151
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Razafsky D, Hodzic D. Bringing KASH under the SUN: the many faces of nucleo-cytoskeletal connections. ACTA ACUST UNITED AC 2009; 186:461-72. [PMID: 19687252 PMCID: PMC2733748 DOI: 10.1083/jcb.200906068] [Citation(s) in RCA: 197] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The nucleus is the most prominent cellular organelle, and its sharp boundaries suggest the compartmentalization of the nucleoplasm from the cytoplasm. However, the recent identification of evolutionarily conserved linkers of the nucleoskeleton to the cytoskeleton (LINC) complexes, a family of macromolecular assemblies that span the double membrane of the nuclear envelope, reveals tight physical connections between the two compartments. Here, we review the structure and evolutionary conservation of SUN and KASH domain–containing proteins, whose interaction within the perinuclear space forms the “nuts and bolts” of LINC complexes. Moreover, we discuss the function of these complexes in nuclear, centrosomal, and chromosome dynamics, and their connection to human disease.
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Affiliation(s)
- David Razafsky
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO 63110, USA
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152
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Lazar IM. Recent advances in capillary and microfluidic platforms with MS detection for the analysis of phosphoproteins. Electrophoresis 2009; 30:262-75. [PMID: 19156662 DOI: 10.1002/elps.200800427] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Reversible protein phosphorylation represents a key regulatory mechanism that triggers essential cellular signaling events. The large-scale characterization of protein phosphorylation in a cell represents, therefore, the objective of many biological studies that aim at elucidating the complex signaling pathways that are involved in the progression and/or regression of a disease. The recent implementation of novel MS detection strategies has significantly advanced the capabilities for interrogating the complex cellular phosphoproteome. Simultaneously, the current advent of miniaturized technologies has clearly demonstrated the superior performance of microfluidic instrumentation for bioanalytical and biological applications that cope with speed, sensitivity and throughput-related demands. This review aims at providing an update on the latest developments regarding the interfacing of microfluidic devices with MS detection for exploring the challenging area of phosphoproteomics.
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Affiliation(s)
- Iulia M Lazar
- Virginia Bioinformatics Institute and Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.
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153
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Condina MR, Guthridge MA, McColl SR, Hoffmann P. A sensitive magnetic bead method for the detection and identification of tyrosine phosphorylation in proteins by MALDI-TOF/TOF MS. Proteomics 2009; 9:3047-57. [DOI: 10.1002/pmic.200701179] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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154
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Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJR, Mohammed S. Lys-N and Trypsin Cover Complementary Parts of the Phosphoproteome in a Refined SCX-Based Approach. Anal Chem 2009; 81:4493-501. [DOI: 10.1021/ac9004309] [Citation(s) in RCA: 221] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sharon Gauci
- Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands and The Netherlands Proteomics Center
| | - Andreas O. Helbig
- Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands and The Netherlands Proteomics Center
| | - Monique Slijper
- Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands and The Netherlands Proteomics Center
| | - Jeroen Krijgsveld
- Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands and The Netherlands Proteomics Center
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands and The Netherlands Proteomics Center
| | - Shabaz Mohammed
- Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands and The Netherlands Proteomics Center
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155
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156
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Abstract
Human cerebrospinal fluid (CSF), which circulates within the ventricles of the brain and the subarachnoid space of the central nervous system (CNS), is an excellent source for proteomic discovery of biomarkers in neurodegenerative disorders, including Alzheimer's and Parkinson's disease. Protein glycosylation is an abundant and biologically significant posttranslational modification. Glycoproteins, commonly associated with membrane and secreted proteins, are highly enriched in body fluids, including CSF. Focusing on glycoproteins also improves the dynamic range of proteomic profiling of the CSF, where low abundance proteins are difficult to identify because of the CSF's enormous complexity. As an ongoing process to define the human CSF proteome, we have recently employed a complementary proteomic approach, with integrated lectin affinity column and hydrazide chemistry, for CSF glycoprotein identification. This investigation has revealed many proteins of low abundance that are related to the CNS structurally and/or functionally. This review centers on the technical details involved in various steps in sample preparation as well as proteomic analysis of CSF glycoproteins.
