1
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Suski JM, Ratnayeke N, Braun M, Zhang T, Strmiska V, Michowski W, Can G, Simoneau A, Snioch K, Cup M, Sullivan CM, Wu X, Nowacka J, Branigan TB, Pack LR, DeCaprio JA, Geng Y, Zou L, Gygi SP, Walter JC, Meyer T, Sicinski P. CDC7-independent G1/S transition revealed by targeted protein degradation. Nature 2022; 605:357-365. [PMID: 35508654 PMCID: PMC9106935 DOI: 10.1038/s41586-022-04698-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 03/29/2022] [Indexed: 12/30/2022]
Abstract
The entry of mammalian cells into the DNA synthesis phase (S phase) represents a key event in cell division1. According to current models of the cell cycle, the kinase CDC7 constitutes an essential and rate-limiting trigger of DNA replication, acting together with the cyclin-dependent kinase CDK2. Here we show that CDC7 is dispensable for cell division of many different cell types, as determined using chemical genetic systems that enable acute shutdown of CDC7 in cultured cells and in live mice. We demonstrate that another cell cycle kinase, CDK1, is also active during G1/S transition both in cycling cells and in cells exiting quiescence. We show that CDC7 and CDK1 perform functionally redundant roles during G1/S transition, and at least one of these kinases must be present to allow S-phase entry. These observations revise our understanding of cell cycle progression by demonstrating that CDK1 physiologically regulates two distinct transitions during cell division cycle, whereas CDC7 has a redundant function in DNA replication.
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Affiliation(s)
- Jan M Suski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Nalin Ratnayeke
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, USA
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Marcin Braun
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Chair of Oncology, Medical University of Lodz, Lodz, Poland
| | - Tian Zhang
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Vladislav Strmiska
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Wojciech Michowski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Geylani Can
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Antoine Simoneau
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Konrad Snioch
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Mikolaj Cup
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Caitlin M Sullivan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Xiaoji Wu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Joanna Nowacka
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Timothy B Branigan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Lindsey R Pack
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, USA
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - James A DeCaprio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Yan Geng
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Johannes C Walter
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Tobias Meyer
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, USA.
| | - Piotr Sicinski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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2
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Phosphoproteomics Meets Chemical Genetics: Approaches for Global Mapping and Deciphering the Phosphoproteome. Int J Mol Sci 2020; 21:ijms21207637. [PMID: 33076458 PMCID: PMC7588962 DOI: 10.3390/ijms21207637] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 12/14/2022] Open
Abstract
Protein kinases are important enzymes involved in the regulation of various cellular processes. To function properly, each protein kinase phosphorylates only a limited number of proteins among the thousands present in the cell. This provides a rapid and dynamic regulatory mechanism that controls biological functions of the proteins. Despite the importance of protein kinases, most of their substrates remain unknown. Recently, the advances in the fields of protein engineering, chemical genetics, and mass spectrometry have boosted studies on identification of bona fide substrates of protein kinases. Among the various methods in protein kinase specific substrate identification, genetically engineered protein kinases and quantitative phosphoproteomics have become promising tools. Herein, we review the current advances in the field of chemical genetics in analog-sensitive protein kinase mutants and highlight selected strategies for identifying protein kinase substrates and studying the dynamic nature of protein phosphorylation.
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3
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Michowski W, Chick JM, Chu C, Kolodziejczyk A, Wang Y, Suski JM, Abraham B, Anders L, Day D, Dunkl LM, Li Cheong Man M, Zhang T, Laphanuwat P, Bacon NA, Liu L, Fassl A, Sharma S, Otto T, Jecrois E, Han R, Sweeney KE, Marro S, Wernig M, Geng Y, Moses A, Li C, Gygi SP, Young RA, Sicinski P. Cdk1 Controls Global Epigenetic Landscape in Embryonic Stem Cells. Mol Cell 2020; 78:459-476.e13. [PMID: 32240602 DOI: 10.1016/j.molcel.2020.03.010] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 01/26/2020] [Accepted: 03/08/2020] [Indexed: 12/13/2022]
Abstract
The cyclin-dependent kinase 1 (Cdk1) drives cell division. To uncover additional functions of Cdk1, we generated knockin mice expressing an analog-sensitive version of Cdk1 in place of wild-type Cdk1. In our study, we focused on embryonic stem cells (ESCs), because this cell type displays particularly high Cdk1 activity. We found that in ESCs, a large fraction of Cdk1 substrates is localized on chromatin. Cdk1 phosphorylates many proteins involved in epigenetic regulation, including writers and erasers of all major histone marks. Consistent with these findings, inhibition of Cdk1 altered histone-modification status of ESCs. High levels of Cdk1 in ESCs phosphorylate and partially inactivate Dot1l, the H3K79 methyltransferase responsible for placing activating marks on gene bodies. Decrease of Cdk1 activity during ESC differentiation de-represses Dot1l, thereby allowing coordinated expression of differentiation genes. These analyses indicate that Cdk1 functions to maintain the epigenetic identity of ESCs.
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Affiliation(s)
- Wojciech Michowski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Joel M Chick
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Chen Chu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Aleksandra Kolodziejczyk
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Yichen Wang
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Jan M Suski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Brian Abraham
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Lars Anders
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Daniel Day
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Lukas M Dunkl
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Mitchell Li Cheong Man
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Tian Zhang
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Phatthamon Laphanuwat
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Nickolas A Bacon
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Lijun Liu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Anne Fassl
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Samanta Sharma
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Tobias Otto
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Emanuelle Jecrois
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Richard Han
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Katharine E Sweeney
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Samuele Marro
- Institute for Stem Cell Biology and Regenerative Medicine and Department of Pathology, Stanford University Medical School, Stanford, CA 94305, USA
| | - Marius Wernig
- Institute for Stem Cell Biology and Regenerative Medicine and Department of Pathology, Stanford University Medical School, Stanford, CA 94305, USA
| | - Yan Geng
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Alan Moses
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3B2, Canada; Center for Analysis of Genome Evolution and Function, Toronto, ON M5S 3B2, Canada
| | - Cheng Li
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Piotr Sicinski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
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4
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Abstract
The cyclin-dependent kinase 5 (CDK5), originally described as a neuronal-specific kinase, is also frequently activated in human cancers. Using conditional CDK5 knockout mice and a mouse model of highly metastatic melanoma, we found that CDK5 is dispensable for the growth of primary tumors. However, we observed that ablation of CDK5 completely abrogated the metastasis, revealing that CDK5 is essential for the metastatic spread. In mouse and human melanoma cells CDK5 promotes cell invasiveness by directly phosphorylating an intermediate filament protein, vimentin, thereby inhibiting assembly of vimentin filaments. Chemical inhibition of CDK5 blocks the metastatic spread of patient-derived melanomas in patient-derived xenograft (PDX) mouse models. Hence, inhibition of CDK5 might represent a very potent therapeutic strategy to impede the metastatic dissemination of malignant cells.
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5
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Arrington JV, Hsu CC, Elder SG, Andy Tao W. Recent advances in phosphoproteomics and application to neurological diseases. Analyst 2018; 142:4373-4387. [PMID: 29094114 DOI: 10.1039/c7an00985b] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Phosphorylation has an incredible impact on the biological behavior of proteins, altering everything from intrinsic activity to cellular localization and complex formation. It is no surprise then that this post-translational modification has been the subject of intense study and that, with the advent of faster, more accurate instrumentation, the number of large-scale mass spectrometry-based phosphoproteomic studies has swelled over the past decade. Recent developments in sample preparation, phosphorylation enrichment, quantification, and data analysis strategies permit both targeted and ultra-deep phosphoproteome profiling, but challenges remain in pinpointing biologically relevant phosphorylation events. We describe here technological advances that have facilitated phosphoproteomic analysis of cells, tissues, and biofluids and note applications to neuropathologies in which the phosphorylation machinery may be dysregulated, much as it is in cancer.
