1
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Rhee KY, Jansen RS, Grundner C. Activity-based annotation: the emergence of systems biochemistry. Trends Biochem Sci 2022; 47:785-794. [PMID: 35430135 PMCID: PMC9378515 DOI: 10.1016/j.tibs.2022.03.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/10/2022] [Accepted: 03/22/2022] [Indexed: 01/21/2023]
Abstract
Current tools to annotate protein function have failed to keep pace with the speed of DNA sequencing and exponentially growing number of proteins of unknown function (PUFs). A major contributing factor to this mismatch is the historical lack of high-throughput methods to experimentally determine biochemical activity. Activity-based methods, such as activity-based metabolite and protein profiling, are emerging as new approaches for unbiased, global, biochemical annotation of protein function. In this review, we highlight recent experimental, activity-based approaches that offer new opportunities to determine protein function in a biologically agnostic and systems-level manner.
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Affiliation(s)
- Kyu Y Rhee
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
| | - Robert S Jansen
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands.
| | - Christoph Grundner
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA; Department of Global Health, University of Washington, Seattle, WA, USA; Department of Pediatrics, University of Washington, Seattle, WA, USA.
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2
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Miao W, Yin J, Porter DF, Jiang X, Khavari PA, Wang Y. Targeted Proteomic Approaches for Proteome-Wide Characterizations of the AMP-Binding Capacities of Kinases. J Proteome Res 2022; 21:2063-2070. [PMID: 35820187 PMCID: PMC9357193 DOI: 10.1021/acs.jproteome.2c00225] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Kinases play important roles in cell signaling, and adenosine monophosphate (AMP) is known to modulate cellular energy homeostasis through AMP-activated protein kinase (AMPK). Here, we explored novel AMP-binding kinases by employing a desthiobiotin-conjugated AMP acyl-phosphate probe to enrich efficiently AMP-binding proteins. Together with a parallel-reaction monitoring-based targeted proteomic approach, we uncovered 195 candidate AMP-binding kinases. We also enriched desthiobiotin-labeled peptides from adenine nucleotide-binding sites of kinases and analyzed them using LC-MS/MS in the multiple-reaction monitoring mode, which resulted in the identification of 44 peptides derived from 43 kinases displaying comparable or better binding affinities toward AMP relative to adenosine triphosphate (ATP). Moreover, our proteomic data revealed a potential involvement of AMP in the MAPK pathway through binding directly to the relevant kinases, especially MEK2 and MEK3. Together, we revealed the AMP-binding capacities of a large number of kinases, and our work built a strong foundation for understanding how AMP functions as a second messenger to modulate cell signaling.
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Affiliation(s)
- Weili Miao
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, United States
| | | | - Douglas F Porter
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, United States
| | | | - Paul A Khavari
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, United States
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3
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Cai R, Bade D, Liu X, Huang M, Qi TF, Wang Y. Targeted Quantitative Profiling of GTP-Binding Proteins Associated with Metastasis of Melanoma Cells. J Proteome Res 2021; 20:5189-5195. [PMID: 34694799 DOI: 10.1021/acs.jproteome.1c00708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Metastasis is a major obstacle in the therapeutic intervention of melanoma, and several GTP-binding proteins were found to play important roles in regulating cancer metastasis. To assess systematically the regulatory roles of these proteins in melanoma metastasis, we employed a targeted chemoproteomic method, which relies on the application of stable isotope-labeled desthiobiotin-GTP acyl phosphate probes in conjunction with scheduled multiple-reaction monitoring (MRM), for profiling quantitatively the GTP-binding proteins. Following probe labeling, tryptic digestion, and affinity pull-down of desthiobiotin-conjugated peptides, differences in expression levels of GTP-binding proteins in two matched pairs of primary/metastatic melanoma cell lines were measured using liquid chromatography-MRM analysis. We also showed that among the top upregulated proteins in metastatic melanoma cells, AK4 promotes the migration and invasion of melanoma cells; overexpression of AK4 in primary melanoma cells leads to augmented migration and invasion, and reciprocally, knockdown of AK4 in metastatic melanoma cells results in repressed invasiveness. In summary, we examined the relative expression levels of GTP-binding proteins in two pairs of primary/metastatic melanoma cell lines. Our results confirmed some previously reported regulators of melanoma metastasis and revealed a potential role of AK4 in promoting melanoma metastasis.
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Affiliation(s)
- Rong Cai
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, United States.,Suzhou Research Institute, Shandong University, Suzhou, Jiangsu 215123, China
| | - David Bade
- Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, California 92521, United States
| | - Xiaochuan Liu
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, United States
| | - Ming Huang
- Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, California 92521, United States
| | - Tianyu F Qi
- Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, California 92521, United States
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, United States.,Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, California 92521, United States
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4
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Liu Y, Qu M, Pan M, Zheng X, Sheng Y, Ji Y, You C, Dai X. Chemical proteomic profiling of UTP-binding proteins in human cells. Anal Chim Acta 2021; 1168:338607. [PMID: 34052001 DOI: 10.1016/j.aca.2021.338607] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/22/2021] [Accepted: 05/03/2021] [Indexed: 12/20/2022]
Abstract
Nucleotide-binding proteins play important roles in a variety of biological processes. While ATP- and GTP-binding proteins have been well studied, the systematical identification of UTP-interacting proteins remains under investigated. Here, we developed a chemical proteomic strategy using a biotinylated UTP affinity probe coupled with liquid chromatography tandem mass spectrometry (LC-MS/MS) method to enrich, identify and quantify UTP-binding proteins at the entire proteome scale. By performing labeling reactions with high vs low concentrations of UTP probe (100 and 10 μM) or with the UTP probe in the presence of free UTP in stable isotope labeling by amino acids in cell culture (SILAC) experiments, we identified more than 70 potential UTP-binding proteins which are involved in multiple cellular processes, such as translational elongation and protein folding. We also validated the UTP-binding capability of the cytoskeletal protein ACTB by using cellular thermal shift assay (CETSA). Together, we performed a high-throughput chemical proteomics-based analysis to identify, for the first time, UTP-binding proteins in human proteome, which should be applicable for the identification and quantification of UTP-binding proteins in other organisms.
