Friedrich
- Institute of Human Genetics, University of Regensburg, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany
| | - Shyamtanu Datta
- Institute of Human Genetics, University of Regensburg, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany
| | - Thomas Schubert
- Department of Biochemistry, University of Regensburg, 2bind GmbH, Josef Engert Straße 13, 93053 Regensburg, Germany
| | - Karolina Plössl
- Institute of Human Genetics, University of Regensburg, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany
| | | | - Felix Grassmann
- Institute of Human Genetics, University of Regensburg, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany
| | | | - Klaus-Jürgen Tiefenbach
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany and
| | - Gernot Längst
- Department of Biochemistry, University of Regensburg
| | - Bernhard H F Weber
- Institute of Human Genetics, University of Regensburg, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany,
| |
Collapse
|
15
|
Tzeranis DS, Soller EC, Buydash MC, So PTC, Yannas IV. In Situ Quantification of Surface Chemistry in Porous Collagen Biomaterials. Ann Biomed Eng 2015; 44:803-15. [PMID: 26369635 DOI: 10.1007/s10439-015-1445-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Accepted: 09/01/2015] [Indexed: 01/28/2023]
Abstract
Cells inside a 3D matrix (such as tissue extracellular matrix or biomaterials) sense their insoluble environment through specific binding interactions between their adhesion receptors and ligands present on the matrix surface. Despite the critical role of the insoluble matrix in cell regulation, there exist no widely-applicable methods for quantifying the chemical stimuli provided by a matrix to cells. Here, we describe a general-purpose technique for quantifying in situ the density of ligands for specific cell adhesion receptors of interest on the surface of a 3D matrix. This paper improves significantly the accuracy of the procedure introduced in a previous publication by detailed marker characterization, optimized staining, and improved data interpretation. The optimized methodology is utilized to quantify the ligands of integrins α 1 β 1, α 2 β 1 on two kinds of matched porous collagen scaffolds, which are shown to possess significantly different ligand density, and significantly different ability to induce peripheral nerve regeneration in vivo. Data support the hypothesis that cell adhesion regulates contractile cell phenotypes, recently shown to be inversely related to organ regeneration. The technique provides a standardized way to quantify the surface chemistry of 3D matrices, and a means for introducing matrix effects in quantitative biological models.
Collapse
Affiliation(s)
- Dimitrios S Tzeranis
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. .,Department of Mechanical Engineering, National Technical University of Athens, 15780, Zografou, Greece.
| | - Eric C Soller
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Melissa C Buydash
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Peter T C So
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Ioannis V Yannas
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| |
Collapse
|
16
|
Cserép GB, Herner A, Kele P. Bioorthogonal fluorescent labels: a review on combined forces. Methods Appl Fluoresc 2015; 3:042001. [DOI: 10.1088/2050-6120/3/4/042001] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
|
17
|
Yan Q, Bruchez MP. Advances in chemical labeling of proteins in living cells. Cell Tissue Res 2015; 360:179-94. [PMID: 25743694 PMCID: PMC4380784 DOI: 10.1007/s00441-015-2145-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 02/02/2015] [Indexed: 01/07/2023]
Abstract
The pursuit of quantitative biological information via imaging requires robust labeling approaches that can be used in multiple applications and with a variety of detectable colors and properties. In addition to conventional fluorescent proteins, chemists and biologists have come together to provide a range of approaches that combine dye chemistry with the convenience of genetic targeting. This hybrid-tagging approach amalgamates the rational design of properties available through synthetic dye chemistry with the robust biological targeting available with genetic encoding. In this review, we discuss the current range of approaches that have been exploited for dye targeting or for targeting and activation and some of the recent applications that are uniquely permitted by these hybrid-tagging approaches.
Collapse
Affiliation(s)
- Qi Yan
- Sharp Edge Laboratories, Inc. Pittsburgh, PA
| | - Marcel P. Bruchez
- Sharp Edge Laboratories, Inc. Pittsburgh, PA
- Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, PA
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA
| |
Collapse
|
18
|
Mahalingam M, Fessenden JD. Methods for labeling skeletal muscle ion channels site-specifically with fluorophores suitable for FRET-based structural analysis. Methods Enzymol 2015; 556:455-74. [PMID: 25857795 DOI: 10.1016/bs.mie.2014.11.049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Skeletal muscle excitation-contraction coupling is triggered by the concerted action of two enormous Ca(2+) channel complexes, the dihydropyridine receptor and the type 1 ryanodine receptor. Recent advances in our understanding of the structure of these large Ca(2+) channels have been driven by fluorescence resonance energy transfer (FRET)-based analysis. A methodological challenge in conducting these FRET measurements is the ability to site-specifically label these huge ion channels with donor and acceptor fluorophores capable of undergoing energy transfer. In this chapter, we detail specific protocols for tagging large membrane proteins with these fluorescent probes using three orthogonal labeling methods: fluorescent protein fusions, biarsenical reagents directed to engineered tetracysteine tags, and Cy3/5 nitrilotriacetic acid conjugates that bind to poly-histidine tags.