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6
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An iterative compound screening contest method for identifying target protein inhibitors using the tyrosine-protein kinase Yes. Sci Rep 2017; 7:12038. [PMID: 28931921 PMCID: PMC5607274 DOI: 10.1038/s41598-017-10275-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 08/07/2017] [Indexed: 01/03/2023] Open
Abstract
We propose a new iterative screening contest method to identify target protein inhibitors. After conducting a compound screening contest in 2014, we report results acquired from a contest held in 2015 in this study. Our aims were to identify target enzyme inhibitors and to benchmark a variety of computer-aided drug discovery methods under identical experimental conditions. In both contests, we employed the tyrosine-protein kinase Yes as an example target protein. Participating groups virtually screened possible inhibitors from a library containing 2.4 million compounds. Compounds were ranked based on functional scores obtained using their respective methods, and the top 181 compounds from each group were selected. Our results from the 2015 contest show an improved hit rate when compared to results from the 2014 contest. In addition, we have successfully identified a statistically-warranted method for identifying target inhibitors. Quantitative analysis of the most successful method gave additional insights into important characteristics of the method used.
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7
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Fajer M, Meng Y, Roux B. The Activation of c-Src Tyrosine Kinase: Conformational Transition Pathway and Free Energy Landscape. J Phys Chem B 2017; 121:3352-3363. [PMID: 27715044 PMCID: PMC5398919 DOI: 10.1021/acs.jpcb.6b08409] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Tyrosine kinases are important cellular signaling allosteric enzymes that regulate cell growth, proliferation, metabolism, differentiation, and migration. Their activity must be tightly controlled, and malfunction can lead to a variety of diseases, particularly cancer. The nonreceptor tyrosine kinase c-Src, a prototypical model system and a representative member of the Src-family, functions as complex multidomain allosteric molecular switches comprising SH2 and SH3 domains modulating the activity of the catalytic domain. The broad picture of self-inhibition of c-Src via the SH2 and SH3 regulatory domains is well characterized from a structural point of view, but a detailed molecular mechanism understanding is nonetheless still lacking. Here, we use advanced computational methods based on all-atom molecular dynamics simulations with explicit solvent to advance our understanding of kinase activation. To elucidate the mechanism of regulation and self-inhibition, we have computed the pathway and the free energy landscapes for the "inactive-to-active" conformational transition of c-Src for different configurations of the SH2 and SH3 domains. Using the isolated c-Src catalytic domain as a baseline for comparison, it is observed that the SH2 and SH3 domains, depending upon their bound orientation, promote either the inactive or active state of the catalytic domain. The regulatory structural information from the SH2-SH3 tandem is allosterically transmitted via the N-terminal linker of the catalytic domain. Analysis of the conformational transition pathways also illustrates the importance of the conserved tryptophan 260 in activating c-Src, and reveals a series of concerted events during the activation process.
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Affiliation(s)
| | | | - Benoît Roux
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, 60637, USA
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8
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Sugiyama N, Ishihama Y. Large-scale profiling of protein kinases for cellular signaling studies by mass spectrometry and other techniques. J Pharm Biomed Anal 2016; 130:264-272. [DOI: 10.1016/j.jpba.2016.05.046] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/26/2016] [Accepted: 05/27/2016] [Indexed: 01/26/2023]
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9
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Kumar V, Weng YC, Geldenhuys WJ, Wang D, Han X, Messing RO, Chou WH. Generation and characterization of ATP analog-specific protein kinase Cδ. J Biol Chem 2014; 290:1936-51. [PMID: 25505183 DOI: 10.1074/jbc.m114.598698] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To better study the role of PKCδ in normal function and disease, we developed an ATP analog-specific (AS) PKCδ that is sensitive to specific kinase inhibitors and can be used to identify PKCδ substrates. AS PKCδ showed nearly 200 times higher affinity (Km) and 150 times higher efficiency (kcat/Km) than wild type (WT) PKCδ toward N(6)-(benzyl)-ATP. AS PKCδ was uniquely inhibited by 1-(tert-butyl)-3-(1-naphthyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine (1NA-PP1) and 1-(tert-butyl)-3-(2-methylbenzyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine (2MB-PP1) but not by other 4-amino-5-(4-methylphenyl)-7-(t-butyl)pyrazolo[3,4-d]pyrimidine (PP1) analogs tested, whereas WT PKCδ was insensitive to all PP1 analogs. To understand the mechanisms for specificity and affinity of these analogs, we created in silico WT and AS PKCδ homology models based on the crystal structure of PKCι. N(6)-(Benzyl)-ATP and ATP showed similar positioning within the purine binding pocket of AS PKCδ, whereas N(6)-(benzyl)-ATP was displaced from the pocket of WT PKCδ and was unable to interact with the glycine-rich loop that is required for phosphoryl transfer. The adenine rings of 1NA-PP1 and 2MB-PP1 matched the adenine ring of ATP when docked in AS PKCδ, and this interaction prevented the potential interaction of ATP with Lys-378, Glu-428, Leu-430, and Phe-633 residues. 1NA-PP1 failed to effectively dock within WT PKCδ. Other PP1 analogs failed to interact with either AS PKCδ or WT PKCδ. These results provide a structural basis for the ability of AS PKCδ to efficiently and specifically utilize N(6)-(benzyl)-ATP as a phosphate donor and for its selective inhibition by 1NA-PP1 and 2MB-PP1. Such homology modeling could prove useful in designing molecules to target PKCδ and other kinases to understand their function in cell signaling and to identify unique substrates.
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Affiliation(s)
- Varun Kumar
- From the Department of Biological Sciences, School of Biomedical Sciences, Kent State University, Kent, Ohio 44242
| | - Yi-Chinn Weng
- From the Department of Biological Sciences, School of Biomedical Sciences, Kent State University, Kent, Ohio 44242
| | - Werner J Geldenhuys
- the Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, Ohio 44272
| | - Dan Wang
- the Ernest Gallo Clinic and Research Center, Department of Neurology, University of California, San Francisco, Emeryville, California 94608, and
| | - Xiqian Han
- From the Department of Biological Sciences, School of Biomedical Sciences, Kent State University, Kent, Ohio 44242
| | - Robert O Messing
- the Ernest Gallo Clinic and Research Center, Department of Neurology, University of California, San Francisco, Emeryville, California 94608, and the Division of Pharmacology and Toxicology, College of Pharmacy, University of Texas, Austin, Texas 78712
| | - Wen-Hai Chou
- From the Department of Biological Sciences, School of Biomedical Sciences, Kent State University, Kent, Ohio 44242, the Ernest Gallo Clinic and Research Center, Department of Neurology, University of California, San Francisco, Emeryville, California 94608, and
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10
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Abstract
Kinases catalyse the phosphorylation of target substrates on hydroxy group-containing residues as a means to nucleate multi-component complexes or to stabilize unique conformational states. Through this biochemical activity, kinases play critical roles in many signal transduction and disease pathways. Pseudokinases constitute a subclass of these enzymes that were originally predicted as inactive on the basis of mutations of key conserved active-site residues. However, recent biochemical and structural analyses have revealed several enzymatically active pseudokinases, suggesting either that novel mechanisms of phosphorylation are at play or that the constraints for highly conserved active-site residues are looser than originally anticipated. The purpose of the present review is to summarize several of the active pseudokinases, and one in particular termed KSR (kinase suppressor of Ras), which was recently found to possess a kinase activity that can become accelerated through an allosteric mechanism. Utilization of catalytic activity or structural features of the kinase fold may be key to the function of many pseudokinases.
