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Tan W, Zhang Q, Wang J, Yi M, He H, Xu B. Enzymatic Assemblies of Thiophosphopeptides Instantly Target Golgi Apparatus and Selectively Kill Cancer Cells*. Angew Chem Int Ed Engl 2021; 60:12796-12801. [PMID: 33783926 PMCID: PMC8159897 DOI: 10.1002/anie.202102601] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/19/2021] [Indexed: 01/01/2023]
Abstract
Changing an oxygen atom of the phosphoester bond in phosphopeptides by a sulfur atom enables instantly targeting Golgi apparatus (GA) and selectively killing cancer cells by enzymatic self-assembly. Specifically, conjugating cysteamine S-phosphate to the C-terminal of a self-assembling peptide generates a thiophosphopeptide. Being a substrate of alkaline phosphatase (ALP), the thiophosphopeptide undergoes rapid ALP-catalyzed dephosphorylation to form a thiopeptide that self-assembles. The thiophosphopeptide enters cells via caveolin-mediated endocytosis and macropinocytosis and instantly accumulates in GA because of dephosphorylation and formation of disulfide bonds in Golgi by themselves and with Golgi proteins. Moreover, the thiophosphopeptide potently and selectively inhibits cancer cells (HeLa) with the IC50 (about 3 μM), which is an order of magnitude more potent than that of the parent phosphopeptide.
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Affiliation(s)
- Weiyi Tan
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA, 02453, USA
| | - Qiuxin Zhang
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA, 02453, USA
| | - Jiaqing Wang
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA, 02453, USA
| | - Meihui Yi
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA, 02453, USA
| | - Hongjian He
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA, 02453, USA
| | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA, 02453, USA
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Tan W, Zhang Q, Wang J, Yi M, He H, Xu B. Enzymatic Assemblies of Thiophosphopeptides Instantly Target Golgi Apparatus and Selectively Kill Cancer Cells**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102601] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Weiyi Tan
- Department of Chemistry Brandeis University 415 South Street Waltham MA 02453 USA
| | - Qiuxin Zhang
- Department of Chemistry Brandeis University 415 South Street Waltham MA 02453 USA
| | - Jiaqing Wang
- Department of Chemistry Brandeis University 415 South Street Waltham MA 02453 USA
| | - Meihui Yi
- Department of Chemistry Brandeis University 415 South Street Waltham MA 02453 USA
| | - Hongjian He
- Department of Chemistry Brandeis University 415 South Street Waltham MA 02453 USA
| | - Bing Xu
- Department of Chemistry Brandeis University 415 South Street Waltham MA 02453 USA
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Salehi Marzijarani N, Lam YH, Wang X, Klapars A, Qi J, Song Z, Sherry BD, Liu Z, Ji Y. New Mechanism for Cinchona Alkaloid-Catalysis Allows for an Efficient Thiophosphorylation Reaction. J Am Chem Soc 2020; 142:20021-20029. [PMID: 33180475 DOI: 10.1021/jacs.0c09192] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
An efficient synthesis of nucleoside 5'-monothiophosphates under mild reaction conditions using commercially available thiophosphoryl chloride was achieved with a cinchona alkaloid catalyst. A detailed mechanistic study of the reaction was undertaken, employing a combination of reaction kinetics, NMR spectroscopy, and computational modeling, to better understand the observed reactivity. Taken collectively, the results support an unprecedented mechanism for this class of organocatalyst.