Collapse
Affiliation(s)
- Mohana Mahalingam
- Department of Anesthesia, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - James D Fessenden
- Department of Anesthesia, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.
| |
Collapse
|
19
|
Hussey AM, Chambers JJ. Methods to locate and track ion channels and receptors expressed in live neurons. ACS Chem Neurosci 2015; 6:189-98. [PMID: 25307447 DOI: 10.1021/cn5002057] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Brain cells use electrical and chemical signaling to communicate with each other and to send and receive information from the body. These neurons also encode information such as memories and are constantly adapting to changes as a result of positive alterations, such as learning, or negative events, such as neurological insults or neurodegeneration. In the last two decades, it has become clear that the placement of minute branches of neurons and, more importantly for the topic of this review, the placement of individual protein molecules, are the key events that enable neuronal network building and pruning. Advances in both electrophysiology and light-based imaging have allowed neuroscientists to answer fundamental questions about the key proteins involved in memory formation, maintenance, and loss. These findings have been enabled often through the clever use of chemical biology, biotechnology, and genetic engineering. In this review, we highlight numerous examples where chemical biology was used to provide new tools to answer difficult and near impossible questions in neurobiology.
Collapse
Affiliation(s)
- Amanda M. Hussey
- Department
of Chemistry, University of Massachusetts, Amherst, Amherst, Massachusetts 01003, United States
| | - James J. Chambers
- Department
of Chemistry, University of Massachusetts, Amherst, Amherst, Massachusetts 01003, United States
- Neuroscience
and Behavior Program, University of Massachusetts, Amherst, Amherst, Massachusetts 01003, United States
| |
Collapse
|
20
|
Griffin BA, Adams SR, Tsien RY. How FlAsH got its sparkle: historical recollections of the biarsenical-tetracysteine tag. Methods Mol Biol 2015; 1266:1-6. [PMID: 25560064 DOI: 10.1007/978-1-4939-2272-7_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The biarsenical-tetracysteine tagging system was the first of (and inspiration for) the now numerous methods for site-specifically labeling proteins in living cells with small molecules such as fluorophores. This historical recollection describes its conception and the trial-and-error chemical development required to become a versatile technique.
Collapse
|
21
|
Lang K, Chin JW. Cellular incorporation of unnatural amino acids and bioorthogonal labeling of proteins. Chem Rev 2014; 114:4764-806. [PMID: 24655057 DOI: 10.1021/cr400355w] [Citation(s) in RCA: 791] [Impact Index Per Article: 79.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kathrin Lang
- Medical Research Council Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | | |
Collapse
|
22
|
Yang Y, Zhang CY. Visualizing and quantifying protein polySUMOylation at the single-molecule level. Anal Chem 2014; 86:967-72. [PMID: 24383460 DOI: 10.1021/ac403753r] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Protein polySUMOylation, the attachment of small ubiquitin-like modifier (SUMO) chains to the target protein, is associated with a variety of physiological processes. However, the analysis of protein polySUMOylation is often complicated by the heterogeneity of SUMO-target conjugates. Here, we develop a new strategy to visualize and quantify polySUMOylation at the single-molecule level by integrating the tetracysteine (TC) tag labeling technology and total internal reflection fluorescence (TIRF)-based single-molecule imaging. As a proof-of-concept, we employ the human SUMO-2 as the model. The addition of TC tag to SUMO-2 can specifically translate the SUMO-mediated modification into visible fluorescence signal without disturbing the function of SUMO-2. The SUMO monomers display homogeneous fluorescence spots at the single-molecule level, whereas the mixed SUMO chains exhibit nonuniform fluorescence spots with a wide range of intensities. Analysis of the number and the brightness of fluorescence spots enable quantitative measurement of the polySUMOylation degree inside the cells under different physiological conditions. Due to the frequent occurrence of posttranslational modification by polymeric chains in cells, this single-molecule strategy has the potential to be broadly applied for studying protein posttranslational modification in normal cellular physiology and disease etiology.
Collapse
Affiliation(s)
- Yong Yang
- Single-molecule Detection and Imaging Laboratory, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences , Shenzhen, Guangdong 518055, China
| | | |
Collapse
|
23
|
Cornell TA, Fu J, Newland SH, Orner BP. Detection of Specific Protein–Protein Interactions in Nanocages by Engineering Bipartite FlAsH Binding Sites. J Am Chem Soc 2013; 135:16618-24. [DOI: 10.1021/ja4085034] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Thomas A. Cornell
- Department
of Chemistry, King’s College London, London, SE1 1DB, United Kingdom
- Division
of Chemistry and Biological Chemistry, Nanyang Technological University, Singapore, 637371
| | - Jing Fu
- Division
of Chemistry and Biological Chemistry, Nanyang Technological University, Singapore, 637371
| | - Stephanie H. Newland
- School
of Chemistry, University of Southampton, Southampton, SO17 1BJ, United Kingdom
| | - Brendan P. Orner
- Department
of Chemistry, King’s College London, London, SE1 1DB, United Kingdom
| |
Collapse
|
24
|
Krumm SA, Takeda M, Plemper RK. The measles virus nucleocapsid protein tail domain is dispensable for viral polymerase recruitment and activity. J Biol Chem 2013; 288:29943-53. [PMID: 24003217 DOI: 10.1074/jbc.m113.503862] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Paramyxovirus genomes are ribonucleoprotein (RNP) complexes consisting of nucleoprotein (N)-encapsidated viral RNA. Measles virus (MeV) N features an amino-terminal RNA-binding core and a 125-residue tail domain, of which only the last 75 residues are considered fully mobile on the nucleocapsid surface. A molecular recognition element (MoRE) domain mediates binding of the viral phosphoprotein (P). This P N-tail interaction is considered instrumental for recruiting the polymerase complex to the template. We have engineered MeV N variants with tail truncations progressively eliminating the MoRE domain and upstream tail sections. Confirming previous reports, RNPs with N truncations lacking the carboxyl-terminal 43-residues harboring the MoRE domain cannot serve as polymerase template. Remarkably, further removal of all tail residues predicted to be surface-exposed significantly restores RNP bioactivity. Insertion of structurally dominant tags into the central N-tail section reduces bioactivity, but the negative regulatory effect of exposed N-tail stems is sequence-independent. Bioactive nucleocapsids lacking exposed N-tail sections are unable to sustain virus replication, because of weakened interaction of the advancing polymerase complex with the template. Deletion of the N-MoRE-binding domain in P abrogates polymerase recruitment to standard nucleocapsids, but polymerase activity is partially restored when N-tail truncated RNPs serve as template. Revising central elements of the current replication model, these data reveal that MeV polymerase is capable of productively docking directly to the nucleocapsid core. Dispensable for polymerase recruitment, N-MoRE binding to P-tail stabilizes the advancing polymerase-RNP complex and may rearrange unstructured central tail sections to facilitate polymerase access to the template.