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11
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Corden JL. RNA polymerase II C-terminal domain: Tethering transcription to transcript and template. Chem Rev 2013; 113:8423-55. [PMID: 24040939 PMCID: PMC3988834 DOI: 10.1021/cr400158h] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jeffry L Corden
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine , 725 North Wolfe Street, Baltimore Maryland 21205, United States
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12
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Zhang C, Lopez MS, Dar AC, LaDow E, Finkbeiner S, Yun CH, Eck MJ, Shokat KM. Structure-guided inhibitor design expands the scope of analog-sensitive kinase technology. ACS Chem Biol 2013; 8:1931-8. [PMID: 23841803 DOI: 10.1021/cb400376p] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Engineered analog-sensitive (AS) protein kinases have emerged as powerful tools for dissecting phospho-signaling pathways, for elucidating the cellular function of individual kinases, and for deciphering unanticipated effects of clinical therapeutics. A crucial and necessary feature of this technology is a bioorthogonal small molecule that is innocuous toward native cellular systems but potently inhibits the engineered kinase. In order to generalize this method, we sought a molecule capable of targeting divergent AS-kinases. Here we employ X-ray crystallography and medicinal chemistry to unravel the mechanism of current inhibitors and use these insights to design the most potent, selective, and general AS-kinase inhibitors reported to date. We use large-scale kinase inhibitor profiling to characterize the selectivity of these molecules as well as examine the consequences of potential off-target effects in chemical genetic experiments. The molecules reported here will serve as powerful tools in efforts to extend AS-kinase technology to the entire kinome and the principles discovered may help in the design of other engineered enzyme/ligand pairs.
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Affiliation(s)
- Chao Zhang
- Howard Hughes Medical Institute and Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, California 94158, United States
| | - Michael S. Lopez
- Howard Hughes Medical Institute and Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, California 94158, United States
- Chemistry
and Chemical Biology
Graduate Program, University of California, San Francisco, 600 16th Street, MC2280, San Francisco, California 94158, United
States
| | - Arvin C. Dar
- Howard Hughes Medical Institute and Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, California 94158, United States
| | - Eva LaDow
- Gladstone Institute of Neurological Disease, San Francisco, California 94158,
United States
| | - Steven Finkbeiner
- Gladstone Institute of Neurological Disease, San Francisco, California 94158,
United States
| | - Cai-Hong Yun
- Department
of Biological Chemistry
and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Michael J. Eck
- Department
of Biological Chemistry
and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Kevan M. Shokat
- Howard Hughes Medical Institute and Department of Cellular & Molecular Pharmacology, University of California, San Francisco, San Francisco, California 94158, United States
- Department of Chemistry, University of California, Berkeley, Berkeley, California
94720, United States
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13
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Fleißner A. Turning the switch: using chemical genetics to elucidate protein kinase functions in filamentous fungi. FUNGAL BIOL REV 2013. [DOI: 10.1016/j.fbr.2013.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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14
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Lourido S, Jeschke GR, Turk BE, Sibley LD. Exploiting the unique ATP-binding pocket of toxoplasma calcium-dependent protein kinase 1 to identify its substrates. ACS Chem Biol 2013; 8:1155-62. [PMID: 23530747 PMCID: PMC3691715 DOI: 10.1021/cb400115y] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
![]()
Apicomplexan parasites rely on calcium
as a second messenger to
regulate a variety of essential cellular processes. Calcium-dependent
protein kinases (CDPK), which transduce these signals, are conserved
among apicomplexans but absent from mammalian hosts, making them attractive
targets for therapeutic intervention. Despite their importance, the
signaling pathways CDPK regulate remain poorly characterized, and
their protein substrates are completely unknown. In Toxoplasma
gondii, CDPK1 is required for calcium-regulated secretion
from micronemes, thereby controlling motility, invasion, and egress
from host cells. CDPK1 is unique among parasite and mammalian kinases
in containing glycine at the key “gatekeeper” residue,
which results in an expanded ATP-binding pocket. In the present study,
we use a synthetic ATPγS analogue that displays steric complementarity
to the ATP-binding pocket and hence allows identification of protein
substrates based on selective thiophosphorylation. The specificity
of this approach was validated by the concordance between the identified
phosphorylation sites and the in vitro substrate
preference of CDPK1. We further demonstrate that the phosphorylation
of predicted substrates is dependent on CDPK1 both in vivo and in vitro. This combined strategy for identifying
the targets of specific protein kinases provides a platform for defining
the roles of CDPKs in apicomplexans.
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Affiliation(s)
- Sebastian Lourido
- Department of Molecular Microbiology, Washington University School of Medicine, 660 S. Euclid
Ave., St. Louis, Missouri 63110, United States
| | - Grace R. Jeschke
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar St.,
New Haven, Connecticut 06520, United States
| | - Benjamin E. Turk
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar St.,
New Haven, Connecticut 06520, United States
| | - L. David Sibley
- Department of Molecular Microbiology, Washington University School of Medicine, 660 S. Euclid
Ave., St. Louis, Missouri 63110, United States
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15
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Chen X, Zhao X, Abeyweera TP, Rotenberg SA. Analysis of substrates of protein kinase C isoforms in human breast cells by the traceable kinase method. Biochemistry 2012; 51:7087-97. [PMID: 22897107 DOI: 10.1021/bi300999c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A previous report [Abeyweera, T. P., and Rotenberg, S. A. (2007) Biochemistry 46, 2364-2370] described the application of the traceable kinase method in identifying substrates of protein kinase Cα (PKC-α) in nontransformed human breast MCF-10A cells. Here, a nonradioactive variation of this method compared the phosphoprotein profiles of three traceable PKC isoforms (α, δ, and ζ) for the purpose of identifying novel, isoform-selective substrates. Each FLAG-tagged traceable kinase was expressed and co-immunoprecipitated along with high-affinity substrates. The isolated kinase and its associated substrates were subjected to an in vitro phosphorylation reaction with traceable kinase-specific N(6)-phenyl-ATP, and the resulting phosphoproteins were analyzed by Western blotting with an antibody that recognizes the phosphorylated PKC consensus site. Phosphoprotein profiles generated by PKC-α and -δ were similar and differed markedly from that of PKC-ζ. Mass spectrometry of selected bands revealed known PKC substrates and several potential substrates that included the small GTPase-associated Cdc42 effector protein-4 (CEP4). Of those potential substrates tested, only CEP4 was phosphorylated by pure PKC-α, -δ, and -ζ isoforms in vitro, and by endogenous PKC isoforms in MCF-10A cells treated with DAG-lactone, a membrane permeable PKC activator. Under these conditions, the stoichiometry of CEP4 phosphorylation was 3.2 ± 0.5 (moles of phospho-CEP4 per mole of CEP4). Following knockdown with isoform-specific shRNA-encoding plasmids, the level of phosphorylation of CEP4 was substantially decreased in response to silencing of each of the three isoforms (PKC-α, -δ, and -ζ), whereas testing of kinase-dead mutants supported a role for only PKC-α and -δ in CEP4 phosphorylation. These findings identify CEP4 as a novel intracellular PKC substrate that is phosphorylated by multiple PKC isoforms.