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Affiliation(s)
| | - Yu-Hong Lam
- Department of Computational and Structural Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Xiao Wang
- Department of Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Artis Klapars
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Ji Qi
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States.,Department of Process Research and Development, MSD R&D (China) Co., Ltd., Building 21 Rongda Road, Wangjing R&D Base, Zhongguancun Electronic Zone West Zone, Beijing 100012, China
| | - Zhiyan Song
- Department of Synthetic Chemistry, Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, China
| | - Benjamin D Sherry
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Zhijian Liu
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Yining Ji
- Department of Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
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Chi Y, Carter JH, Swanger J, Mazin AV, Moritz RL, Clurman BE. A novel landscape of nuclear human CDK2 substrates revealed by in situ phosphorylation. SCIENCE ADVANCES 2020; 6:eaaz9899. [PMID: 32494624 PMCID: PMC7164936 DOI: 10.1126/sciadv.aaz9899] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 01/23/2020] [Indexed: 05/03/2023]
Abstract
Cyclin-dependent kinase 2 (CDK2) controls cell division and is central to oncogenic signaling. We used an "in situ" approach to identify CDK2 substrates within nuclei isolated from cells expressing CDK2 engineered to use adenosine 5'-triphosphate analogs. We identified 117 candidate substrates, ~40% of which are known CDK substrates. Previously unknown candidates were validated to be CDK2 substrates, including LSD1, DOT1L, and Rad54. The identification of many chromatin-associated proteins may have been facilitated by labeling conditions that preserved nuclear architecture and physiologic CDK2 regulation by endogenous cyclins. Candidate substrates include proteins that regulate histone modifications, chromatin, transcription, and RNA/DNA metabolism. Many of these proteins also coexist in multi-protein complexes, including epigenetic regulators, that may provide new links between cell division and other cellular processes mediated by CDK2. In situ phosphorylation thus revealed candidate substrates with a high validation rate and should be readily applicable to other nuclear kinases.
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Affiliation(s)
- Yong Chi
- Divisions of Clinical Research and Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N. Seattle, WA 98109, USA
- Institute for Systems Biology, 401 Terry Avenue, N. Seattle, WA 98109, USA
| | - John H. Carter
- Division of Hematology/Medical Oncology, Oregon Health & Science University School of Medicine, 3181 S.W. Sam Jackson Park Rd., Portland, OR 97239-3098, USA
| | - Jherek Swanger
- Divisions of Clinical Research and Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N. Seattle, WA 98109, USA
| | - Alexander V. Mazin
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 N 15th Street, Philadelphia, PA 19102-1192, USA
| | - Robert L. Moritz
- Institute for Systems Biology, 401 Terry Avenue, N. Seattle, WA 98109, USA
| | - Bruce E. Clurman
- Divisions of Clinical Research and Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N. Seattle, WA 98109, USA
- Corresponding author.
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5
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Auto-thiophosphorylation activity of Src tyrosine kinase. BMC BIOCHEMISTRY 2016; 17:13. [PMID: 27387461 PMCID: PMC4936181 DOI: 10.1186/s12858-016-0071-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 06/29/2016] [Indexed: 11/22/2022]
Abstract
Background Intermolecular autophosphorylation at Tyr416 is a conserved mechanism of activation among the members of the Src family of nonreceptor tyrosine kinases. Like several other tyrosine kinases, Src can catalyze the thiophosphorylation of peptide and protein substrates using ATPγS as a thiophosphodonor, although the efficiency of the reaction is low. Results Here, we have characterized the ability of Src to auto-thiophosphorylate. Auto-thiophosphorylation of Src at Tyr416 in the activation loop proceeds efficiently in the presence of Ni2+, resulting in kinase activation. Other tyrosine kinases (Ack1, Hck, and IGF1 receptor) also auto-thiophosphorylate in the presence of Ni2+. Tyr416-thiophosphorylated Src is resistant to dephosphorylation by PTP1B phosphatase. Conclusions Src and other tyrosine kinases catalyze auto-thiophosphorylation in the presence of Ni2+. Thiophosphorylation of Src occurs at Tyr416 in the activation loop, and results in enhanced kinase activity. Tyr416-thiophosphorylated Src could serve as a stable, persistently-activated mimic of Src. Electronic supplementary material The online version of this article (doi:10.1186/s12858-016-0071-z) contains supplementary material, which is available to authorized users.