Collapse
Affiliation(s)
- Stefanie A Krumm
- From the Center for Inflammation, Immunity & Infection, Georgia State University, Atlanta, Georgia 30303 and
| | | | | |
Collapse
|
25
|
Taguchi Y, Hohsfield LA, Hollister JR, Baron GS. Effects of FlAsH/tetracysteine (TC) Tag on PrP proteolysis and PrPres formation by TC-scanning. Chembiochem 2013; 14:1597-610, 1510. [PMID: 23943295 DOI: 10.1002/cbic.201300255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Indexed: 11/09/2022]
Abstract
Protein-protein interactions associated with proteolytic processing and aggregation are integral to normal and pathological aspects of prion protein (PrP) biology. Characterization of these interactions requires the identification of amino acid residues involved. The FlAsH/tetracysteine (FlAsH/TC) tag is a small fluorescent tag amenable to insertion at internal sites in proteins. In this study, we used serial FlAsH/TC insertions (TC-scanning) as a probe to characterize sites of protein-protein interaction between PrP and other molecules. To explore this application in the context of substrate-protease interactions, we analyzed the effect of FlAsH/TC insertions on proteolysis of cellular prion protein (PrPsen) in in vitro reactions and generation of the C1 metabolic fragment of PrPsen in live neuroblastoma cells. The influence of FlAsH/TC insertion was evaluated by TC-scanning across the cleavage sites of each protease. The results showed that FlAsH/TC inhibited protease cleavage only within limited ranges of the cleavage sites, which varied from about one to six residues in width, depending on the protease, providing an estimate of the PrP residues interacting with each protease. TC-scanning was also used to probe a different type of protein-protein interaction: the conformational conversion of FlAsH-PrPsen to the prion disease-associated isoform, PrPres. PrP constructs with FlAsH/TC insertions at residues 90-96 but not 97-101 were converted to FlAsH-PrPres, identifying a boundary separating loosely versus compactly folded regions of PrPres. Our observations demonstrate that TC-scanning with the FlAsH/TC tag can be a versatile method for probing protein-protein interactions and folding processes.
Collapse
Affiliation(s)
- Yuzuru Taguchi
- Rocky Mountain Laboratories, NIAID, NIH, Laboratory of Persistent Viral Diseases, 903 S. 4th St., Hamilton, MT 59840 (USA); Currently at the Department of Comparative Biology & Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, T2N 4Z6 (Canada).
| | | | | | | |
Collapse
|
26
|
Fessenden JD, Mahalingam M. Site-specific labeling of the type 1 ryanodine receptor using biarsenical fluorophores targeted to engineered tetracysteine motifs. PLoS One 2013; 8:e64686. [PMID: 23724080 PMCID: PMC3665623 DOI: 10.1371/journal.pone.0064686] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 04/16/2013] [Indexed: 12/02/2022] Open
Abstract
The type 1 ryanodine receptor (RyR1) is an intracellular Ca2+ release channel that mediates skeletal muscle excitation contraction coupling. While the overall shape of RyR1 has been elucidated using cryo electron microscopic reconstructions, fine structural details remain elusive. To better understand the structure of RyR1, we have previously used a cell-based fluorescence resonance energy transfer (FRET) method using a fused green fluorescent protein (GFP) donor and a fluorescent acceptor, Cy3NTA that binds specifically to short poly-histidine ‘tags’ engineered into RyR1. However, the need to permeabilize cells to allow Cy3NTA entry as well as the noncovalent binding of Cy3NTA to the His tag limits future applications of this technique for studying conformational changes of the RyR. To overcome these problems, we used a dodecapeptide sequence containing a tetracysteine (Tc) motif to target the biarsenical fluorophores, FlAsH and ReAsH to RyR1. These compounds freely cross intact cell membranes where they then bind covalently to the tetracysteine motif. First, we used this system to conduct FRET measurements in intact cells by fusing a yellow fluorescent protein (YFP) FRET donor to the N-terminus of RyR1 and then targeting the FRET acceptor, ReAsH to an adjacent Tc tag. Moderate energy transfer (∼33%) was observed whereas ReAsH incubation of a YFPRyR1 fusion protein lacking the Tc tag resulted in no detectable FRET. We also developed a FRET-based system that did not require RyR fluorescent protein fusions by labeling N-terminal Tc-tagged RyR1 with FlAsH, a FRET donor and then targeting the FRET acceptor Cy3NTA to an adjacent decahistidine (His10) tag. A high degree of energy transfer (∼66%) indicated proper binding of both compounds to these unique recognition sequences in RyR1. Thus, these two systems should provide unprecedented flexibility in future FRET-based structural determinations of RyR1.