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Affiliation(s)
- Hye Jin Hwang
- Department of Pathology, Harborview Medical Center, University of Washington School of Medicine, Seattle, WA, USA
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157
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Dengjel J, Kratchmarova I, Blagoev B. Receptor tyrosine kinase signaling: a view from quantitative proteomics. MOLECULAR BIOSYSTEMS 2009; 5:1112-21. [DOI: 10.1039/b909534a] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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158
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Blackburn K, Goshe MB. Challenges and strategies for targeted phosphorylation site identification and quantification using mass spectrometry analysis. BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS 2008; 8:90-103. [DOI: 10.1093/bfgp/eln051] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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159
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Chen Y, Tang CE, Ouyang GL, Ruan L, Li MY, Zhang PF, Li C, Yi H, Peng F, Li JL, Chen ZC, Xiao ZQ. Identification of RKIP as a differentially tyrosine-phosphorylated protein in nasopharyngeal carcinoma and normal nasopharyngeal epithelial tissues by phosphoproteomic approach. Med Oncol 2008; 26:463-70. [PMID: 19096942 DOI: 10.1007/s12032-008-9147-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2008] [Accepted: 12/02/2008] [Indexed: 11/25/2022]
Abstract
AIMS To screen for differentially tyrosine-phosphorylated proteins between nasopharyngeal carcinoma (NPC) and normal nasopharyngeal epithelial tissues (NNET) to provide a basis for elucidate the molecular mechanisms of NPC carcinogenesis. METHODS Two-dimensional (2-D) electrophoresis was applied to separate proteins from NPC and NNET, respectively, and 2-D Western blotting was performed to detect tyrosine-phosphorylated proteins using antiphosphotyrosine antibody. Differentially tyrosine-phosphorylated proteins were identified by electrospray ionization-quadrupole time-of-flight MS (ESI-Q-TOF MS). NetPhos software was used to predict the tyrosine-phosphorylation sites of the identified proteins, and Western blotting was used to detect the tyrosine-phosphorylated levels of RKIP in NPC and NNET. RESULTS Twenty-five differentially tyrosine-phosphorylated proteins in the two types of tissues were found, 13 of which were identified by ESI-Q-TOF MS. Among the 13 identified proteins, tyrosine-phosphorylated levels of 7 proteins were increased, and those of 6 proteins were decreased in NPC compared with NNET. NetPhos software prediction showed that all the 13 identified proteins contained tyrosine phosphorylation sites, and the differentially tyrosine-phosphorylated level of RKIP in NPC and NNET was confirmed. CONCLUSION The 13 differentially tyrosine-phosphorylated proteins may be involved in the development and progression of NPC.
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Affiliation(s)
- Yan Chen
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, 410008, Hunan Province, China
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160
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Sakai M, Furuya M, Endo H, Yamaoka K, Kondo S, Koike T. An Efficient Identification Method of a Specific Binding Protein for a Bioactive Compound Using On-Bead Digestion and Mass Spectrometry. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2008. [DOI: 10.1246/bcsj.81.1599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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161
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Schreiber TB, Mäusbacher N, Breitkopf SB, Grundner-Culemann K, Daub H. Quantitative phosphoproteomics--an emerging key technology in signal-transduction research. Proteomics 2008; 8:4416-32. [PMID: 18837465 DOI: 10.1002/pmic.200800132] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Protein phosphorylation is the most important type of reversible post-translational modification involved in the regulation of cellular signal-transduction processes. In addition to controlling normal cellular physiology on the molecular level, perturbations of phosphorylation-based signaling networks and cascades have been implicated in the onset and progression of various human diseases. Recent advances in mass spectrometry-based proteomics helped to overcome many of the previous limitations in protein phosphorylation analysis. Improved isotope labeling and phosphopeptide enrichment strategies in conjunction with more powerful mass spectrometers and advances in data analysis have been integrated in highly efficient phosphoproteomics workflows, which are capable of monitoring up to several thousands of site-specific phosphorylation events within one large-scale analysis. Combined with ongoing efforts to define kinase-substrate relationships in intact cells, these major achievements have considerable potential to assess phosphorylation-based signaling networks on a system-wide scale. Here, we provide an overview of these exciting developments and their potential to transform signal-transduction research into a technology-driven, high-throughput science.