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Molden RC, Goya J, Khan Z, Garcia BA. Stable isotope labeling of phosphoproteins for large-scale phosphorylation rate determination. Mol Cell Proteomics 2014; 13:1106-18. [PMID: 24532841 DOI: 10.1074/mcp.o113.036145] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Signals that control responses to stimuli and cellular function are transmitted through the dynamic phosphorylation of thousands of proteins by protein kinases. Many techniques have been developed to study phosphorylation dynamics, including several mass spectrometry (MS)-based methods. Over the past few decades, substantial developments have been made in MS techniques for the large-scale identification of proteins and their post-translational modifications. Nevertheless, all of the current MS-based techniques for quantifying protein phosphorylation dynamics rely on the measurement of changes in peptide abundance levels, and many methods suffer from low confidence in phosphopeptide identification due to poor fragmentation. Here we have optimized an approach for the stable isotope labeling of amino acids by phosphate using [γ-¹⁸O₄]ATP in nucleo to determine global site-specific phosphorylation rates. The advantages of this metabolic labeling technique are increased confidence in phosphorylated peptide identification, direct labeling of phosphorylation sites, measurement phosphorylation rates, and the identification of actively phosphorylated sites in a cell-like environment. In this study we calculated approximate rate constants for over 1,000 phosphorylation sites based on labeling progress curves. We measured a wide range of phosphorylation rate constants from 0.34 min⁻¹ to 0.001 min⁻¹. Finally, we applied stable isotope labeling of amino acids by phosphate to identify sites that have different phosphorylation kinetics during G1/S and M phase. We found that most sites had very similar phosphorylation rates under both conditions; however, a small subset of sites on proteins involved in the mitotic spindle were more actively phosphorylated during M phase, whereas proteins involved in DNA replication and transcription were more actively phosphorylated during G1/S phase. The data have been deposited to the ProteomeXchange with the identifier PXD000680.
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Affiliation(s)
- Rosalynn C Molden
- Department of Chemistry, Frick Laboratory, Princeton University, Princeton, New Jersey 08544
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Parker LL, Kron SJ. Kinase activation in circulating cells: opportunities for biomarkers for diagnosis and therapeutic monitoring. ACTA ACUST UNITED AC 2013; 2:33-46. [PMID: 23485115 DOI: 10.1517/17530059.2.1.33] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
A clinically useful tool to assay phosphorylation-dependent signaling in circulating cells has the potential to provide a wealth of information about a patient's health, including information unavailable by any other method. Patterns of kinase activation, such as the abnormal signaling characteristic of myeloproliferative disorders, may offer highly specific biomarkers for diagnosis or monitoring the efficacy of therapeutics. For assays of kinase activity in circulating leukocytes to be standardized, let alone made practical for the clinic, numerous technical hurdles must be overcome. In this review the current status of analysis of kinase signaling in circulating cells and recent progress in biomarker discovery and validation is discussed. Looking forward, the potential value of signaling patterns as complex biomarkers and the resulting need for future development of robust, multiplexed assays of kinase activation is addressed.
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Affiliation(s)
- Laurie L Parker
- University of Chicago, Ludwig Center for Metastasis Research, Knapp R322, 924 E. 57th Street, Chicago, IL 6063, USA
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Senevirathne C, Pflum MKH. Biotinylated phosphoproteins from kinase-catalyzed biotinylation are stable to phosphatases: implications for phosphoproteomics. Chembiochem 2013; 14:381-7. [PMID: 23335220 PMCID: PMC4524292 DOI: 10.1002/cbic.201200626] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Indexed: 11/11/2022]
Abstract
Kinase-catalyzed protein phosphorylation is involved in a wide variety of cellular events. Development of methods to monitor phosphorylation is critical to understand cell biology. Our lab recently discovered kinase-catalyzed biotinylation, where ATP-biotin is utilized by kinases to label phosphopeptides or phosphoproteins with a biotin tag. To exploit kinase-catalyzed biotinylation for phosphoprotein purification and identification in a cellular context, the susceptibility of the biotin tag to phosphatases was characterized. We found that the phosphorylbiotin group on peptide and protein substrates was relatively insensitive to protein phosphatases. To understand how phosphatase stability would impact phosphoproteomics research applications, kinase-catalyzed biotinylation of cell lysates was performed in the presence of kinase or phosphatase inhibitors. We found that biotinylation with ATP-biotin was sensitive to inhibitors, although with variable effects compared to ATP phosphorylation. The results suggest that kinase-catalyzed biotinylation is well suited for phosphoproteomics studies, with particular utility towards monitoring low-abundance phosphoproteins or characterizing the influence of inhibitor drugs on protein phosphorylation.