Collapse
Affiliation(s)
- James D Fessenden
- Department of Anesthesia, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America.
| | | |
Collapse
|
27
|
Chao JA, Yoon YJ, Singer RH. Imaging translation in single cells using fluorescent microscopy. Cold Spring Harb Perspect Biol 2012; 4:cshperspect.a012310. [PMID: 22960595 DOI: 10.1101/cshperspect.a012310] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The regulation of translation provides a mechanism to control not only the abundance of proteins, but also the precise time and subcellular location that they are synthesized. Much of what is known concerning the molecular basis for translational control has been gleaned from experiments (e.g., luciferase assays and polysome analysis) that measure average changes in the protein synthesis of a population of cells, however, mechanistic insights can be obscured in ensemble measurements. The development of fluorescent microscopy techniques and reagents has allowed translation to be studied within its cellular context. Here we highlight recent methodologies that can be used to study global changes in protein synthesis or regulation of specific mRNAs in single cells. Imaging of translation has provided direct evidence for local translation of mRNAs at synapses in neurons and will become an important tool for studying translational control.
Collapse
Affiliation(s)
- Jeffrey A Chao
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | | | | |
Collapse
|
28
|
Scheck RA, Lowder MA, Appelbaum JS, Schepartz A. Bipartite tetracysteine display reveals allosteric control of ligand-specific EGFR activation. ACS Chem Biol 2012; 7:1367-76. [PMID: 22667988 DOI: 10.1021/cb300216f] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Aberrant activation of the epidermal growth factor receptor (EGFR), a prototypic receptor tyrosine kinase, is critical to the biology of many common cancers. The molecular events that define how EGFR transmits an extracellular ligand binding event through the membrane are not understood. Here we use a chemical tool, bipartite tetracysteine display, to report on ligand-specific conformational changes that link ligand binding and kinase activation for full-length EGFR on the mammalian cell surface. We discover that EGF binding is communicated to the cytosol through formation of an antiparallel coiled coil within the intracellular juxtamembrane (JM) domain. This conformational transition is functionally coupled to receptor activation by EGF. In contrast, TGFα binding is communicated to the cytosol through formation of a discrete, alternative helical interface. These findings suggest that the JM region can differentially decode extracellular signals and transmit them to the cell interior. Our results provide new insight into how EGFR communicates ligand-specific information across the membrane.
Collapse
Affiliation(s)
| | | | - Jacob S. Appelbaum
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut
06510, United States
| | | |
Collapse
|
29
|
Detection of SNARE complexes with FRET using the tetracysteine system. Biotechniques 2012; 52:103-8. [DOI: 10.2144/000113811] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Accepted: 12/30/2011] [Indexed: 11/23/2022] Open
Abstract
The three proteins synaptosomal-associated protein 25 (SNAP-25), Syntaxin-1a and vesicle-associated membrane protein (VAMP-2) are collectively called SNAREs (soluble N-ethylmaleimide-sensitive factor attachment protein receptors). By assembling into an exocytic complex, the three SNAREs help in catalyzing membrane fusion. Due to lack of probes that adequately reconstitute the intracellular behavior of endogenous SNAREs, the dynamics of SNARE complexes in living cells is poorly understood. Here we describe a new FRET-based probe, called Cerulean-SNAP-25-C4 (CSNAC), that can track the conformational changes undergone by SNAP-25 as exocytic complexes assemble. The fluorescent protein Cerulean was attached to the N terminus and served as a FRET donor. The biarsenical dye FlAsH served as a FRET acceptor and was attached to a short tetracysteine motif (C4) motif inserted into the so-called linker domain of SNAP-25. CSNAC reported successive FRET changes when first Syntaxin-1a and then VAMP-2 were added in vitro. Small tetracysteine insertions used as a FRET acceptor are expected to have less steric hindrance than previously used GFP-based fluorophores. We propose that genetically-encoded tetracysteine tags can be used to study regulated SNARE complex assembly in vivo.