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Affiliation(s)
- Yunming Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China
| | - Minghui Qu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China
| | - Mengting Pan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China
| | - Xiaofang Zheng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China
| | - Yuwei Sheng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China
| | - Yongqin Ji
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China
| | - Changjun You
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China.
| | - Xiaoxia Dai
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China.
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5
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Huang M, Wang Y. GLOBAL AND TARGETED PROFILING OF GTP-BINDING PROTEINS IN BIOLOGICAL SAMPLES BY MASS SPECTROMETRY. MASS SPECTROMETRY REVIEWS 2021; 40:215-235. [PMID: 32519381 PMCID: PMC7725852 DOI: 10.1002/mas.21637] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 05/04/2020] [Accepted: 05/15/2020] [Indexed: 05/05/2023]
Abstract
GTP-binding proteins are among the most important enzyme families that are involved in a plethora of biological processes. However, owing to the enormous diversity of the nucleotide-binding protein family, comprehensive analyses of the expression level, structure, activity, and regulatory mechanisms of GTP-binding proteins remain challenging with the use of conventional approaches. The many advances in mass spectrometry (MS) instrumentation and data acquisition methods, together with a variety of enrichment approaches in sample preparation, render MS a powerful tool for the comprehensive characterizations of the activities and expression levels of various GTP-binding proteins. We review herein the recent developments in the application of MS-based techniques, together with general and widely used affinity enrichment approaches, for the proteome-wide and targeted capture, identification, and quantification of GTP-binding proteins. The working principles, advantages, and limitations of various strategies for profiling the expression level, activity, posttranslational modifications, and interactome of GTP-binding proteins are discussed. It can be envisaged that future applications of MS-based proteomics will lead to a better understanding about the roles of GTP-binding proteins in different biological processes and human diseases. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Ming Huang
- Environmental Toxicology Graduate Program, University of California Riverside, Riverside, CA 92521, USA
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program, University of California Riverside, Riverside, CA 92521, USA
- Department of Chemistry, University of California Riverside, Riverside, CA 92521, USA
- Correspondence author: Yinsheng Wang. Telephone: (951)827-2700;
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6
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Cai R, Dong X, Yu K, He X, Liu X, Wang Y. Chemical Proteomic Profiling of the Interacting Proteins of Isoprenoid Pyrophosphates. Anal Chem 2020; 92:8031-8036. [PMID: 32420730 DOI: 10.1021/acs.analchem.0c01676] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Isoprenoid pyrophosphates are involved in protein prenylation and assume regulatory roles in cells; however, little is known about the cellular proteins that can interact with isoprenoid pyrophosphates. Here, we devised a chemical proteomic strategy, capitalizing on the use of a desthiobiotin-geranyl pyrophosphate (GPP) acyl phosphate probe for the enrichment and subsequent identification of GPP-binding proteins using liquid chromatography-tandem mass spectrometry (LC-MS/MS). By combining stable isotope labeling by amino acids in cell culture (SILAC) and competitive labeling with low vs high concentrations of GPP probe, with ATP vs GPP acyl phosphate probes, or with the GPP probe in the presence of different concentrations of free GPP, we uncovered a number of candidate GPP-binding proteins. We also discovered, for the first time, histone deacetylase 1 (HDAC1) as a GPP-binding protein. Furthermore, we found that the enzymatic activity of HDAC1 could be modulated by isoprenoid pyrophosphates. Together, we developed a novel chemical proteomic method for the proteome-wide discovery of GPP-binding proteins, which sets the stage for a better understanding about the biological functions of isoprenoids.
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Affiliation(s)
- Rong Cai
- Department of Chemistry, University of California Riverside, Riverside, California 92521-0403, United States.,School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong 250012, China
| | - Xuejiao Dong
- Department of Chemistry, University of California Riverside, Riverside, California 92521-0403, United States
| | - Kailin Yu
- Department of Chemistry, University of California Riverside, Riverside, California 92521-0403, United States
| | - Xiaomei He
- Department of Chemistry, University of California Riverside, Riverside, California 92521-0403, United States
| | - Xiaochuan Liu
- Department of Chemistry, University of California Riverside, Riverside, California 92521-0403, United States
| | - Yinsheng Wang
- Department of Chemistry, University of California Riverside, Riverside, California 92521-0403, United States
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7
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Alqahtani FM, Arivett BA, Taylor ZE, Handy ST, Farone AL, Farone MB. Chemogenomic profiling to understand the antifungal action of a bioactive aurone compound. PLoS One 2019; 14:e0226068. [PMID: 31825988 PMCID: PMC6905557 DOI: 10.1371/journal.pone.0226068] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 11/18/2019] [Indexed: 12/15/2022] Open
Abstract
Every year, more than 250,000 invasive candidiasis infections are reported with 50,000 deaths worldwide. The limited number of antifungal agents necessitates the need for alternative antifungals with potential novel targets. The 2-benzylidenebenzofuran-3-(2H)-ones have become an attractive scaffold for antifungal drug design. This study aimed to determine the antifungal activity of a synthetic aurone compound and characterize its mode of action. Using the broth microdilution method, aurone SH1009 exhibited inhibition against C. albicans, including resistant isolates, as well as C. glabrata, and C. tropicalis with IC50 values of 4-29 μM. Cytotoxicity assays using human THP-1, HepG2, and A549 human cell lines showed selective toxicity toward fungal cells. The mode of action for SH1009 was characterized using chemical-genetic interaction via haploinsufficiency (HIP) and homozygous (HOP) profiling of a uniquely barcoded Saccharomyces cerevisiae mutant collection. Approximately 5300 mutants were competitively treated with SH1009 followed by DNA extraction, amplification of unique barcodes, and quantification of each mutant using multiplexed next-generation sequencing. Barcode post-sequencing analysis revealed 238 sensitive and resistant mutants that significantly (FDR P values ≤ 0.05) responded to aurone SH1009. The enrichment analysis of KEGG pathways and gene ontology demonstrated the cell cycle pathway as the most significantly enriched pathway along with DNA replication, cell division, actin cytoskeleton organization, and endocytosis. Phenotypic studies of these significantly enriched responses were validated in C. albicans. Flow cytometric analysis of SH1009-treated C. albicans revealed a significant accumulation of cells in G1 phase, indicating cell cycle arrest. Fluorescence microscopy detected abnormally interrupted actin dynamics, resulting in enlarged, unbudded cells. RT-qPCR confirmed the effects of SH1009 in differentially expressed cell cycle, actin polymerization, and signal transduction genes. These findings indicate the target of SH1009 as a cell cycle-dependent organization of the actin cytoskeleton, suggesting a novel mode of action of the aurone compound as an antifungal inhibitor.
