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Asiimwe N, Al Mazid MF, Murale DP, Kim YK, Lee J. Recent advances in protein modifications techniques for the targeting
N‐terminal
cysteine. Pept Sci (Hoboken) 2021. [DOI: 10.1002/pep2.24235] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Nicholas Asiimwe
- Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology (KIST) Seoul Korea
- Bio‐Med Program, KIST‐School UST Seoul Korea
| | | | | | - Yun Kyung Kim
- Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology (KIST) Seoul Korea
- Bio‐Med Program, KIST‐School UST Seoul Korea
| | - Jun‐Seok Lee
- Department of Pharmacology Korea University College of Medicine Seoul Korea
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Biswas S, Avan I, Basak AK, Abo-Dya NE, Asiri A, Katritzky AR. Photophysics of novel coumarin-labeled depsipeptides in solution: sensing interactions with SDS micelle via TICT model. Amino Acids 2013; 45:159-70. [PMID: 23553487 DOI: 10.1007/s00726-013-1483-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 02/23/2013] [Indexed: 12/12/2022]
Abstract
N-Acylbenzotriazoles enable the synthesis (69-92% yield) of blue to green fluorescent coumarin-labeled depsidipeptides 8a-f (quantum yields 0.004-0.97) and depsitripeptides 12a-d (quantum yields 0.02-0.96). Detailed photophysical studies of fluorescent coumarin-labeled depsipeptides 8a-f and 12a-d are reported for both polar protic and polar aprotic solvents. 7-Methoxy and 7-diethylaminocoumarin-3-ylcarbonyl depsipeptides 8c,f and 12d are highly solvent sensitive. These highly fluorescent compounds could be useful for peptide assays. Further photophysical studies of 7-diethylaminocoumarin-labeled depsipeptides 8c,12d within the micellar microenvironment of SDS reflect their ability to bind with the biological membrane, suggesting potential applications in the fields of bio- and medicinal chemistry.
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Affiliation(s)
- Suvendu Biswas
- Department of Chemistry, Center for Heterocyclic Compounds, University of Florida, Gainesville, FL 32611-7200, USA
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Uzagare MC, Claußnitzer I, Gerrits M, Bannwarth W. Site specific chemoselective labelling of proteins with robust and highly sensitive Ru(ii) bathophenanthroline complexes. Org Biomol Chem 2012; 10:2223-6. [DOI: 10.1039/c2ob06684j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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5
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Watanabe S, Mizukami S, Akimoto Y, Hori Y, Kikuchi K. Intracellular protein labeling with prodrug-like probes using a mutant β-lactamase tag. Chemistry 2011; 17:8342-9. [PMID: 21656862 DOI: 10.1002/chem.201100973] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Indexed: 01/15/2023]
Abstract
Intracellular protein labeling with small molecular probes that do not require a washing step for the removal of excess probe is greatly desired for real-time investigation of protein dynamics in living cells. Successful labeling of proteins on the cell membrane has been performed using mutant β-lactamase tag (BL-tag) technology. In the present study, intracellular protein labeling with novel cell membrane permeable probes based on β-lactam prodrugs is described. The prodrug-based probes quickly permeated the plasma membranes of living mammalian cells, and efficiently labeled intracellular proteins at low probe concentrations. Because these cell-permeable probes were activated only inside cells, simultaneous discriminative labeling of intracellular and cell surface BL-tag fusion proteins was attained by using cell-permeable and impermeable probes. Thus, this technology enables adequate discrimination of the location of proteins labeled with the same protein tag, in conjunction with different color probes, by dual-color fluorescence. Moreover, the combination of BL-tag technology and the prodrug-based probes enabled the labeling of target proteins without requiring a washing step, owing to the efficient entry of probes into cells and the fast covalent labeling achieved with BL-tag technology after bioactivation. This prodrug-based probe design strategy for BL-tags provides a simple experimental procedure with application to cellular studies with the additional advantage of reduced stress to living cells.