Collapse
|
30
|
Stafforst T. A FlAsH Reporter for Protein-Dimerization Triggers. Chembiochem 2012; 13:505-7. [DOI: 10.1002/cbic.201100787] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Indexed: 11/10/2022]
|
31
|
Hu Y, Su B, Zheng H, Kim JR. A peptide probe for detection of various beta-amyloid oligomers. MOLECULAR BIOSYSTEMS 2012; 8:2741-52. [DOI: 10.1039/c2mb25148e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
32
|
Scheck RA, Schepartz A. Surveying protein structure and function using bis-arsenical small molecules. Acc Chem Res 2011; 44:654-65. [PMID: 21766813 DOI: 10.1021/ar2001028] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Exploration across the fields of biology, chemical biology, and medicine has led to an increasingly complex, albeit incomplete, view of the interactions that drive life's processes. The ability to monitor and track the movement, activity, and interactions of biomolecules in living cells is an essential part of this investigation. In our laboratory, we have endeavored to develop tools that are capable not only of monitoring protein localization but also reporting on protein structure and function. Central to our efforts is a new strategy, bipartite tetracysteine display, that relies on the specific and high-affinity interaction between a fluorogenic, bis-arsenical small molecule and a unique protein sequence, conformation, or assembly. In 1998, a small-molecule analogue of fluorescein with two arsenic atoms, FlAsH, was shown by Tsien and coworkers to fluoresce upon binding to a linear amino acid sequence, Cys-Cys-Arg-Glu-Cys-Cys. Later work demonstrated that substituting Pro-Gly for Arg-Glu optimized both binding and fluorescence yield. Our strategy of bipartite tetracysteine display emanated from the idea that it would be possible to replace the intervening Pro-Gly dipeptide in this sequence with a protein or protein partnership, provided the assembled protein fold successfully reproduced the approximate placement of the two Cys-Cys pairs. In this Account, we describe our recent progress in this area, with an emphasis on the fundamental concepts that underlie the successful use of bis-arsenicals such as FlAsH and the related ReAsH for bipartite display experiments. In particular, we highlight studies that have explored how broadly bipartite tetracysteine display can be employed and that have navigated the conformational boundary conditions favoring success. To emphasize the utility of these principles, we outline two recently reported applications of bipartite tetracysteine display. The first is a novel, encodable, selective, Src kinase sensor that lacks fluorescent proteins but possesses a fluorescent readout exceeding that of most sensors based on Förster resonance energy transfer (FRET). The second is a unique method, called complex-edited electron microscopy (CE-EM), that facilitates visualization of protein-protein complexes with electron microscopy. Exciting as these applications may be, the continued development of small-molecule tools with improved utility in living cells, let alone in vivo, will demand a more nuanced understanding of the fundamental photophysics that lead to fluorogenicity, as well as creative approaches toward the synthesis and identification of new and orthogonal dye-tag pairs that can be applied facilely in tandem. We describe one example of a dye-sequence tag pair that is chemically distinct from bis-arsenical chemistry. Through further effort, we expect that that bipartite tetracysteine display will find successful use in the study of sophisticated biological questions that are essential to the fields of biochemistry and biology as well as to our progressive understanding of human disease.
Collapse
Affiliation(s)
- Rebecca A. Scheck
- Departments of Chemistry and Molecular, Cellular and Developmental Biology, Yale University, 225 Prospect Street, New Haven, Connecticut 06520-8107, United States
| | - Alanna Schepartz
- Departments of Chemistry and Molecular, Cellular and Developmental Biology, Yale University, 225 Prospect Street, New Haven, Connecticut 06520-8107, United States
| |
Collapse
|
33
|
Crivat G, Taraska JW. Imaging proteins inside cells with fluorescent tags. Trends Biotechnol 2011; 30:8-16. [PMID: 21924508 DOI: 10.1016/j.tibtech.2011.08.002] [Citation(s) in RCA: 189] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 08/04/2011] [Accepted: 08/04/2011] [Indexed: 11/30/2022]
Abstract
Watching biological molecules provides clues to their function and regulation. Some of the most powerful methods of labeling proteins for imaging use genetically encoded fluorescent fusion tags. There are four standard genetic methods of covalently tagging a protein with a fluorescent probe for cellular imaging. These use (i) autofluorescent proteins, (ii) self-labeling enzymes, (iii) enzymes that catalyze the attachment of a probe to a target sequence, and (iv) biarsenical dyes that target tetracysteine motifs. Each of these techniques has advantages and disadvantages. In this review, we cover new developments in these methods and discuss practical considerations for their use in imaging proteins inside living cells.
Collapse
Affiliation(s)
- Georgeta Crivat
- University of Maryland, College Park, Department of Entomology and Program in Cell and Molecular Biology, College Park, MD 20742, USA
| | | |
Collapse
|
34
|
Whitt MA, Mire CE. Utilization of fluorescently-labeled tetracysteine-tagged proteins to study virus entry by live cell microscopy. Methods 2011; 55:127-36. [PMID: 21939769 DOI: 10.1016/j.ymeth.2011.09.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Revised: 09/01/2011] [Accepted: 09/02/2011] [Indexed: 10/24/2022] Open
Abstract
Viruses exploit cellular machinery to gain entry and initiate their replication cycle within host cells. The development of methods to visualize virus entry in live cells has provided new insights to the cellular processes involved in virus entry and the intracellular locations where viral payloads are deposited. The use of fluorescently labeled virus and high-resolution microscopy is currently the method of choice to study virus entry in live cells. While fluorescent protein fusions (e.g. viral proteins fused to GFP) have been used, the labeling of viral proteins that contain a small tetracysteine (tc) tag with biarsenical fluorescent compounds (e.g. FlAsH, ReAsH, Lumio-x) offers several advantages over conventional xFP-fusion constructs. This article describes methods for generating fluorescently labeled viruses encoding tc-tagged proteins that are suitable for the study of virus entry in live cells by fluorescence microscopy. Critical parameters required to quantify fluorescence signals from the labeled, tc-tagged proteins in individual virus particles during the entry process and the subsequent fate of the labeled viral proteins after virus uncoating are also described.