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Affiliation(s)
- Fatmah M. Alqahtani
- Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, United States of America
| | - Brock A. Arivett
- Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, United States of America
| | - Zachary E. Taylor
- Department of Chemistry, Middle Tennessee State University, Murfreesboro, Tennessee, United States of America
| | - Scott T. Handy
- Department of Chemistry, Middle Tennessee State University, Murfreesboro, Tennessee, United States of America
| | - Anthony L. Farone
- Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, United States of America
| | - Mary B. Farone
- Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, United States of America
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8
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Abbruzzese C, Matteoni S, Persico M, Ascione B, Schenone S, Musumeci F, Amato R, Perrotti N, Matarrese P, Paggi MG. The small molecule SI113 hinders epithelial-to-mesenchymal transition and subverts cytoskeletal organization in human cancer cells. J Cell Physiol 2019; 234:22529-22542. [PMID: 31099037 DOI: 10.1002/jcp.28816] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 04/05/2019] [Accepted: 04/24/2019] [Indexed: 02/06/2023]
Abstract
The small molecule SI113 is an inhibitor of the kinase activity of SGK1, a key biological regulator acting on the PI3K/mTOR signal transduction pathway. Several studies demonstrate that this compound is able to strongly restrain cancer growth in vitro and in vivo, alone or in associative antineoplastic treatments, being able to elicit an autophagic response, either cytotoxic or cytoprotective. To elucidate more exhaustively the molecular mechanisms targeted by SI113, we performed activity-based protein profiling (ABPP) proteomic analysis using a kinase enrichment procedure. This technique allowed the identification via mass spectrometry of novel targets of this compound, most of them involved in functions concerning cell motility and cytoskeletal architecture. Using a glioblastoma multiforme, hepatocarcinoma and colorectal carcinoma cell line, we recognized an inhibitory effect of SI113 on cell migration, invading, and epithelial-to-mesenchymal transition. In addition, these cancer cells, when exposed to this compound, showed a remarkable subversion of the cytoskeletal architecture characterized by F-actin destabilization, phospho-FAK delocalization, and tubulin depolimerization. These results were definitely concordant in attributing to SI113 a key role in hindering cancer cell malignancy and, due to its negligible in vivo toxicity, can sustain performing a Phase I clinical trial to employ this drug in associative cancer therapy.
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Affiliation(s)
- Claudia Abbruzzese
- Division of Cellular Networks and Molecular Therapeutic Targets, Proteomics Unit, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
| | - Silvia Matteoni
- Division of Cellular Networks and Molecular Therapeutic Targets, Proteomics Unit, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
| | - Michele Persico
- Division of Cellular Networks and Molecular Therapeutic Targets, Proteomics Unit, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
| | - Barbara Ascione
- Center for Gender Specific Medicine, Oncology Unit, Istituto Superiore di Sanità, Rome, Italy
| | | | | | - Rosario Amato
- Department of "Scienze della Salute", University "Magna Graecia" of Catanzaro, Catanzaro, Italy
| | - Nicola Perrotti
- Department of "Scienze della Salute", University "Magna Graecia" of Catanzaro, Catanzaro, Italy
| | - Paola Matarrese
- Center for Gender Specific Medicine, Oncology Unit, Istituto Superiore di Sanità, Rome, Italy
| | - Marco G Paggi
- Division of Cellular Networks and Molecular Therapeutic Targets, Proteomics Unit, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
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9
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Miao W, Wang Y. Quantitative Interrogation of the Human Kinome Perturbed by Two BRAF Inhibitors. J Proteome Res 2019; 18:2624-2631. [PMID: 30994353 DOI: 10.1021/acs.jproteome.9b00134] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Oncogenic BRAF mutations contribute to the development of a number of cancers, and small-molecule BRAF inhibitors have been approved by the Food and Drug Administration (FDA) for anticancer therapy. In this study, we employed two targeted quantitative proteomics approaches for monitoring separately the alterations in protein expression and ATP binding affinities of kinases in cultured human melanoma cells elicited by two FDA-approved small-molecule BRAF inhibitors, dabrafenib and vemurafenib. Our results showed that treatment with the two inhibitors led to markedly different reprograming of the human kinome. Furthermore, we confirmed that vemurafenib could compromise the ATP binding capacity of MAP2K5 in vitro and inhibit its kinase activity in cells. Together, our targeted quantitative proteomic methods revealed profound changes in expression levels of kinase proteins in cultured melanoma cells upon treatment with clinically used BRAF inhibitors and led to the discovery of novel putative target kinases for these inhibitors.