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Affiliation(s)
- Xiangyu Chen
- Department of Chemistry and Biochemistry, Queens College, The City University of New York, 65-30 Kissena Boulevard, Flushing, NY 11367, USA
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16
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SH3 domains: modules of protein-protein interactions. Biophys Rev 2012; 5:29-39. [PMID: 28510178 DOI: 10.1007/s12551-012-0081-z] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 05/29/2012] [Indexed: 01/01/2023] Open
Abstract
Src homology 3 (SH3) domains are involved in the regulation of important cellular pathways, such as cell proliferation, migration and cytoskeletal modifications. Recognition of polyproline and a number of noncanonical sequences by SH3 domains has been extensively studied by crystallography, nuclear magnetic resonance and other methods. High-affinity peptides that bind SH3 domains are used in drug development as candidates for anticancer treatment. This review summarizes the latest achievements in deciphering structural determinants of SH3 function.
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17
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Abstract
Identification of protein kinase targets and specific inhibition of individual kinase isoforms on the protein level in planta are important techniques to elucidate signal transduction pathways. The use of ATP-binding pocket mutants, the so-called gatekeeper mutants, that accommodate N(6)-enlarged nucleotides and kinase inhibitors has allowed a dramatic increase in kinase isoform selectivity. In this chapter, we describe protocols for the identification and mutation of the gatekeeper residue, radiolabeling of N(6)-modified nucleotides, analysis of protein targets by using [(32)P]-labeled N(6)-modified nucleotides, and in vivo inhibition of kinase activity combined with subsequent molecular readouts. The chapter includes alternative approaches for the described techniques, considerations for other kinases and recommendations toward a setup of a substrate labeling experiment using total cell lysate.
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Affiliation(s)
- Maik Böhmer
- Institute for Biology and Biotechnology of Plants, University of Münster, Münster, Germany.
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18
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A kinase cascade leading to Rab11-FIP5 controls transcytosis of the polymeric immunoglobulin receptor. Nat Cell Biol 2010; 12:1143-53. [PMID: 21037565 DOI: 10.1038/ncb2118] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2010] [Accepted: 10/06/2010] [Indexed: 01/26/2023]
Abstract
Polymeric immunoglobulin A (pIgA) transcytosis, mediated by the polymeric immunoglobulin receptor (pIgR), is a central component of mucosal immunity and a model for regulation of polarized epithelial membrane traffic. Binding of pIgA to pIgR stimulates transcytosis in a process requiring Yes, a Src family tyrosine kinase (SFK). We show that Yes directly phosphorylates EGF receptor (EGFR) on liver endosomes. Injection of pIgA into rats induced EGFR phosphorylation. Similarly, in MDCK cells, pIgA treatment significantly increased phosphorylation of EGFR on various sites, subsequently activating extracellular signal-regulated protein kinase (ERK). Furthermore, we find that the Rab11 effector Rab11-FIP5 is a substrate of ERK. Knocking down Yes or Rab11-FIP5, or inhibition of the Yes-EGFR-ERK cascade, decreased pIgA-pIgR transcytosis. Finally, we demonstrate that Rab11-FIP5 phosphorylation by ERK controls Rab11a endosome distribution and pIgA-pIgR transcytosis. Our results reveal a novel Yes-EGFR-ERK-FIP5 signalling network for regulation of pIgA-pIgR transcytosis.
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19
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Haan C, Behrmann I, Haan S. Perspectives for the use of structural information and chemical genetics to develop inhibitors of Janus kinases. J Cell Mol Med 2010; 14:504-27. [PMID: 20132407 PMCID: PMC3823453 DOI: 10.1111/j.1582-4934.2010.01018.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Gain-of-function mutations in the genes encoding Janus kinases have been discovered in various haematologic diseases. Jaks are composed of a FERM domain, an SH2 domain, a pseudokinase domain and a kinase domain, and a complex interplay of the Jak domains is involved in regulation of catalytic activity and association to cytokine receptors. Most activating mutations are found in the pseudokinase domain. Here we present recently discovered mutations in the context of our structural models of the respective domains. We describe two structural hotspots in the pseudokinase domain of Jak2 that seem to be associated either to myeloproliferation or to lymphoblastic leukaemia, pointing at the involvement of distinct signalling complexes in these disease settings. The different domains of Jaks are discussed as potential drug targets. We present currently available inhibitors targeting Jaks and indicate structural differences in the kinase domains of the different Jaks that may be exploited in the development of specific inhibitors. Moreover, we discuss recent chemical genetic approaches which can be applied to Jaks to better understand the role of these kinases in their biological settings and as drug targets.
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Affiliation(s)
- Claude Haan
- Life Sciences Research Unit, University of Luxembourg, 162A, av. de la Faïencerie, 1511 Luxembourg, Luxembourg.
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20
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Koch A, Hauf S. Strategies for the identification of kinase substrates using analog-sensitive kinases. Eur J Cell Biol 2010; 89:184-93. [PMID: 20061049 DOI: 10.1016/j.ejcb.2009.11.024] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Phosphorylation of proteins is a prevalent post-translational modification, which affects intracellular signaling in many ways. About 2% of all eukaryotic genes code for protein kinases catalyzing phosphorylation events. Despite technological advances that have made it possible to identify thousands of phosphorylation sites simultaneously, identification of the substrates of a given kinase remains an exceptionally challenging task. Here, we summarize approaches for substrate identification that make use of genetically engineered 'analog-sensitive' kinases.
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Affiliation(s)
- André Koch
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstrasse 39, 72076 Tübingen, Germany
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21
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Elphick LM, Lee SE, Child ES, Prasad A, Pignocchi C, Thibaudeau S, Anderson AA, Bonnac L, Gouverneur V, Mann DJ. A quantitative comparison of wild-type and gatekeeper mutant cdk2 for chemical genetic studies with ATP analogues. Chembiochem 2009; 10:1519-26. [PMID: 19437469 DOI: 10.1002/cbic.200900052] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Chemical genetic studies with enlarged ATP binding sites and unnatural ATP analogues have been applied to protein kinases for characterisation and substrate identification. Although this system is becoming widely used, there are limited data available about the kinetic profile of the modified system. Here we describe a detailed comparison of the wild-type cdk2 and the mutant gatekeeper kinase to assess the relative efficiencies of these kinases with ATP and unnatural ATP analogues. Our data demonstrate that mutation of the kinase alters neither the substrate specificity nor the phosphorylation site specificity. We find comparable K(M)/V(max) values for mutant cdk2 and wild-type kinase. Furthermore, F80G cdk2 is efficiently able to compensate for a defective cdk in a biological setting.
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Affiliation(s)
- Lucy M Elphick
- Division of Cell and Molecular Biology, Imperial College, London SW72AZ, UK
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22
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Abeyweera TP, Chen X, Rotenberg SA. Phosphorylation of alpha6-tubulin by protein kinase Calpha activates motility of human breast cells. J Biol Chem 2009; 284:17648-56. [PMID: 19406749 PMCID: PMC2719404 DOI: 10.1074/jbc.m902005200] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2009] [Indexed: 11/06/2022] Open
Abstract
Engineered overexpression of protein kinase Calpha (PKCalpha) was previously shown to endow nonmotile MCF-10A human breast cells with aggressive motility. A traceable mutant of PKCalpha (Abeyweera, T. P., and Rotenberg, S. A. (2007) Biochemistry 46, 2364-2370) revealed that alpha6-tubulin is phosphorylated in cells expressing traceable PKCalpha and in vitro by wild type PKCalpha. Gain-of-function, single site mutations (Ser-->Asp) were constructed at each PKC consensus site in alpha6-tubulin (Ser158, Ser165, Ser241, and Thr337) to simulate phosphorylation. Following expression of each construct in MCF-10A cells, motility assays identified Ser165 as the only site in alpha6-tubulin whose pseudophosphorylation reproduced the motile behavior engendered by PKCalpha. Expression of a phosphorylation-resistant mutant (S165N-alpha6-tubulin) resulted in suppression of MCF-10A cell motility stimulated either by expression of PKCalpha or by treatment with PKCalpha-selective activator diacylglycerol-lactone. MCF-10A cells treated with diacylglycerol-lactone showed strong phosphorylation of endogenous alpha-tubulin that could be blocked when S165N-alpha6-tubulin was expressed. The S165N mutant also inhibited intrinsically motile human breast tumor cells that express high endogenous PKCalpha levels (MDA-MB-231 cells) or lack PKCalpha and other conventional isoforms (MDA-MB-468 cells). Comparison of Myc-tagged wild type alpha6-tubulin and S165N-alpha6-tubulin expressed in MDA-MB-468 cells demonstrated that Ser165 is also a major site of phosphorylation for endogenously active, nonconventional PKC isoforms. PKC-stimulated motility of MCF-10A cells was nocodazole-sensitive, thereby implicating microtubule elongation in the mechanism. These findings support a model in which PKC phosphorylates alpha-tubulin at Ser165, leading to microtubule elongation and motility.