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Affiliation(s)
- Shuji Watanabe
- Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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Sadhu KK, Mizukami S, Hori Y, Kikuchi K. Switching Modulation for Protein Labeling with Activatable Fluorescent Probes. Chembiochem 2011; 12:1299-308. [DOI: 10.1002/cbic.201100137] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Indexed: 12/14/2022]
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7
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Lee J, Lee KH, Jeon J, Dragulescu-Andrasi A, Xiao F, Rao J. Combining SELEX screening and rational design to develop light-up fluorophore-RNA aptamer pairs for RNA tagging. ACS Chem Biol 2010; 5:1065-74. [PMID: 20809562 DOI: 10.1021/cb1001894] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We report here a new small molecule fluorogen and RNA aptamer pair for RNA labeling. The small-molecule fluorogen is designed on the basis of fluorescently quenched sulforhodamine dye. The SELEX (Systematic Evolution of Ligands by EXponential enrichment) procedure and fluorescence screening in E. coli have been applied to discover the aptamer that can specifically activate the fluorogen with micromolar binding affinity. The systematic mutation and truncation study on the aptamer structure determined the minimum binding domain of the aptamer. A series of rationally modified fluorogen analogues have been made to probe the interacting groups of fluorogen with the aptamer. These results led to the design of a much improved fluorogen ASR 7 that displayed a 33-fold increase in the binding affinity for the selected aptamer in comparison to the original ASR 1 and an 88-fold increase in the fluorescence emission after the aptamer binding. This study demonstrates the value of combining in vitro SELEX and E. coli fluorescence screening with rational modifications in discovering and optimizing new fluorogen-RNA aptamer labeling pairs.
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Affiliation(s)
| | - Kyung Hyun Lee
- Molecular Imaging Program at Stanford (MIPS), Department of Radiology
| | - Jongho Jeon
- Molecular Imaging Program at Stanford (MIPS), Department of Radiology
| | | | - Fei Xiao
- Molecular Imaging Program at Stanford (MIPS), Department of Radiology
| | - Jianghong Rao
- Department of Chemistry
- Molecular Imaging Program at Stanford (MIPS), Department of Radiology
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Nguyen UTT, Goody RS, Alexandrov K. Understanding and exploiting protein prenyltransferases. Chembiochem 2010; 11:1194-201. [PMID: 20432425 DOI: 10.1002/cbic.200900727] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Uyen T T Nguyen
- Laboratory of Synthetic Protein Chemistry, The Rockefeller University, New York, NY 10065, USA
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9
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Ren H, Xiao F, Zhan K, Kim YP, Xie H, Xia Z, Rao J. A Biocompatible Condensation Reaction for the Labeling of Terminal Cysteine Residues on Proteins. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200903627] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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10
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Serwa R, Wilkening I, Del Signore G, Mühlberg M, Claußnitzer I, Weise C, Gerrits M, Hackenberger C. Chemoselektive Staudinger-Phosphit-Reaktion von Aziden für die Phosphorylierung von Proteinen. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200902118] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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11
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Serwa R, Wilkening I, Del Signore G, Mühlberg M, Claußnitzer I, Weise C, Gerrits M, Hackenberger C. Chemoselective Staudinger-Phosphite Reaction of Azides for the Phosphorylation of Proteins. Angew Chem Int Ed Engl 2009; 48:8234-9. [DOI: 10.1002/anie.200902118] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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12
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Katritzky AR, Narindoshvili T. Fluorescent amino acids: advances in protein-extrinsic fluorophores. Org Biomol Chem 2009; 7:627-34. [DOI: 10.1039/b818908k] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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13
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Ren H, Xiao F, Zhan K, Kim YP, Xie H, Xia Z, Rao J. A biocompatible condensation reaction for the labeling of terminal cysteine residues on proteins. Angew Chem Int Ed Engl 2009; 48:9658-62. [PMID: 19924746 PMCID: PMC4878437 DOI: 10.1002/anie.200903627] [Citation(s) in RCA: 198] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
This communication describes a novel protein labeling method that uses a single amino-acid tag — N-terminal cysteine residue — and small-molecule probes carrying the cyanobenzothiazole unit for specific labeling of proteins in vitro and at the surface of live cells. This simple ligation reaction proceeds with a high degree of specificity in physiological conditions, and should offer an important alternative to currently available protein labeling methods.