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Affiliation(s)
- Weili Miao
- Department of Chemistry , University of California , Riverside , California 92521-0403 , United States
| | - Yinsheng Wang
- Department of Chemistry , University of California , Riverside , California 92521-0403 , United States
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10
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Cai R, Huang M, Wang Y. Targeted Quantitative Profiling of GTP-Binding Proteins in Cancer Cells Using Isotope-Coded GTP Probes. Anal Chem 2018; 90:14339-14346. [PMID: 30433760 PMCID: PMC6434709 DOI: 10.1021/acs.analchem.8b03727] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
GTP-binding proteins play important roles in many essential biological processes, including cell signaling, trafficking, and protein synthesis. To assess quantitatively these proteins at the whole proteome level, we developed a high-throughput targeted proteomic method based on the use of isotope-coded GTP probes and multiple-reaction monitoring (MRM) analysis. Targeted proteins were labeled with desthiobiotin-GTP probes, digested with trypsin, and the ensuing desthiobiotin-conjugated peptides were enriched with streptavidin beads for LC-MS/MS analysis. We also established a Skyline MRM library based on shotgun proteomic data acquired for 12 different human cell lines. The library contained 605 tryptic peptides derived from 217 GTP-binding proteins, representing approximately 60% of the annotated human GTP-binding proteome. By using this library, in conjunction with isotope-coded GTP probes and scheduled LC-MRM analysis, we investigated the differential expression of GTP-binding proteins in a pair of primary/metastatic colon cancer cell lines (SW480 and SW620). We were able to quantify 97 GTP-binding proteins, and we further validated the differential expression of several GTP-binding proteins by Western blot analysis. Together, we developed a facile targeted quantitative proteomic method for the high-throughput analysis of GTP-binding proteins and applied the method for probing the altered expression of these proteins involved in colon cancer metastasis.
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Affiliation(s)
- Rong Cai
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, United States
| | - Ming Huang
- Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, California 92521, United States
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, United States
- Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, California 92521, United States
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11
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Lim YT, Prabhu N, Dai L, Go KD, Chen D, Sreekumar L, Egeblad L, Eriksson S, Chen L, Veerappan S, Teo HL, Tan CSH, Lengqvist J, Larsson A, Sobota RM, Nordlund P. An efficient proteome-wide strategy for discovery and characterization of cellular nucleotide-protein interactions. PLoS One 2018; 13:e0208273. [PMID: 30521565 PMCID: PMC6283526 DOI: 10.1371/journal.pone.0208273] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 11/14/2018] [Indexed: 12/03/2022] Open
Abstract
Metabolite-protein interactions define the output of metabolic pathways and regulate many cellular processes. Although diseases are often characterized by distortions in metabolic processes, efficient means to discover and study such interactions directly in cells have been lacking. A stringent implementation of proteome-wide Cellular Thermal Shift Assay (CETSA) was developed and applied to key cellular nucleotides, where previously experimentally confirmed protein-nucleotide interactions were well recaptured. Many predicted, but never experimentally confirmed, as well as novel protein-nucleotide interactions were discovered. Interactions included a range of different protein families where nucleotides serve as substrates, products, co-factors or regulators. In cells exposed to thymidine, a limiting precursor for DNA synthesis, both dose- and time-dependence of the intracellular binding events for sequentially generated thymidine metabolites were revealed. Interactions included known cancer targets in deoxyribonucleotide metabolism as well as novel interacting proteins. This stringent CETSA based strategy will be applicable for a wide range of metabolites and will therefore greatly facilitate the discovery and studies of interactions and specificities of the many metabolites in human cells that remain uncharacterized.
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Affiliation(s)
- Yan Ting Lim
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Nayana Prabhu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Lingyun Dai
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Ka Diam Go
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Dan Chen
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Lekshmy Sreekumar
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Louise Egeblad
- Department of Anatomy, Physiology and Biochemistry, The Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Staffan Eriksson
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Liyan Chen
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Saranya Veerappan
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Hsiang Ling Teo
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
| | - Chris Soon Heng Tan
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore
| | - Johan Lengqvist
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Andreas Larsson
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Radoslaw M. Sobota
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore
- * E-mail: (PN); (RMS)
| | - Pär Nordlund
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore
- * E-mail: (PN); (RMS)
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12
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Joachimiak Ł, Błażewska KM. Phosphorus-Based Probes as Molecular Tools for Proteome Studies: Recent Advances in Probe Development and Applications. J Med Chem 2018; 61:8536-8562. [DOI: 10.1021/acs.jmedchem.8b00249] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Łukasz Joachimiak
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego Street 116, 90-924 Łódź, Poland
| | - Katarzyna M. Błażewska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego Street 116, 90-924 Łódź, Poland
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13
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Ortega C, Frando A, Webb-Robertson BJ, Anderson LN, Fleck N, Flannery EL, Fishbaugher M, Murphree TA, Hansen JR, Smith RD, Kappe SHI, Wright AT, Grundner C. A Global Survey of ATPase Activity in Plasmodium falciparum Asexual Blood Stages and Gametocytes. Mol Cell Proteomics 2017; 17:111-120. [PMID: 29079720 DOI: 10.1074/mcp.ra117.000088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 10/03/2017] [Indexed: 01/12/2023] Open
Abstract
Effective malaria control and elimination in hyperendemic areas of the world will require treatment of the Plasmodium falciparum (Pf) blood stage that causes disease as well as the gametocyte stage that is required for transmission from humans to the mosquito vector. Most currently used therapies do not kill gametocytes, a highly specialized, non-replicating sexual parasite stage. Further confounding next generation drug development against Pf is the unknown metabolic state of the gametocyte and the lack of known biochemical activity for most parasite gene products in general. Here, we take a systematic activity-based proteomics approach to survey the activity of the large and druggable ATPase family in replicating blood stage asexual parasites and transmissible, non-replicating sexual gametocytes. ATPase activity broadly changes during the transition from asexual schizonts to sexual gametocytes, indicating altered metabolism and regulatory roles of ATPases specific for each lifecycle stage. We further experimentally confirm existing annotation and predict ATPase function for 38 uncharacterized proteins. By mapping the activity of ATPases associated with gametocytogenesis, we assign biochemical activity to a large number of uncharacterized proteins and identify new candidate transmission blocking targets.