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Affiliation(s)
- Thushara P. Abeyweera
- From the Department of Chemistry and Biochemistry of Queens College and
- the Graduate Center of the City University of New York, Flushing, New York 11367
| | - Xiangyu Chen
- From the Department of Chemistry and Biochemistry of Queens College and
- the Graduate Center of the City University of New York, Flushing, New York 11367
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23
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Ghose AK, Herbertz T, Pippin DA, Salvino JM, Mallamo JP. Knowledge based prediction of ligand binding modes and rational inhibitor design for kinase drug discovery. J Med Chem 2008; 51:5149-71. [PMID: 18710211 DOI: 10.1021/jm800475y] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Arup K Ghose
- Department of Medicinal Chemistry, Cephalon, Inc., 145 Brandywine Parkway, West Chester, Pennsylvania 19380, USA.
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24
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Mori Y, Hirokawa T, Aoki K, Satomi H, Takeda S, Aburada M, Miyamoto KI. Structure activity relationships of quinoxalin-2-one derivatives as platelet-derived growth factor-beta receptor (PDGFbeta R) inhibitors, derived from molecular modeling. Chem Pharm Bull (Tokyo) 2008; 56:682-7. [PMID: 18451558 DOI: 10.1248/cpb.56.682] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We previously reported a quinoxalin-2-one compound (Compound 1) that had inhibitory activity equivalent to existing platelet-derived growth factor-beta receptor (PDGFbeta R) inhibitors. Lead optimization of Compound 1 to increase its activity and selectivity, using structural information regarding PDGFbeta R-ligand interactions, is urgently needed. Here we present models of the PDGFbeta R kinase domain complexed with quinoxalin-2-one derivatives. The models were constructed using comparative modeling, molecular dynamics (MD) and ligand docking. In particular, conformations derived from MD, and ligand binding site information presented by alpha-spheres in the pre-docking processing, allowed us to identify optimal protein structures for docking of target ligands. By carrying out molecular modeling and MD of PDGFbeta R in its inactive state, we obtained two structural models having good Compound 1 binding potentials. In order to distinguish the optimal candidate, we evaluated the structural activity relationships (SAR) between the ligand-binding free energies and inhibitory activity values (IC50 values) for available quinoxalin-2-one derivatives. Consequently, a final model with a high SAR was identified. This model included a molecular interaction between the hydrophobic pocket behind the ATP binding site and the substitution region of the quinoxalin-2-one derivatives. These findings should prove useful in lead optimization of quinoxalin-2-one derivatives as PDGFb R inhibitors.
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25
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Blethrow J, Zhang C, Shokat KM, Weiss EL. Design and use of analog-sensitive protein kinases. ACTA ACUST UNITED AC 2008; Chapter 18:Unit 18.11. [PMID: 18265343 DOI: 10.1002/0471142727.mb1811s66] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Many protein kinases can be engineered to accept analogs of ATP that are not efficiently used by wild-type kinases. These engineered kinases, which are referred to as "analog-sensitive" or "-as" alleles, are also often sensitive to protein kinase inhibitor variants that do not block the activity of nonmutant kinases. Selective in vitro use of radiolabeled ATP analogs by -as kinases can be exploited to identify the direct phosphorylation targets of individual kinases in complex extracts. In organisms in which it is practical to replace wild-type kinase genes with engineered alleles, the in vivo activity of a -as kinase can be reversibly blocked with an allele-specific inhibitor. Thus, analog-sensitive kinases can be effective tools for discovery of the cellular functions and phosphorylation targets of individual enzymes. A theoretical background for the design and use of these alleles is discussed, as are strategies for construction of candidate -as alleles of any kinase.
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Affiliation(s)
- Justin Blethrow
- University of California at San Francisco, San Francisco, California, USA
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26
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Turk BE. Understanding and exploiting substrate recognition by protein kinases. Curr Opin Chem Biol 2008; 12:4-10. [PMID: 18282484 DOI: 10.1016/j.cbpa.2008.01.018] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2007] [Accepted: 01/15/2008] [Indexed: 10/22/2022]
Abstract
Protein kinases play a virtually universal role in cellular regulation and are emerging as an important class of new drug targets, yet the cellular functions of most human kinases largely remain obscure. Aspects of substrate recognition common to all kinases in the ATP nucleotide binding site have been exploited in the generation of analog-specific mutants for exploring kinase function and discovering novel protein substrates. Likewise, understanding interactions with the protein substrate, which differ substantially between kinases, can also help to identify substrates and to produce tools for studying kinase pathways, including fluorescent biosensors. Principles of kinase substrate recognition are particularly valuable in guiding bioinformatics and phosphoproteomics approaches that impact our understanding of signaling pathways and networks on a global scale.
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Affiliation(s)
- Benjamin E Turk
- Department of Pharmacology, Yale University School of Medicine, P.O. Box 208066, 333 Cedar Street, New Haven, CT 06520, United States.
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27
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Affiliation(s)
- Daniel P Walsh
- Department of Chemistry, New York University, New York, New York 10003, USA
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28
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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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29
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Allen JJ, Li M, Brinkworth CS, Paulson JL, Wang D, Hübner A, Chou WH, Davis RJ, Burlingame AL, Messing RO, Katayama CD, Hedrick SM, Shokat KM. A semisynthetic epitope for kinase substrates. Nat Methods 2007; 4:511-6. [PMID: 17486086 PMCID: PMC2932705 DOI: 10.1038/nmeth1048] [Citation(s) in RCA: 251] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2007] [Accepted: 03/30/2007] [Indexed: 12/31/2022]
Abstract
The ubiquitous nature of protein phosphorylation makes it challenging to map kinase-substrate relationships, which is a necessary step toward defining signaling network architecture. To trace the activity of individual kinases, we developed a semisynthetic reaction scheme, which results in the affinity tagging of substrates of the kinase in question. First, a kinase, engineered to use a bio-orthogonal ATPgammaS analog, catalyzes thiophosphorylation of its direct substrates. Second, alkylation of thiophosphorylated serine, threonine or tyrosine residues creates an epitope for thiophosphate ester-specific antibodies. We demonstrated the generality of semisynthetic epitope construction with 13 diverse kinases: JNK1, p38alpha MAPK, Erk1, Erk2, Akt1, PKCdelta, PKCepsilon, Cdk1/cyclinB, CK1, Cdc5, GSK3beta, Src and Abl. Application of this approach, in cells isolated from a mouse that expressed endogenous levels of an analog-specific (AS) kinase (Erk2), allowed purification of a direct Erk2 substrate.