Collapse
Affiliation(s)
- Michael A Whitt
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
| | | |
Collapse
|
35
|
Wang M, Zhang P, Zong W, Xu Q, Liu R. The charge ratio between O and N on amide bonds: a new approach to the mobile proton model. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2011; 79:1915-1919. [PMID: 21689971 DOI: 10.1016/j.saa.2011.05.088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Revised: 05/24/2011] [Accepted: 05/25/2011] [Indexed: 05/30/2023]
Abstract
The influence of charge distribution on the cleavage of the peptides was investigated by fragmentation efficiency curves and quantum chemical calculations in order to clarify the fragmentation mechanism in this paper. The peptide Arg-Gly-Asp-Cys (RGDC) was oxidized to change the charge distribution, but its main sequence was retained. Under this study, it was illustrated that the fragmentation of the peptide RGDC became easier with each addition of an O atom to the Cys hydrosulfide group and the relative charge ratios between O and N (QO/QN) in the amide bonds had much to do with the cleavage of the peptide RGDC. For each amide bond, the situations coincided with overall conclusion: the increase of the QO/QN values results in a higher fragmentation efficiency and vice versa. The methods which combined fragmentation efficiency curves with the charge distribution of peptides provided a way to refine the mobile proton model for peptide fragmentation and to probe the discrepant fragmentation of peptides in peptide/protein identification.
Collapse
Affiliation(s)
- Meijie Wang
- Shandong Key Laboratory of Water Pollution Control and Resource 4 Reuse, School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 27# Shanda South Road, Jinan 250100, PR China
| | | | | | | | | |
Collapse
|
36
|
Newman RH, Fosbrink MD, Zhang J. Genetically encodable fluorescent biosensors for tracking signaling dynamics in living cells. Chem Rev 2011; 111:3614-66. [PMID: 21456512 PMCID: PMC3092831 DOI: 10.1021/cr100002u] [Citation(s) in RCA: 260] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Robert H. Newman
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Matthew D. Fosbrink
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Jin Zhang
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| |
Collapse
|
37
|
Hu Y, Su B, Kim CS, Hernandez M, Rostagno A, Ghiso J, Kim JR. A strategy for designing a peptide probe for detection of β-amyloid oligomers. Chembiochem 2011; 11:2409-18. [PMID: 21031399 DOI: 10.1002/cbic.201000435] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Aggregation of β-amyloid (Aβ) is implicated in the pathology of Alzheimer's disease. Development of a robust strategy to detect Aβ oligomeric intermediates, which have been identified as significant toxic agents, would be highly beneficial in the screening of drug candidates as well as enhancing our understanding of Aβ oligomerization. Rapid, specific and quantitative detection, currently unavailable, would be highly preferred for accurate and reliable probing of transient Aβ oligomers. Here, we report the development of a novel peptide probe, PG46, based on the nature of Aβ self-assembly and the conformation-sensitive fluorescence of the biarsenical dye, FlAsH. PG46 was found to bind to Aβ oligomers and displayed an increase in FlAsH fluorescence upon binding. No such event was observed when PG46 was co-incubated with Aβ low-molecular-weight species or Aβ fibrils. Aβ oligomer detection was fast, and occurred within one hour without any additional sample incubation or preparation. We anticipate that the development of a strategy for detection of amyloid oligomers described in this study will be directly relevant to a host of other amyloidogenic proteins.
Collapse
Affiliation(s)
- Yang Hu
- Othmer-Jacobs Department of Chemical and Biological Engineering, Polytechnic Institute of New York University, 6 MetroTech Center, Brooklyn, NY 11201, USA
| | | | | | | | | | | | | |
Collapse
|
38
|
Pomorski A, Krężel A. Exploration of biarsenical chemistry--challenges in protein research. Chembiochem 2011; 12:1152-67. [PMID: 21538762 DOI: 10.1002/cbic.201100114] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Indexed: 11/07/2022]
Abstract
The fluorescent modification of proteins (with genetically encoded low-molecular-mass fluorophores, affinity probes, or other chemically active species) is extraordinarily useful for monitoring and controlling protein functions in vitro, as well as in cell cultures and tissues. The large sizes of some fluorescent tags, such as fluorescent proteins, often perturb normal activity and localization of the protein of interest, as well as other effects. Of the many fluorescent-labeling strategies applied to in vitro and in vivo studies, one is very promising. This requires a very short (6- to 12-residue), appropriately spaced, tetracysteine sequence (-CCXXCC-); this is either placed at a protein terminus, within flexible loops, or incorporated into secondary structure elements. Proteins that contain the tetracysteine motif become highly fluorescent upon labeling with a nonluminescent biarsenical probe, and form very stable covalent complexes. We focus on the development, growth, and multiple applications of this protein research methodology, both in vitro and in vivo. Its application is not limited to intact-cell protein visualization; it has tremendous potential in other protein research disciplines, such as protein purification and activity control, electron microscopy imaging of cells or tissue, protein-protein interaction studies, protein stability, and aggregation studies.