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Affiliation(s)
- Corrie Ortega
- From the ‡Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, Washington 98109
| | - Andrew Frando
- From the ‡Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, Washington 98109.,§Department of Global Health, University of Washington, Seattle, Washington 98195
| | - Bobbie-Jo Webb-Robertson
- ¶Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Lindsey N Anderson
- ¶Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Neil Fleck
- From the ‡Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, Washington 98109
| | - Erika L Flannery
- From the ‡Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, Washington 98109
| | - Matthew Fishbaugher
- From the ‡Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, Washington 98109
| | - Taylor A Murphree
- ¶Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Joshua R Hansen
- ¶Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Richard D Smith
- ¶Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Stefan H I Kappe
- From the ‡Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, Washington 98109.,§Department of Global Health, University of Washington, Seattle, Washington 98195
| | - Aaron T Wright
- ¶Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Christoph Grundner
- From the ‡Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, Washington 98109; .,§Department of Global Health, University of Washington, Seattle, Washington 98195
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14
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Ermert S, Marx A, Hacker SM. Phosphate-Modified Nucleotides for Monitoring Enzyme Activity. Top Curr Chem (Cham) 2017; 375:28. [PMID: 28251563 DOI: 10.1007/s41061-017-0117-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 01/30/2017] [Indexed: 02/07/2023]
Abstract
Nucleotides modified at the terminal phosphate position have been proven to be interesting entities to study the activity of a variety of different protein classes. In this chapter, we present various types of modifications that were attached as reporter molecules to the phosphate chain of nucleotides and briefly describe the chemical reactions that are frequently used to synthesize them. Furthermore, we discuss a variety of applications of these molecules. Kinase activity, for instance, was studied by transfer of a phosphate modified with a reporter group to the target proteins. This allows not only studying the activity of kinases, but also identifying their target proteins. Moreover, kinases can also be directly labeled with a reporter at a conserved lysine using acyl-phosphate probes. Another important application for phosphate-modified nucleotides is the study of RNA and DNA polymerases. In this context, single-molecule sequencing is made possible using detection in zero-mode waveguides, nanopores or by a Förster resonance energy transfer (FRET)-based mechanism between the polymerase and a fluorophore-labeled nucleotide. Additionally, fluorogenic nucleotides that utilize an intramolecular interaction between a fluorophore and the nucleobase or an intramolecular FRET effect have been successfully developed to study a variety of different enzymes. Finally, also some novel techniques applying electron paramagnetic resonance (EPR)-based detection of nucleotide cleavage or the detection of the cleavage of fluorophosphates are discussed. Taken together, nucleotides modified at the terminal phosphate position have been applied to study the activity of a large diversity of proteins and are valuable tools to enhance the knowledge of biological systems.
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Affiliation(s)
- Susanne Ermert
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78464, Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78464, Konstanz, Germany
| | - Stephan M Hacker
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78464, Konstanz, Germany.
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15
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Xiong Y, Lu J, Hunter J, Li L, Scott D, Choi HG, Lim SM, Manandhar A, Gondi S, Sim T, Westover KD, Gray NS. Covalent Guanosine Mimetic Inhibitors of G12C KRAS. ACS Med Chem Lett 2017; 8:61-66. [PMID: 28105276 DOI: 10.1021/acsmedchemlett.6b00373] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 11/30/2016] [Indexed: 12/21/2022] Open
Abstract
Ras proteins are members of a large family of GTPase enzymes that are commonly mutated in cancer where they act as dominant oncogenes. We previously developed an irreversible guanosine-derived inhibitor, SML-8-73-1, of mutant G12C RAS that forms a covalent bond with cysteine 12. Here we report exploration of the structure-activity relationships (SAR) of hydrolytically stable analogues of SML-8-73-1 as covalent G12C KRAS inhibitors. We report the discovery of difluoromethylene bisphosphonate analogues such as compound 11, which, despite exhibiting reduced efficiency as covalent G12C KRAS inhibitors, remove the liability of the hydrolytic instability of the diphosphate moiety present in SML-8-73-1 and provide the foundation for development of prodrugs to facilitate cellular uptake. The SAR and crystallographic results reaffirm the exquisite molecular recognition that exists in the diphosphate region of RAS for guanosine nucleotides which must be considered in the design of nucleotide-competitive inhibitors.
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Affiliation(s)
- Yuan Xiong
- Department
of Cancer Biology, Dana Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02115, United States
- Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Jia Lu
- Departments
of Biochemistry and Radiation Oncology, The University of Texas, Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
| | - John Hunter
- Departments
of Biochemistry and Radiation Oncology, The University of Texas, Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
| | - Lianbo Li
- Departments
of Biochemistry and Radiation Oncology, The University of Texas, Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
| | - David Scott
- Department
of Cancer Biology, Dana Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02115, United States
- Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Hwan Geun Choi
- New
Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu 41061, Republic of Korea
| | - Sang Min Lim
- Center
for Neuro-Medicine, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Anuj Manandhar
- Departments
of Biochemistry and Radiation Oncology, The University of Texas, Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
| | - Sudershan Gondi
- Departments
of Biochemistry and Radiation Oncology, The University of Texas, Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
| | - Taebo Sim
- Chemical
Kinomics Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
- KU-KIST
Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Republic of Korea
| | - Kenneth D. Westover
- Departments
of Biochemistry and Radiation Oncology, The University of Texas, Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
| | - Nathanael S. Gray
- Department
of Cancer Biology, Dana Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02115, United States
- Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
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16
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Miao W, Xiao Y, Guo L, Jiang X, Huang M, Wang Y. A High-Throughput Targeted Proteomic Approach for Comprehensive Profiling of Methylglyoxal-Induced Perturbations of the Human Kinome. Anal Chem 2016; 88:9773-9779. [PMID: 27626823 DOI: 10.1021/acs.analchem.6b02816] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Kinases are one of the most important families of enzymes that are involved in numerous cell signaling processes. Existing methods for studying kinase expression and activation have limited kinome coverage. Herein we established a multiple-reaction monitoring (MRM)-based targeted proteomic method that provided an unprecedented coverage (∼80%) of the human kinome. We employed this method for profiling comprehensively the alterations of the global kinome of HEK293T human embryonic kidney cells upon treatment with methylglyoxal, a glycolysis byproduct that is present at elevated levels in blood and tissues of diabetic patients and is thought to contribute to diabetic complications. Our results led to the quantification of 328 unique kinases. In particular, we found that methylglyoxal treatment gave rise to altered expression of a number of kinases in the MAPK pathway and diminished expression of several receptor tyrosine kinases, including epidermal growth factor receptor (EGFR), insulin growth factor 2 receptor (IGF2R), fibroblast growth factor receptor (FGFR), etc. Furthermore, we demonstrated that the diminished expression of EGFR occurred through a mechanism that is distinct from the reduced expression of IGF2R and FGFR1. Together, our targeted kinome profiling method offers a powerful resource for exploring kinase-mediated signaling pathways that are altered by extracellular stimuli, and the results from the present study suggest new mechanisms underlying the development of diabetic complications.