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Affiliation(s)
- Jasmina J Allen
- Graduate Program in Chemistry and Chemical Biology, University of California, San Francisco, San Francisco, California 94143, USA
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30
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Blair JA, Rauh D, Kung C, Yun CH, Fan QW, Rode H, Zhang C, Eck MJ, Weiss WA, Shokat KM. Structure-guided development of affinity probes for tyrosine kinases using chemical genetics. Nat Chem Biol 2007; 3:229-38. [PMID: 17334377 DOI: 10.1038/nchembio866] [Citation(s) in RCA: 166] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2006] [Accepted: 02/05/2007] [Indexed: 12/20/2022]
Abstract
As key components in nearly every signal transduction pathway, protein kinases are attractive targets for the regulation of cellular signaling by small-molecule inhibitors. We report the structure-guided development of 6-acrylamido-4-anilinoquinazoline irreversible kinase inhibitors that potently and selectively target rationally designed kinases bearing two selectivity elements that are not found together in any wild-type kinase: an electrophile-targeted cysteine residue and a glycine gatekeeper residue. Cocrystal structures of two irreversible quinazoline inhibitors bound to either epidermal growth factor receptor (EGFR) or engineered c-Src show covalent inhibitor binding to the targeted cysteine (Cys797 in EGFR and Cys345 in engineered c-Src). To accommodate the new covalent bond, the quinazoline core adopts positions that are different from those seen in kinase structures with reversible quinazoline inhibitors. Based on these structures, we developed a fluorescent 6-acrylamido-4-anilinoquinazoline affinity probe to report the fraction of kinase necessary for cellular signaling, and we used these reagents to quantitate the relationship between EGFR stimulation by EGF and its downstream outputs-Akt, Erk1 and Erk2.
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Affiliation(s)
- Jimmy A Blair
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, USA
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31
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Kim S, Shah K. Dissecting yeast Hog1 MAP kinase pathway using a chemical genetic approach. FEBS Lett 2007; 581:1209-16. [PMID: 17346711 DOI: 10.1016/j.febslet.2007.02.032] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2007] [Revised: 02/09/2007] [Accepted: 02/16/2007] [Indexed: 12/20/2022]
Abstract
Using a chemical genetic approach, we identified four novel physiological substrates of Hog1 kinase (Krs1, Tdh3, Hsp26, and Shm2). These substrates suggest plausible mechanisms for actin reorganization, cell cycle arrest and regulation of protein synthesis observed upon osmotic stress. We further show that the human homolog of Shm2 (SHMT1) is a novel physiological substrate of p38 MAP kinase in vitro and in vivo. Down-regulation of its enzymatic activity was observed following p38-mediated phosphorylation revealing a potential cancer-modulating property of p38 MAP kinase. This screen has uncovered several novel Hog1 substrates that provide new avenues for investigation into the mechanism of osmoadaptation by this kinase.
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Affiliation(s)
- Sungjoon Kim
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, USA
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32
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Abeyweera TP, Rotenberg SA. Design and characterization of a traceable protein kinase Calpha. Biochemistry 2007; 46:2364-70. [PMID: 17279776 DOI: 10.1021/bi0622017] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein kinase Calpha (PKCalpha) is a critical component of pathways that govern cancer-related phenotypes such as invasion and proliferation. Proteins that serve as immediate substrates for PKCalpha offer potential targets for anticancer drug design. To identify specific substrates, a mutant of PKCalpha (M417A) was constructed at the ATP binding site such that it could bind a sterically large ATP analogue derivatized through the N6 amino group of adenosine ([gamma-32P]-N6-phenyl-ATP). Because this analogue could be utilized by the mutant kinase but not by wild-type PKCalpha (or presumably other protein kinase) to phosphorylate peptide or protein substrates, 32P-labeled products were the direct result of the mutant PKCalpha. Kinetic analysis with [gamma-32P]-N6-phenyl-ATP revealed that the mutant retained undiminished affinity for the peptide substrate (Km = 12.4 microM) and a Vmax value (10.3 pmol/min) that was only 3-fold lower than that exhibited by the wild-type enzyme with natural ATP. However, with [gamma-32P]ATP, the mutant had a somewhat lower affinity (Km = 82.8 microM) than the wild-type enzyme (Km = 9.3 microM) in vitro but was competent in causing aggressive motility in nonmotile MCF-10A human breast cells (with endogenous ATP), as previously described for wild-type PKCalpha. The FLAG-tagged PKCalpha mutant was expressed in MCF-10A cells and used to co-immunoprecipitate high-affinity substrates from lysates. Immunopellets were reacted with [gamma-32P]-N6-phenyl-ATP, and radiolabeled products were analyzed by SDS-PAGE and autoradiography. Mass spectrometry of selected bands identified several known substrates of PKC, thereby validating the methods used in these studies. These findings provide a foundation for future applications of this traceable PKCalpha mutant.
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Affiliation(s)
- Thushara P Abeyweera
- Department of Chemistry and Biochemistry of Queens College, The City University of New York, Flushing, New York 11367-1597, USA
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33
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Shah K, Vincent F. Divergent roles of c-Src in controlling platelet-derived growth factor-dependent signaling in fibroblasts. Mol Biol Cell 2005; 16:5418-32. [PMID: 16135530 PMCID: PMC1266437 DOI: 10.1091/mbc.e05-03-0263] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The vast complexity of platelet-derived growth factor (PDGF)-induced downstream signaling pathways is well known, but the precise roles of critical players still elude us due to our lack of specific and temporal control over their activities. Accordingly, although Src family members are some of the better characterized effectors of PDGFbeta signaling, considerable controversy still surrounds their precise functions. To address these questions and limitations, we applied a chemical-genetic approach to study the role of c-Src at the cellular level, in defined signaling cascades; we also uncovered novel phosphorylation targets and defined its influence on transcriptional events. The spectacular control of c-Src on actin reorganization and chemotaxis was delineated by global substrate labeling and transcriptional analysis, revealing multiple cytoskeletal proteins and chemotaxis promoting genes to be under c-Src control. Additionally, this tool revealed the contrasting roles of c-Src in controlling DNA synthesis, where it transmits conflicting inputs via the phosphatidylinositol 3 kinase and Ras pathways. Finally, this study reveals a mechanism by which Src family kinases may control PDGF-mediated responses both at transcriptional and translational levels.
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Affiliation(s)
- Kavita Shah
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA.
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34
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Abstract
The ubiquitous ATP binding site offers a global target for protein kinase inhibitors. The corollary is that molecular selectivity with such agents may be difficult to achieve and ascertain. A relevant example is discussed in terms of design and biomedical rationale.
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Affiliation(s)
- Peter M Fischer
- Cyclacel Limited, James Lindsay Place, Dundee, DD1 5JJ, Scotland
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35
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Whitney JA. Reference Systems for Kinase Drug Discovery: Chemical Genetic Approaches to Cell-Based Assays. Assay Drug Dev Technol 2004; 2:417-29. [PMID: 15357923 DOI: 10.1089/adt.2004.2.417] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Protein kinases play key roles in a number of diseases, including cancer, inflammation, and diabetes. Disregulation of kinase-based signal transduction networks results in aberrant cell differentiation, activation, proliferation, and invasion. The growing importance of kinases as a major class of drug targets across multiple large clinical indications, together with the large number of kinases in the genome (~518), has generated a critical need for technologies that enable the identification of potent and selective kinase inhibitors with good drug-like properties. In this review, we describe methods used for developing cell-based assays for kinase inhibitors, discuss advantages and disadvantages of each approach, and describe new chemical genetic methods as reference systems for establishing cell-based assays and their use for functional selectivity profiling of kinase inhibitors.
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Affiliation(s)
- J Andrew Whitney
- Department of Research Informatics, Cellular Genomics, Inc., Branford, CT, USA.