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Affiliation(s)
| | - Mary Kay H. Pflum
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, Fax: (+)
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Martić S, Kraatz HB. Chemical biology toolkit for exploring protein kinase catalyzed phosphorylation reactions. Chem Sci 2013. [DOI: 10.1039/c2sc20846f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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Zhou G, Khan F, Dai Q, Sylvester JE, Kron SJ. Photocleavable peptide-oligonucleotide conjugates for protein kinase assays by MALDI-TOF MS. MOLECULAR BIOSYSTEMS 2012; 8:2395-404. [PMID: 22772337 DOI: 10.1039/c2mb25163a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Robust methods for highly parallel, quantitative analysis of cellular protein tyrosine kinase activities may provide tools critically needed to decipher oncogenic signaling, discover new targeted drugs, diagnose cancer and monitor patients. Here, we describe proof-of-principle for a novel protein kinase assay with the potential to help overcome these challenges. MALDI-TOF mass spectrometry provides an ideal tool for label-free multiplexed analysis of peptide phosphorylation, but is poorly matched to homogeneous assays and complex samples. Thus, we conjugated a common oligonucleotide tag to multiple peptide substrates, offering efficient capture from solution-phase kinase reactions by annealing to the complementary sequence tethered to PEG-passivated superparamagnetic microparticles. To enable reversible conjugation, we developed a novel bifunctional cross-linker allowing simple and efficient preparation of photocleavable peptide-oligonucleotide conjugates. After washing away contaminants and following photorelease, MALDI-TOF analysis yielded relative phosphorylation of each peptide with high sensitivity and specificity. Validating the hybridization-mediated multiplexed kinase assay, when three peptide substrate-oligonucleotide conjugates were mixed with the tyrosine kinase c-Abl and ATP, we readily observed their differential phosphorylation yet measured a common IC(50) for the Abl kinase inhibitor imatinib. This new assay enables analysis of protein kinase activities in a multiplexed format amenable to screening inhibitors against multiple kinases in parallel, an important capability for drug discovery and predictive diagnostics.
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Affiliation(s)
- Guangchang Zhou
- Department of Molecular Genetics and Cell Biology, Gordon Center for Integrative Sciences, W522A, The University of Chicago, Chicago, IL 60637, USA
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11
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Chi Y, Clurman BE. Mass spectrometry-based identification of protein kinase substrates utilizing engineered kinases and thiophosphate labeling. CURRENT PROTOCOLS IN CHEMICAL BIOLOGY 2010; 2:ch100151. [PMID: 21743840 PMCID: PMC3131159 DOI: 10.1002/9780470559277.ch100151] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Protein kinases constitute a large enzyme family with key roles in cellular signal transduction. One way to elucidate the functions of protein kinases is to systematically identify their downstream targets. We present here a simple and effective method to identify direct protein kinase substrates in native cell lysates. First, we isolate the activity of the kinase of interest by engineering the normal kinase to utilize bulky ATP analogs that cannot be used by normal cellular kinases. This allows specific labeling of substrates with thiophosphate tags by performing kinase reactions in cell lysates that also include bulky ATP-γ-S analogs. After digesting the proteins in the reaction mixture, thiophosphopeptides are isolated using a single-step capture-and-release protocol and identified by mass spectrometry. This technique is easy to use and generally applicable.