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Affiliation(s)
- Weili Miao
- Department of Chemistry, and ‡Environmental Toxicology Graduate Program, University of California , Riverside, California 92521-0403, United States
| | - Yongsheng Xiao
- Department of Chemistry, and ‡Environmental Toxicology Graduate Program, University of California , Riverside, California 92521-0403, United States
| | - Lei Guo
- Department of Chemistry, and ‡Environmental Toxicology Graduate Program, University of California , Riverside, California 92521-0403, United States
| | - Xiaogang Jiang
- Department of Chemistry, and ‡Environmental Toxicology Graduate Program, University of California , Riverside, California 92521-0403, United States
| | - Ming Huang
- Department of Chemistry, and ‡Environmental Toxicology Graduate Program, University of California , Riverside, California 92521-0403, United States
| | - Yinsheng Wang
- Department of Chemistry, and ‡Environmental Toxicology Graduate Program, University of California , Riverside, California 92521-0403, United States
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17
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Xiao Y, Wang Y. Global discovery of protein kinases and other nucleotide-binding proteins by mass spectrometry. MASS SPECTROMETRY REVIEWS 2016; 35:601-19. [PMID: 25376990 PMCID: PMC5609854 DOI: 10.1002/mas.21447] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Revised: 08/08/2014] [Accepted: 08/09/2014] [Indexed: 05/11/2023]
Abstract
Nucleotide-binding proteins, such as protein kinases, ATPases and GTP-binding proteins, are among the most important families of proteins that are involved in a number of pivotal cellular processes. However, global study of the structure, function, and expression level of nucleotide-binding proteins as well as protein-nucleotide interactions can hardly be achieved with the use of conventional approaches owing to enormous diversity of the nucleotide-binding protein family. Recent advances in mass spectrometry (MS) instrumentation, coupled with a variety of nucleotide-binding protein enrichment methods, rendered MS-based proteomics a powerful tool for the comprehensive characterizations of the nucleotide-binding proteome, especially the kinome. Here, we review the recent developments in the use of mass spectrometry, together with general and widely used affinity enrichment approaches, for the proteome-wide capture, identification and quantification of nucleotide-binding proteins, including protein kinases, ATPases, GTPases, and other nucleotide-binding proteins. The working principles, advantages, and limitations of each enrichment platform in identifying nucleotide-binding proteins as well as profiling protein-nucleotide interactions are summarized. The perspectives in developing novel MS-based nucleotide-binding protein detection platform are also discussed. © 2014 Wiley Periodicals, Inc. Mass Spec Rev 35:601-619, 2016.
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Affiliation(s)
| | - Yinsheng Wang
- Correspondence to: Yinsheng Wang, Department of Chemistry, University of California, Riverside, CA 92521-0403.
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18
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Geer MA, Fitzgerald MC. Characterization of the Saccharomyces cerevisiae ATP-Interactome using the iTRAQ-SPROX Technique. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:233-243. [PMID: 26530046 DOI: 10.1007/s13361-015-1290-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 09/01/2015] [Accepted: 10/05/2015] [Indexed: 06/05/2023]
Abstract
The stability of proteins from rates of oxidation (SPROX) technique was used in combination with an isobaric mass tagging strategy to identify adenosine triphosphate (ATP) interacting proteins in the Saccharomyces cerevisiae proteome. The SPROX methodology utilized in this work enabled 373 proteins in a yeast cell lysate to be assayed for ATP interactions (both direct and indirect) using the non-hydrolyzable ATP analog, adenylyl imidodiphosphate (AMP-PNP). A total of 28 proteins were identified with AMP-PNP-induced thermodynamic stability changes. These protein hits included 14 proteins that were previously annotated as ATP-binding proteins in the Saccharomyces Genome Database (SGD). The 14 non-annotated ATP-binding proteins included nine proteins that were previously found to be ATP-sensitive in an earlier SPROX study using a stable isotope labeling with amino acids in cell culture (SILAC)-based approach. A bioinformatics analysis of the protein hits identified here and in the earlier SILAC-SPROX experiments revealed that many of the previously annotated ATP-binding protein hits were kinases, ligases, and chaperones. In contrast, many of the newly discovered ATP-sensitive proteins were not from these protein classes, but rather were hydrolases, oxidoreductases, and nucleic acid-binding proteins. Graphical Abstract ᅟ.
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Affiliation(s)
- M Ariel Geer
- Department of Chemistry, Duke University, Durham, NC, 27708-0346, USA
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19
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Vollmer S, Richert C. Effect of preorganization on the affinity of synthetic DNA binding motifs for nucleotide ligands. Org Biomol Chem 2015; 13:5734-42. [PMID: 25902412 DOI: 10.1039/c5ob00508f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Triplexes with a gap in the purine strand have been shown to bind adenosine or guanosine derivatives through a combination of Watson-Crick and Hoogsteen base pairing. Rigidifying the binding site should be advantageous for affinity. Here we report that clamps delimiting the binding site have a modest effect on affinity, while bridging the gap of the purine strand can strongly increase affinity for ATP, cAMP, and FAD. The lowest dissociation constants were measured for two-strand triple helical motifs with a propylene bridge or an abasic nucleoside analog, with Kd values as low as 30 nM for cAMP in the latter case. Taken together, our data suggest that improving preorganization through covalent bridges increases the affinity for nucleotide ligands. But, a bulky bridge may also block one of two alternative binding modes for the adenine base. The results may help to design new receptors, switches, or storage motifs for purine-containing ligands.
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Affiliation(s)
- S Vollmer
- Institute for Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany.