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36
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Vojtechová M, Tuhácková Z, Hlavácek J, Velek J, Sovová V. The v-Src and c-Src tyrosine kinases immunoprecipitated from Rous sarcoma virus-transformed cells display different peptide substrate specificities. Arch Biochem Biophys 2004; 421:277-82. [PMID: 14984208 DOI: 10.1016/j.abb.2003.11.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
In the cells transformed by Rous sarcoma virus (RSV), two Src proteins are expressed: the ubiquitous tyrosine kinase c-Src and the v-Src, the product of the transforming gene of the virus. Using three synthetic peptide substrates widely used for testing Src kinase activity, we show that they are phosphorylated with different efficiencies by the v-Src and c-Src tyrosine kinases immunoprecipitated from the tumor cell line H19. The v-Src displays higher efficiency (Vmax/Km ratio) toward all three peptides used, but the Vmax of v-Src is much lower than Vmax of c-Src with two peptides out of three. This difference in substrate specificity, if ignored, may cause misestimation of the amounts of active c-Src and v-Src in RSV-transformed cells. On the other hand, the different peptide substrate specificities may also reflect different protein substrate specificities of the v-Src and c-Src kinases in vivo.
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Affiliation(s)
- Martina Vojtechová
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, 16637 Prague 6, Czech Republic.
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37
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Hindley AD, Park S, Wang L, Shah K, Wang Y, Hu X, Shokat KM, Kolch W, Sedivy JM, Yeung KC. Engineering the serine/threonine protein kinase Raf-1 to utilise an orthogonal analogue of ATP substituted at the N6 position. FEBS Lett 2004; 556:26-34. [PMID: 14706820 DOI: 10.1016/s0014-5793(03)01352-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
One key area of protein kinase research is the identification of cognate substrates. The search for substrates is hampered by problems in unambiguously assigning substrates to a particular kinase in vitro and in vivo. One solution to this impasse is to engineer the kinase of interest to accept an ATP analogue which is orthogonal (unable to fit into the ATP binding site) for the wild-type enzyme and the majority of other kinases. The acceptance of structurally modified, gamma-(32)P-labelled, nucleotide analogue by active site-modified kinase can provide a unique handle by which the direct substrates of any particular kinase can be displayed in crude mixtures or cell lysates. We have taken this approach with the serine/threonine kinase Raf-1, which plays an essential role in the transduction of stimuli through the Ras-->Raf-->MEK-->ERK/MAP kinase cascade. This cascade plays essential roles in proliferation, differentiation and apoptosis. Here we detail the mutagenesis strategy for the ATP binding pocket of Raf-1, such that it can utilise an N(6)-substituted ATP analogue. We show that these mutations do not alter the substrate specificity and signal transduction through Raf-1. We screen a library of analogues to identify which are orthogonal for Raf-1, and show that mutant Raf-1 can utilise the orthogonal analogue N(6)(2-phenethyl) ATP in vitro to phosphorylate its currently only accepted substrate MEK. Importantly we show that our approach can be used to tag putative direct substrates of Raf-1 kinase with (32)P-N(6)(2-phenethyl) ATP in cell lysates.
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38
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Liu Y, Kung C, Fishburn J, Ansari AZ, Shokat KM, Hahn S. Two cyclin-dependent kinases promote RNA polymerase II transcription and formation of the scaffold complex. Mol Cell Biol 2004; 24:1721-35. [PMID: 14749387 PMCID: PMC344185 DOI: 10.1128/mcb.24.4.1721-1735.2004] [Citation(s) in RCA: 150] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2003] [Revised: 10/13/2003] [Accepted: 11/11/2003] [Indexed: 11/20/2022] Open
Abstract
Three cyclin-dependent kinases, CDK7, -8, and -9, are specifically involved in transcription by RNA polymerase II (Pol II) and target the Pol II C-terminal domain (CTD). The role of CDK7 and CDK8 kinase activity in transcription has been unclear, with CDK7 shown to have variable effects on transcription and CDK8 suggested to repress transcription and/or to target other gene-specific factors. Using a chemical genetics approach, the Saccharomyces cerevisiae homologs of these kinases, Kin28 and Srb10, were engineered to respond to a specific inhibitor and the inhibitor was used to test the role of these kinases in transcription in vivo and in vitro. In vitro, these kinases can both promote transcription, with up to 70% of transcription abolished when both kinases are inhibited together. Similarly, in vivo inhibition of both kinases together gives the strongest decrease in transcription, as measured by chromatin immunoprecipitation of Pol II. Kin28 and Srb10 also have overlapping roles in promoting ATP-dependent dissociation of the preinitiation complex (PIC) into the Scaffold complex. Using the engineered kinases and an ATP analog, specific kinase substrates within the PIC were identified. In addition to the previously known substrate, the Pol II CTD, it was found that Kin28 phosphorylates two subunits of Mediator and Srb10 targets two subunits of TFIID for phosphorylation.
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Affiliation(s)
- Ying Liu
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center and Howard Hughes Medical Institute, Seattle, Washington 98109, USA
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39
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Ubersax JA, Woodbury EL, Quang PN, Paraz M, Blethrow JD, Shah K, Shokat KM, Morgan DO. Targets of the cyclin-dependent kinase Cdk1. Nature 2003; 425:859-64. [PMID: 14574415 DOI: 10.1038/nature02062] [Citation(s) in RCA: 701] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2003] [Accepted: 09/19/2003] [Indexed: 01/17/2023]
Abstract
The events of cell reproduction are governed by oscillations in the activities of cyclin-dependent kinases (Cdks). Cdks control the cell cycle by catalysing the transfer of phosphate from ATP to specific protein substrates. Despite their importance in cell-cycle control, few Cdk substrates have been identified. Here, we screened a budding yeast proteomic library for proteins that are directly phosphorylated by Cdk1 in whole-cell extracts. We identified about 200 Cdk1 substrates, several of which are phosphorylated in vivo in a Cdk1-dependent manner. The identities of these substrates reveal that Cdk1 employs a global regulatory strategy involving phosphorylation of other regulatory molecules as well as phosphorylation of the molecular machines that drive cell-cycle events. Detailed analysis of these substrates is likely to yield important insights into cell-cycle regulation.
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Affiliation(s)
- Jeffrey A Ubersax
- Department of Physiology, University of California, San Francisco, California 94143, USA
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40
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Wan L, de los Santos T, Zhang C, Shokat K, Hollingsworth NM. Mek1 kinase activity functions downstream of RED1 in the regulation of meiotic double strand break repair in budding yeast. Mol Biol Cell 2003; 15:11-23. [PMID: 14595109 PMCID: PMC307523 DOI: 10.1091/mbc.e03-07-0499] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Three meiosis-specific chromosomal components in budding yeast, Mek1, Red1, and Hop1, are required for recombination, proper segregation of homologs, and the meiotic recombination checkpoint. Mek1 is a protein kinase. Mutations that increase the size of the ATP binding pocket of Mek1 (mek1-as1) sensitize the kinase to specific small molecule inhibitors. Experiments using mek1-as1 demonstrate that the requirement for Mek1 kinase activity coincides with the formation of double strand breaks (DSBs) and that this activity is necessary after DSB formation to prevent repair by DMC1-independent pathways. Contrary to previous reports, Red1 is not a substrate for Mek1. Instead, RED1 is required for wild-type levels of Mek1 kinase activity. In addition, activation of Mek1 requires HOP1, the formation of Red1/Hop1 complexes and a functional Mek1 FHA domain. The requirement for RED1 to produce active kinase can be bypassed by a mek1 mutation that creates a constitutively active Mek1 kinase. We propose that Red1 is phosphorylated by a kinase other than MEK1 and that phosphothreonines on Red1 then interact with the Mek1 FHA domain to recruit the kinase to sites of DSBs where Mek1 is activated to prevent DMC1-independent DSB repair.