Collapse
Affiliation(s)
- Adam Pomorski
- Department of Protein Engineering, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | | |
Collapse
|
39
|
Habets RLP, Verstreken P. FlAsH-FALI inactivation of a protein at the third-instar neuromuscular junction. Cold Spring Harb Protoc 2011; 2011:pdb.prot5597. [PMID: 21460046 DOI: 10.1101/pdb.prot5597] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
INTRODUCTIONFluorescein-assisted light inactivation (FALI) is a powerful method for studying acute loss of protein function, even if the corresponding mutations lead to early lethality. In this protocol, FALI is mediated by the membrane-permeable FlAsH (4′,5′-bis(1,3,2-dithioarsolan-2-yl)fluorescein) compound that binds with high specificity to the genetically encoded tetracysteine tag and thus allows the inactivation of protein function in vivo with exquisite spatial (<40 Å) and temporal (<30 sec) resolution. It also enables the analysis of kinetically distinct processes such as synaptic vesicle exocytosis and endocytosis. This protocol describes efficient inactivation of a protein using FlAsH-FALI at the neuromuscular junction (NMJ) of third-instar larvae. Note that FlAsH-FALI in other tissues is also theoretically possible with minor adaptations to the protocol described here. We explain controls for positional effects, for unspecific FlAsH binding to endogenous proteins, and for phototoxicity. Following FlAsH-FALI, protein function can be studied using a number of secondary assays, including electrophysiology, immunohistochemistry, and electron microscopy or FM1-43 labeling of synaptic vesicle pools.
Collapse
|
40
|
Habets RLP, Verstreken P. Construction and expression of tetracysteine-tagged proteins for FlAsH-FALI. Cold Spring Harb Protoc 2011; 2011:pdb.prot5596. [PMID: 21460045 DOI: 10.1101/pdb.prot5596] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
41
|
Ray-Saha S, Schepartz A. Visualizing tyrosine kinase activity with bipartite tetracysteine display. Chembiochem 2011; 11:2089-91. [PMID: 20848632 DOI: 10.1002/cbic.201000234] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sarmistha Ray-Saha
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | | |
Collapse
|
42
|
Spagnuolo C, Joselevich M, Leskow FC, Jares-Erijman EA. Tetracysteine and Bipartite Tags for Biarsenical Organic Fluorophores. ADVANCED FLUORESCENCE REPORTERS IN CHEMISTRY AND BIOLOGY III 2011. [DOI: 10.1007/978-3-642-18035-4_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
43
|
Abstract
In this paper, we provide a general protocol for labeling proteins with the membrane-permeant fluorogenic biarsenical dye fluorescein arsenical hairpin binder-ethanedithiol (FlAsH-EDT₂). Generation of the tetracysteine-tagged protein construct by itself is not described, as this is a protein-specific process. This method allows site-selective labeling of proteins in living cells and has been applied to a wide variety of proteins and biological problems. We provide here a generally applicable labeling procedure and discuss the problems that can occur as well as general considerations that must be taken into account when designing and implementing the procedure. The method can even be applied to proteins with expression below 1 pmol mg⁻¹ of protein, such as G protein-coupled receptors, and it can be used to study the intracellular localization of proteins as well as functional interactions in fluorescence resonance energy transfer experiments. The labeling procedure using FlAsH-EDT₂ as described takes 2-3 h, depending on the number of samples to be processed.
Collapse
|
44
|
Walton ZE, Bishop AC. Target-specific control of lymphoid-specific protein tyrosine phosphatase (Lyp) activity. Bioorg Med Chem 2010; 18:4884-91. [PMID: 20594861 DOI: 10.1016/j.bmc.2010.06.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Revised: 06/01/2010] [Accepted: 06/07/2010] [Indexed: 01/14/2023]
Abstract
Lymphoid-specific protein tyrosine phosphatase (Lyp), a member of the protein tyrosine phosphatase (PTP) superfamily of enzymes, is an important mediator of human-leukocyte signaling. Lyp has also emerged as a potential anti-autoimmune therapeutic target, owing to the association of a Lyp-activating mutation with an array of autoimmune disorders. Toward the goal of generating a selective inhibitor of Lyp activity that could be used for investigating Lyp's roles in cell signaling and autoimmune-disease progression, here we report that Lyp's PTP domain can be readily sensitized to target-specific inhibition by a cell-permeable small molecule. Insertion of a tetracysteine-motif-containing peptide at a conserved position in Lyp's catalytic domain generated a mutant enzyme (Lyp-CCPGCC) that retains activity comparable to that of wild-type Lyp in the absence of added ligand. Upon addition of a tetracysteine-targeting biarsenical compound (FlAsH), however, the activity of the Lyp-CCPGCC drops dramatically, as assayed with either small-molecule or phosphorylated-peptide PTP substrates. We show that FlAsH-induced Lyp-CCPGCC inhibition is potent, specific, rapid, and independent of the nature of the PTP substrate used in the inhibition assay. Moreover, we show that FlAsH can be used to specifically target overexpressed Lyp-CCPGCC in a complex proteomic mixture. Since the mammalian-cell permeability of FlAsH is well established, it is likely that FlAsH-mediated inhibition of Lyp-CCPGCC will be useful for specifically targeting Lyp activity in engineered leukocytes and autoimmune-disease models.