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20
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Guo L, Xiao Y, Fan M, Li JJ, Wang Y. Profiling global kinome signatures of the radioresistant MCF-7/C6 breast cancer cells using MRM-based targeted proteomics. J Proteome Res 2014; 14:193-201. [PMID: 25341124 PMCID: PMC4286165 DOI: 10.1021/pr500919w] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
![]()
Ionizing
radiation is widely used in cancer therapy; however, cancer
cells often develop radioresistance, which compromises the efficacy
of cancer radiation therapy. Quantitative assessment of the alteration
of the entire kinome in radioresistant cancer cells relative to their
radiosensitive counterparts may provide important knowledge to define
the mechanism(s) underlying tumor adaptive radioresistance and uncover
novel target(s) for effective prevention and treatment of tumor radioresistance.
By employing a scheduled multiple-reaction monitoring analysis in
conjunction with isotope-coded ATP affinity probes, we assessed the
global kinome of radioresistant MCF-7/C6 cells and their parental
MCF-7 human breast cancer cells. We rigorously quantified 120 kinases,
of which 1/3 exhibited significant differences
in expression levels or ATP binding affinities. Several kinases involved
in cell cycle progression and DNA damage response were found to be
overexpressed or hyperactivated, including checkpoint kinase 1 (CHK1),
cyclin-dependent kinases 1 and 2 (CDK1 and CDK2), and the catalytic
subunit of DNA-dependent protein kinase. The elevated expression of
CHK1, CDK1, and CDK2 in MCF-7/C6 cells was further validated by Western
blot analysis. Thus, the altered kinome profile of radioresistant
MCF-7/C6 cells suggests the involvement of kinases on cell cycle progression
and DNA repair in tumor adaptive radioresistance. The unique kinome
profiling results also afforded potential effective targets for resensitizing
radioresistant cancer cells and counteracting deleterious effects
of ionizing radiation exposure.
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Affiliation(s)
- Lei Guo
- Environmental Toxicology Graduate Program and ‡Department of Chemistry, University of California , Riverside, California 92521-0403, United States
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21
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Guo L, Xiao Y, Wang Y. Application of adenosine triphosphate affinity probe and scheduled multiple-reaction monitoring analysis for profiling global kinome in human cells in response to arsenite treatment. Anal Chem 2014; 86:10700-7. [PMID: 25301106 PMCID: PMC4222629 DOI: 10.1021/ac502592d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
Phosphorylation of cellular components
catalyzed by kinases plays
important roles in cell signaling and proliferation. Quantitative
assessment of perturbation in global kinome may provide crucial knowledge
for elucidating the mechanisms underlying the cytotoxic effects of
environmental toxicants. Here, we utilized an adenosine triphosphate
(ATP) affinity probe coupled with stable isotope labeling by amino
acids in cell culture (SILAC) to assess quantitatively the arsenite-induced
alteration of global kinome in human cells. We constructed a SILAC-compatible
kinome library for scheduled multiple-reaction monitoring (MRM) analysis
and adopted on-the-fly recalibration of retention time shift, which
provided better throughput of the analytical method and enabled the
simultaneous quantification of the expression of ∼300 kinases
in two LC-MRM runs. With this improved analytical method, we conducted
an in-depth quantitative analysis of the perturbation of kinome of
GM00637 human skin fibroblast cells induced by arsenite exposure.
Several kinases involved in cell cycle progression, including cyclin-dependent
kinases (CDK1 and CDK4) and Aurora kinases A, B, and C, were found
to be hyperactivated, and the altered expression of CDK1 was further
validated by Western analysis. In addition, treatment with a CDK inhibitor,
flavopiridol, partially restored the arsenite-induced growth inhibition
of human skin fibroblast cells. Thus, sodium arsenite may confer its
cytotoxic effect partly through the aberrant activation of CDKs and
the resultant perturbation of cell cycle progression. Together, we
developed a high-throughput, SILAC-compatible, and MRM-based kinome
profiling method and demonstrated that the method is powerful in deciphering
the molecular modes of action of a widespread environmental toxicant.
The method should be generally applicable for uncovering the cellular
pathways triggered by other extracellular stimuli.
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Affiliation(s)
- Lei Guo
- Environmental Toxicology Graduate Program and ‡Department of Chemistry, University of California , Riverside, California 92521-0403, United States
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22
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Adachi J, Kishida M, Watanabe S, Hashimoto Y, Fukamizu K, Tomonaga T. Proteome-wide discovery of unknown ATP-binding proteins and kinase inhibitor target proteins using an ATP probe. J Proteome Res 2014; 13:5461-70. [PMID: 25230287 DOI: 10.1021/pr500845u] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
ATP-binding proteins, including protein kinases, play essential roles in many biological and pathological processes and thus these proteins are attractive as drug targets. Acyl-ATP probes have been developed as efficient probes for kinase enrichment, and these probes have also been used to enrich other ATP-binding proteins. However, a robust method to identify ATP-binding proteins with systematic elimination of nonspecific binding proteins has yet to be established. Here, we describe an ATP competition assay that permitted establishment of a rigorous ATP-binding protein list with virtual elimination of nonspecific proteins. A total of 539 ATP-binding protein candidates were identified, including 178 novel candidates. In informatics analysis, ribosomal proteins were overrepresented in the list of novel candidates. We also found multiple ATP-competitive sites for several kinases, including epidermal growth factor receptor, serine/threonine-protein kinase PRP4 homologue, cyclin-dependent kinase 12, eukaryotic elongation factor 2 kinase, ribosomal protein S6 kinase alpha-1, and SRSF protein kinase 1. Using our cataloged ATP-binding protein list, a selectivity profiling method that covers the kinome and ATPome was established to identify off-target binding sites of ATP-competitive kinase inhibitors, staurosporine and crizotinib.