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Affiliation(s)
- Yong Chi
- Divisions of Clinical Research and Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
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Chi Y, Welcker M, Hizli AA, Posakony JJ, Aebersold R, Clurman BE. Identification of CDK2 substrates in human cell lysates. Genome Biol 2008; 9:R149. [PMID: 18847512 PMCID: PMC2760876 DOI: 10.1186/gb-2008-9-10-r149] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2008] [Revised: 09/29/2008] [Accepted: 10/13/2008] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Protein phosphorylation regulates a multitude of biological processes. However, the large number of protein kinases and their substrates generates an enormously complex phosphoproteome. The cyclin-dependent kinases--the CDKs--comprise a class of enzymes that regulate cell cycle progression and play important roles in tumorigenesis. However, despite intense study, only a limited number of mammalian CDK substrates are known. A comprehensive understanding of CDK function requires the identification of their substrate network. RESULTS We describe a simple and efficient approach to identify potential cyclin A-CDK2 targets in complex cell lysates. Using a kinase engineering strategy combined with chemical enrichment and mass spectrometry, we identified 180 potential cyclin A-CDK2 substrates and more than 200 phosphorylation sites. About 10% of these candidates function within pathways related to cell division, and the vast majority are involved in other fundamental cellular processes. We have validated several candidates as direct cyclin A-CDK2 substrates that are phosphorylated on the same sites that we identified by mass spectrometry, and we also found that one novel substrate, the ribosomal protein RL12, exhibits site-specific CDK2-dependent phosphorylation in vivo. CONCLUSIONS We used methods entailing engineered kinases and thiophosphate enrichment to identify a large number of candidate CDK2 substrates in cell lysates. These results are consistent with other recent proteomic studies, and suggest that CDKs regulate cell division via large networks of cellular substrates. These methods are general and can be easily adapted to identify direct substrates of many other protein kinases.
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Affiliation(s)
- Yong Chi
- Divisions of Clinical Research and Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N., Seattle, WA 98109, USA
- Institute for Systems Biology, 1441 N. 34th Street, Seattle, WA 98103, USA
| | - Markus Welcker
- Divisions of Clinical Research and Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N., Seattle, WA 98109, USA
| | - Asli A Hizli
- Divisions of Clinical Research and Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N., Seattle, WA 98109, USA
| | - Jeffrey J Posakony
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N., Seattle, WA 98109, USA
| | - Ruedi Aebersold
- Institute for Systems Biology, 1441 N. 34th Street, Seattle, WA 98103, USA
- Institute of Molecular Systems Biology, ETH Zurich and Faculty of Science, University of Zurich, 8093 Zurich, Switzerland
| | - Bruce E Clurman
- Divisions of Clinical Research and Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N., Seattle, WA 98109, USA
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Elphick LM, Lee SE, Gouverneur V, Mann DJ. Using chemical genetics and ATP analogues to dissect protein kinase function. ACS Chem Biol 2007; 2:299-314. [PMID: 17518431 DOI: 10.1021/cb700027u] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein kinases catalyze the transfer of the gamma-phosphate of ATP to a protein substrate and thereby profoundly alter the properties of the phosphorylated protein. The identification of the substrates of protein kinases has proven to be a very difficult task because of the multitude of structurally related protein kinases present in cells, their apparent redundancy of function, and the lack of absolute specificity of small-molecule inhibitors. Here, we review approaches that utilize chemical genetics to determine the functions and substrates of protein kinases, focusing on the design of ATP analogues and protein kinase binding site mutants.
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Affiliation(s)
- Lucy M Elphick
- Imperial College London, Cell Cycle Lab, Division of Cell and Molecular Biology, South Kensington, London SW7 2AZ, United Kingdom
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