Collapse
Affiliation(s)
- Zandra E Walton
- Amherst College, Department of Chemistry, Amherst, MA 01002, United States
| | | |
Collapse
|
45
|
Van Engelenburg SB, Nahreini T, Palmer AE. FACS-based selection of tandem tetracysteine peptides with improved ReAsH brightness in live cells. Chembiochem 2010; 11:489-93. [PMID: 20099291 DOI: 10.1002/cbic.200900689] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
46
|
Chang WH, Liu Y. Bio-Orthogonal Protein Labeling Methods for Single Molecule FRET. J CHIN CHEM SOC-TAIP 2010. [DOI: 10.1002/jccs.201000073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
47
|
Pomorski A, Otlewski J, Krężel A. The High ZnII Affinity of the Tetracysteine Tag Affects Its Fluorescent Labeling with Biarsenicals. Chembiochem 2010; 11:1214-8. [DOI: 10.1002/cbic.200900768] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
48
|
Ramdzan YM, Nisbet RM, Miller J, Finkbeiner S, Hill AF, Hatters DM. Conformation sensors that distinguish monomeric proteins from oligomers in live cells. CHEMISTRY & BIOLOGY 2010; 17:371-9. [PMID: 20416508 PMCID: PMC3564667 DOI: 10.1016/j.chembiol.2010.03.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2009] [Revised: 03/10/2010] [Accepted: 03/19/2010] [Indexed: 12/19/2022]
Abstract
Proteins prone to misfolding form large macroscopic deposits in many neurodegenerative diseases. Yet the in situ aggregation kinetics remains poorly understood because of an inability to demarcate precursor oligomers from monomers. We developed a strategy for mapping the localization of soluble oligomers and monomers directly in live cells. Sensors for mutant huntingtin, which forms aggregates in Huntington's disease, were made by introducing a tetracysteine motif into huntingtin that becomes occluded from binding biarsenical fluorophores in oligomers, but not monomers. Up to 70% of the diffusely distributed huntingtin molecules appeared as submicroscopic oligomers in individual neuroblastoma cells expressing mutant huntingtin. We anticipate the sensors to enable insight into cellular mechanisms mediated by oligomers and monomers and for the approach to be adaptable more generally in the study of protein self-association.
Collapse
Affiliation(s)
- Yasmin M. Ramdzan
- Department of Biochemistry and Molecular Biology, The University of Melbourne, VIC 3010, Bio21 Molecular Science and Biotechnology Institute and Mental Health Research Institute, Parkville, VIC
| | - Rebecca M. Nisbet
- Department of Biochemistry and Molecular Biology, The University of Melbourne, VIC 3010, Bio21 Molecular Science and Biotechnology Institute and Mental Health Research Institute, Parkville, VIC
| | - Jason Miller
- Gladstone Institute of Neurological Disease, and the Taube-Koret Center for Huntington’s Disease Research, San Francisco CA
- Medical Scientist Training Program and the Chemistry and Chemical Biology Program, University of California, San Francisco, CA
| | - Steven Finkbeiner
- Gladstone Institute of Neurological Disease, and the Taube-Koret Center for Huntington’s Disease Research, San Francisco CA
- Departments of Neurology and Physiology, University of California, San Francisco, CA
| | - Andrew F. Hill
- Department of Biochemistry and Molecular Biology, The University of Melbourne, VIC 3010, Bio21 Molecular Science and Biotechnology Institute and Mental Health Research Institute, Parkville, VIC
| | - Danny M. Hatters
- Department of Biochemistry and Molecular Biology, The University of Melbourne, VIC 3010, Bio21 Molecular Science and Biotechnology Institute and Mental Health Research Institute, Parkville, VIC
| |
Collapse
|
49
|
Sun F, Liu R, Zong W, Tian Y, Wang M, Zhang P. A Unique Approach to the Mobile Proton Model: Influence of Charge Distribution on Peptide Fragmentation. J Phys Chem B 2010; 114:6350-3. [DOI: 10.1021/jp911772q] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Feng Sun
- School of Environmental Science and Engineering, Shandong University, 27 Shanda South Road, Jinan 250100, P. R. China
| | - Rutao Liu
- School of Environmental Science and Engineering, Shandong University, 27 Shanda South Road, Jinan 250100, P. R. China
| | - Wansong Zong
- School of Environmental Science and Engineering, Shandong University, 27 Shanda South Road, Jinan 250100, P. R. China
| | - Yanmin Tian
- School of Environmental Science and Engineering, Shandong University, 27 Shanda South Road, Jinan 250100, P. R. China
| | - Meijie Wang
- School of Environmental Science and Engineering, Shandong University, 27 Shanda South Road, Jinan 250100, P. R. China
| | - Pengjun Zhang
- School of Environmental Science and Engineering, Shandong University, 27 Shanda South Road, Jinan 250100, P. R. China
| |
Collapse
|
50
|
Tsien RY. Nobel lecture: constructing and exploiting the fluorescent protein paintbox. Integr Biol (Camb) 2010; 2:77-93. [DOI: 10.1039/b926500g] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Roger Y. Tsien
- Howard Hughes Medical Institute and Departments of Pharmacology and Chemistry & Biochemistry, University of California, San Diego 9500 Gilman Drive, La Jolla, CA 92093-0647, USA
| |
Collapse
|