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Affiliation(s)
- Jun Adachi
- Laboratory of Proteome Research, National Institute of Biomedical Innovation , Ibaraki, Osaka 567-0085, Japan
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23
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Xiao Y, Ji D, Guo L, Wang Y. Comprehensive characterization of (S)GTP-binding proteins by orthogonal quantitative (S)GTP-affinity profiling and (S)GTP/GTP competition assays. Anal Chem 2014; 86:4550-8. [PMID: 24689502 PMCID: PMC4014148 DOI: 10.1021/ac500588q] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 04/01/2014] [Indexed: 11/30/2022]
Abstract
Thiopurine drugs are widely used as antileukemic drugs and immunosuppressive agents, and 6-thioguanosine triphosphate ((S)GTP) is a major metabolite for these drugs. Recent studies have suggested that thiopurine drugs may exert their cytotoxic effects partly through binding of (S)GTP to a GTP-binding protein, Rac1. However, it remains unclear whether (S)GTP can also bind to other cellular proteins. Here, we introduced an orthogonal approach, encompassing nucleotide-affinity profiling and nucleotide-binding competition assays, to characterize comprehensively (S)GTP-binding proteins along with the specific binding sites from the entire human proteome. With the simultaneous use of (S)GTP and GTP affinity probes, we identified 165 (S)GTP-binding proteins that are involved in several different biological processes. We also examined the binding selectivities of these proteins toward (S)GTP and GTP, which allowed for the revelation of the relative binding affinities of the two nucleotides toward the nucleotide-binding motif sequence of proteins. Our results suggest that (S)GTP mainly targets GTPases, with strong binding affinities observed for multiple heterotrimeric G proteins. We also demonstrated that (S)GTP binds to several cyclin-dependent kinases (CDKs), which may perturb the CDK-mediated phosphorylation and cell cycle progression. Together, this represents the first comprehensive characterization of (S)GTP-binding property for the entire human proteome. We reason that a similar strategy can be generally employed for the future characterization of the interaction of other modified nucleotides with the global proteome.
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Affiliation(s)
- Yongsheng Xiao
- Department of Chemistry and Environmental Toxicology Graduate
Program, University of California, Riverside, California 92521-0403, United States
| | - Debin Ji
- Department of Chemistry and Environmental Toxicology Graduate
Program, University of California, Riverside, California 92521-0403, United States
| | - Lei Guo
- Department of Chemistry and Environmental Toxicology Graduate
Program, University of California, Riverside, California 92521-0403, United States
| | - Yinsheng Wang
- Department of Chemistry and Environmental Toxicology Graduate
Program, University of California, Riverside, California 92521-0403, United States
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24
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Xiao Y, Guo L, Wang Y. A targeted quantitative proteomics strategy for global kinome profiling of cancer cells and tissues. Mol Cell Proteomics 2014; 13:1065-75. [PMID: 24520089 PMCID: PMC3977184 DOI: 10.1074/mcp.m113.036905] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2013] [Revised: 12/08/2013] [Indexed: 12/28/2022] Open
Abstract
Kinases are among the most intensively pursued enzyme superfamilies as targets for anti-cancer drugs. Large data sets on inhibitor potency and selectivity for more than 400 human kinases became available recently, offering the opportunity to design rationally novel kinase-based anti-cancer therapies. However, the expression levels and activities of kinases are highly heterogeneous among different types of cancer and even among different stages of the same cancer. The lack of effective strategy for profiling the global kinome hampers the development of kinase-targeted cancer chemotherapy. Here, we introduced a novel global kinome profiling method, based on our recently developed isotope-coded ATP-affinity probe and a targeted proteomic method using multiple-reaction monitoring (MRM), for assessing simultaneously the expression of more than 300 kinases in human cells and tissues. This MRM-based assay displayed much better sensitivity, reproducibility, and accuracy than the discovery-based shotgun proteomic method. Approximately 250 kinases could be routinely detected in the lysate of a single cell line. Additionally, the incorporation of iRT into MRM kinome library rendered our MRM kinome assay easily transferrable across different instrument platforms and laboratories. We further employed this approach for profiling kinase expression in two melanoma cell lines, which revealed substantial kinome reprogramming during cancer progression and demonstrated an excellent correlation between the anti-proliferative effects of kinase inhibitors and the expression levels of their target kinases. Therefore, this facile and accurate kinome profiling assay, together with the kinome-inhibitor interaction map, could provide invaluable knowledge to predict the effectiveness of kinase inhibitor drugs and offer the opportunity for individualized cancer chemotherapy.
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Affiliation(s)
| | - Lei Guo
- §Environmental Toxicology Graduate Program, University of California, Riverside, CA 92521-0403
| | - Yinsheng Wang
- From the ‡Department of Chemistry and
- §Environmental Toxicology Graduate Program, University of California, Riverside, CA 92521-0403
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25
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Xiao Y, Guo L, Wang Y. Isotope-coded ATP probe for quantitative affinity profiling of ATP-binding proteins. Anal Chem 2013; 85:7478-86. [PMID: 23841533 DOI: 10.1021/ac401415z] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
ATP-binding proteins play significant roles in numerous cellular processes. Here, we introduced a novel isotope-coded ATP-affinity probe (ICAP) as an acylating agent to simultaneously enrich and incorporate isotope label to ATP-binding proteins. By taking advantage of the quantitative capability of this isotope-coded probe, we devised an affinity profiling strategy to comprehensively characterize ATP-protein interactions at the entire proteome scale. False-positive identification of ATP-binding sites derived from nonspecific labeling was effectively minimized through the comparison of the labeling behaviors of lysine residues with the use of low and high concentrations of the ICAP reagents. A total of 258 previously known ATP-binding proteins from lysates of HeLa-S3 and Jurkat-T cells were validated with this affinity profiling assay. Additionally, we demonstrated that this novel quantitative ATP-affinity profiling strategy is particularly useful for unveiling previously unrecognized nucleotide-binding sites in ATP-binding proteins. For example, our profiling results revealed K356 as a new ATP-binding site in HSP90. Furthermore, 293 proteins without documented ATP-binding GO were predicted to be ATP-binding proteins on the basis of our quantitative affinity profiling results. We also uncovered, for the first time, the ATP-binding capability of human proliferating cell nuclear antigen (PCNA), identified the lysine residue involved in ATP binding, and validated the protein's capacity in ATP binding with an independent assay. The ICAP approach described in the present paper should be generally applicable for the quantitative assessment of ATP-binding proteins in proteomic samples from cells and tissues.
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Affiliation(s)
- Yongsheng Xiao
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
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