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Affiliation(s)
- Lihong Wan
- Institute for Cell and Developmental Biology, Department of Biochemistry and Cell Biology, SUNY Stony Brook, Stony Brook, New York 11794-5215, USA
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41
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Denzel A, Hare KJ, Zhang C, Shokat K, Jenkinson EJ, Anderson G, Hayday A. Cutting edge: a chemical genetic system for the analysis of kinases regulating T cell development. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2003; 171:519-23. [PMID: 12847211 DOI: 10.4049/jimmunol.171.2.519] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
To understand the regulatory activities of kinases in vivo requires their study across a biologically relevant window of activity. To this end, ATP analog-sensitive kinase alleles (ASKAs) specifically sensitive to a competitive inhibitor have been developed. This article tests whether ASKA technology can be applied to complex immunological systems, such as lymphoid development. The results show that when applied to reaggregate thymic organ culture, novel p56(Lck) ASKAs readily expose a dose-dependent correlation of thymocyte development with a range of p56(Lck) activity. By regulating kinase activity, rather than amounts of RNA or protein, ASKA technology offers a general means for assessing the quantitative contributions to immunology of numerous kinases emerging from genomics analyses. It can obviate the generation of multiple lines of mice expressing different levels of kinase transgenes and should permit specific biological effects to be associated with defined biochemical activities.
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Affiliation(s)
- Angela Denzel
- Department of Immunobiology, New Guy's House, Guy's, King's and St. Thomas's School of Medicine, London, United Kingdom
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42
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Ulrich SM, Kenski DM, Shokat KM. Engineering a "methionine clamp" into Src family kinases enhances specificity toward unnatural ATP analogues. Biochemistry 2003; 42:7915-21. [PMID: 12834343 DOI: 10.1021/bi030042a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A single alanine or glycine mutation in the ATP binding site of a protein kinase allows unique use of an unnatural analogue of ATP (N(6)-(benzyl) ATP) as a phosphodonor, which is not accepted by wild-type kinases. Addition of [gamma(32)P] N(6)-(benzyl) ATP to a cell lysate containing an ATP analog-specific kinase allele (as1 allele) results in the exclusive radiolabeling of bona fide substrates of the mutant kinase. Here we report efforts to engineer kinase alleles that have enhanced selectivity for ATP analogues and decreased catalytic activity with ATP, thus increasing the signal-to-noise ratio of substrate labeling. Two conserved leucine residues that contact each face of the adenine ring of ATP were mutated to methionine. The introduction of this "methionine clamp" resulted in Src and Fyn kinase alleles that have markedly improved specificity for unnatural N(6)-substituted ATP analogues over the natural substrate, ATP. This preference for unnatural nucleotides is reflected in more efficient labeling of protein substrates in cell extracts using the new analogue-specific v-Src allele. Kinase alleles with enhanced selectivity for unnatural ATP analogues should greatly facilitate the ultimate goal of labeling kinase substrates in intact cells, where concentrations of ATP and other competing nucleotides are high.
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Affiliation(s)
- Scott M Ulrich
- , Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94107-2280, USA
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43
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Ulrich SM, Sallee NA, Shokat KM. Conformational restraint is a critical determinant of unnatural nucleotide recognition by protein kinases. Bioorg Med Chem Lett 2002; 12:3223-7. [PMID: 12372539 DOI: 10.1016/s0960-894x(02)00616-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
This report describes the synthesis of N(4)-(benzyl) AICAR triphosphate, a conformationally restrained analogue of N(4)-(benzyl) ribavirin triphosphate. Both of these nucleotides were evaluated as phosphodonors for wild-type p38MAP kinase and T106G p38MAP kinase, a designed mutant with expanded nucleotide specificity. The conformationally restrained nucleotide, N(4)-(benzyl) AICAR triphosphate, is orthogonal to (not accepted as a substrate by) wild-type p38MAP kinase, in contrast to N(4)-(benzyl) ribavirin triphosphate. Furthermore, N(4)-(benzyl) AICAR triphosphate, is accepted as a substrate by T106G p38MAP kinase, in contrast to N(4)-(benzyl) ribavirin triphosphate. We hypothesize that the presence of an internal hydrogen bond in N(4)-(benzyl) AICAR and its absence in N(4)-(benzyl) ribavirin triphosphate is the main determinant for their differing structure-activity relationships.
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Affiliation(s)
- Scott M Ulrich
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143-0450, USA.
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44
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Kraybill BC, Elkin LL, Blethrow JD, Morgan DO, Shokat KM. Inhibitor scaffolds as new allele specific kinase substrates. J Am Chem Soc 2002; 124:12118-28. [PMID: 12371851 DOI: 10.1021/ja0264798] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The elucidation of protein kinase signaling networks is challenging due to the large size of the protein kinase superfamily (>500 human kinases). Here we describe a new class of orthogonal triphosphate substrate analogues for the direct labeling of analogue-specific kinase protein targets. These analogues were constructed as derivatives of the Src family kinase inhibitor PP1 and were designed based on the crystal structures of PP1 bound to HCK and N(6)-(benzyl)-ADP bound to c-Src (T338G). 3-Benzylpyrazolopyrimidine triphosphate (3-benzyl-PPTP) proved to be a substrate for a mutant of the MAP kinase p38 (p38-T106G/A157L/L167A). 3-Benzyl-PPTP was preferred by v-Src (T338G) (k(cat)/K(M) = 3.2 x 10(6) min(-)(1) M(-)(1)) over ATP or the previously described ATP analogue, N(6) (benzyl) ATP. For the kinase CDK2 (F80G)/cyclin E, 3-benzyl-PPTP demonstrated catalytic efficiency (k(cat)/K(M) = 2.6 x 10(4) min(-)(1) M(-)(1)) comparable to ATP (k(cat)/K(M) = 5.0 x 10(4) min(-)(1) M(-)(1)) largely due to a significantly better K(M) (6.4 microM vs 530 microM). In kinase protein substrate labeling experiments both 3-benzyl-PPTP and 3-phenyl-PPTP prove to be over 4 times more orthogonal than N(6)-(benzyl)-ATP with respect to the wild-type kinases found in murine spleenocyte cell lysates. These experiments also demonstrate that [gamma-(32)P]-3-benzyl-PPTP is an excellent phosphodonor for labeling the direct protein substrates of CDK2 (F80G)/E in murine spleenocyte cell lysates, even while competing with cellular levels (4 mM) of unlabeled ATP. The fact that this new more highly orthogonal nucleotide is accepted by three widely divergent kinases studied here suggests that it is likely to be generalizable across the entire kinase superfamily.
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Affiliation(s)
- Brian C Kraybill
- Department of Cellular and Molecular Pharmacology, Box 0450, University of California- San Francisco, San Francisco, California 94143, USA
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45
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Shokat K, Velleca M. Novel chemical genetic approaches to the discovery of signal transduction inhibitors. Drug Discov Today 2002; 7:872-9. [PMID: 12546954 DOI: 10.1016/s1359-6446(02)02391-7] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Concurrent advances in both high-throughput chemistry and genomics have given rise to the field of chemical genetics as a discipline for elucidating and validating drug targets, and generating novel therapeutics. Indeed, chemical genetic approaches to drug discovery have now been applied to several important drug target classes, especially those involved in signal transduction. Chemical genetics is distinct from the broader term "chemogenomics" which is defined as the description of all possible drugs against all possible targets (reviewed in [1]). This review covers several "orthogonal" chemical genetic approaches and focuses on a unique analog sensitive kinase technology and its applications to kinase drug discovery.
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Affiliation(s)
- Kevan Shokat
- Dept of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, CA, USA
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