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Affiliation(s)
- Hongjun Ren
- Molecular Imaging Program at Stanford, Departments of Radiology and Chemistry, Stanford University, 1201 Welch Road, Stanford, California 94305-5484 (USA)
| | - Fei Xiao
- Molecular Imaging Program at Stanford, Departments of Radiology and Chemistry, Stanford University, 1201 Welch Road, Stanford, California 94305-5484 (USA)
| | - Ke Zhan
- Molecular Imaging Program at Stanford, Departments of Radiology and Chemistry, Stanford University, 1201 Welch Road, Stanford, California 94305-5484 (USA)
| | - Young-Pil Kim
- Molecular Imaging Program at Stanford, Departments of Radiology and Chemistry, Stanford University, 1201 Welch Road, Stanford, California 94305-5484 (USA)
| | - Hexin Xie
- Molecular Imaging Program at Stanford, Departments of Radiology and Chemistry, Stanford University, 1201 Welch Road, Stanford, California 94305-5484 (USA)
| | - Zuyong Xia
- Molecular Imaging Program at Stanford, Departments of Radiology and Chemistry, Stanford University, 1201 Welch Road, Stanford, California 94305-5484 (USA)
| | - Jianghong Rao
- Molecular Imaging Program at Stanford, Departments of Radiology and Chemistry, Stanford University, 1201 Welch Road, Stanford, California 94305-5484 (USA)
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Hackenberger C, Schwarzer D. Chemoselektive Ligations- und Modifikationsstrategien für Peptide und Proteine. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200801313] [Citation(s) in RCA: 204] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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15
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Hackenberger C, Schwarzer D. Chemoselective Ligation and Modification Strategies for Peptides and Proteins. Angew Chem Int Ed Engl 2008; 47:10030-74. [DOI: 10.1002/anie.200801313] [Citation(s) in RCA: 651] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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16
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So MK, Yao H, Rao J. HaloTag protein-mediated specific labeling of living cells with quantum dots. Biochem Biophys Res Commun 2008; 374:419-23. [PMID: 18621022 DOI: 10.1016/j.bbrc.2008.07.004] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2008] [Accepted: 07/01/2008] [Indexed: 11/24/2022]
Abstract
Quantum dots emerge as an attractive alternative to small molecule fluorophores as fluorescent tags for in vivo cell labeling and imaging. This communication presents a method for specific labeling of live cells using quantum dots. The labeling is mediated by HaloTag protein expressed at the cell surface which forms a stable covalent adduct with its ligand (HaloTag ligand). The labeling can be performed in one single step with quantum dot conjugates that are functionalized with HaloTag ligand, or in two steps with biotinylated HaloTag ligand first and followed by streptavidin coated quantum dots. Live cell fluorescence imaging indicates that the labeling is specific and takes place at the cell surface. This HaloTag protein-mediated cell labeling method should facilitate the application of quantum dots for live cell imaging.
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Affiliation(s)
- Min-kyung So
- Department of Radiology, Stanford University School of Medicine, 1201 Welch Road, P093, Mail code 5484, Stanford, CA 94305, USA
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Selective Chemical Labeling of Proteins with Small Fluorescent Molecules Based on Metal-Chelation Methodology. SENSORS 2008; 8:1004-1024. [PMID: 27879749 PMCID: PMC3927527 DOI: 10.3390/s8021004] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2008] [Accepted: 02/13/2008] [Indexed: 11/16/2022]
Abstract
Site-specific chemical labeling utilizing small fluorescent molecules is a powerful and attractive technique for in vivo and in vitro analysis of cellular proteins, which can circumvent some problems in genetic encoding labeling by large fluorescent proteins. In particular, affinity labeling based on metal-chelation, advantageous due to the high selectivity/simplicity and the small tag-size, is promising, as well as enzymatic covalent labeling, thereby a variety of novel methods have been studied in recent years. This review describes the advances in chemical labeling of proteins, especially highlighting the metal-chelation methodology.
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