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Affiliation(s)
- Thiemo B Schreiber
- Department of Molecular Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
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162
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Dai J, Wang LS, Wu YB, Sheng QH, Wu JR, Shieh CH, Zeng R. Fully Automatic Separation and Identification of Phosphopeptides by Continuous pH-Gradient Anion Exchange Online Coupled with Reversed-Phase Liquid Chromatography Mass Spectrometry. J Proteome Res 2008; 8:133-41. [DOI: 10.1021/pr800381w] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Jie Dai
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Lian-Shui Wang
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yi-Bo Wu
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Quan-Hu Sheng
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jia-Rui Wu
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chia-Hui Shieh
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Rong Zeng
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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163
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Carrascal M, Ovelleiro D, Casas V, Gay M, Abian J. Phosphorylation Analysis of Primary Human T Lymphocytes Using Sequential IMAC and Titanium Oxide Enrichment. J Proteome Res 2008; 7:5167-76. [DOI: 10.1021/pr800500r] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Montserrat Carrascal
- CSIC/UAB Proteomics Laboratory, IIBB-CSIC, IDIBAPS, Facultad de Medicina, Campus UAB, 08193 Bellaterra, Spain
| | - David Ovelleiro
- CSIC/UAB Proteomics Laboratory, IIBB-CSIC, IDIBAPS, Facultad de Medicina, Campus UAB, 08193 Bellaterra, Spain
| | - Vanessa Casas
- CSIC/UAB Proteomics Laboratory, IIBB-CSIC, IDIBAPS, Facultad de Medicina, Campus UAB, 08193 Bellaterra, Spain
| | - Marina Gay
- CSIC/UAB Proteomics Laboratory, IIBB-CSIC, IDIBAPS, Facultad de Medicina, Campus UAB, 08193 Bellaterra, Spain
| | - Joaquin Abian
- CSIC/UAB Proteomics Laboratory, IIBB-CSIC, IDIBAPS, Facultad de Medicina, Campus UAB, 08193 Bellaterra, Spain
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164
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Preisinger C, von Kriegsheim A, Matallanas D, Kolch W. Proteomics and phosphoproteomics for the mapping of cellular signalling networks. Proteomics 2008; 8:4402-15. [DOI: 10.1002/pmic.200800136] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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165
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Schmidt A, Csaszar E, Ammerer G, Mechtler K. Enhanced detection and identification of multiply phosphorylated peptides using TiO2enrichment in combination with MALDI TOF/TOF MS. Proteomics 2008; 8:4577-92. [DOI: 10.1002/pmic.200800279] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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166
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ZHANG Y, LU HJ, YANG PY. Enhanced Ionization of Phosphopeptide Using Ammonium Phosphate as Matrix Additive by MALDI-MS. CHINESE J CHEM 2008. [DOI: 10.1002/cjoc.200890336] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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167
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Abstract
Protein phosphorylation is one of the most important mechanisms of regulating protein function in cells, and it plays an important role in controlling diverse biological processes, including cellular proliferation, migration, and metabolism. The term "phosphoproteome" refers to the complement of proteins that undergoes phosphorylation, the extent of their phosphorylation status at the level of individual residues, as well as the dynamics of the phosphorylation events in response to various stimuli. This unit provides methods for enrichment of phosphorylated proteins and peptides using anti-phosphotyrosine antibodies or titanium dioxide, respectively. Support protocols are provided for two detergent-free cell lysis methods, fractionation of proteins prior to enrichment, and use of stable isotope labeling by amino acids in cell culture (SILAC) method for studying dynamics of phosphorylation events.
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Affiliation(s)
- Jun Zhong
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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168
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Sopko R, Andrews BJ. Linking the kinome and phosphorylome--a comprehensive review of approaches to find kinase targets. MOLECULAR BIOSYSTEMS 2008; 4:920-33. [PMID: 18704230 DOI: 10.1039/b801724g] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Protein phosphorylation is associated with most cell signaling and developmental processes in eukaryotes. Despite the vast extent of the phosphoproteome within the cell, connecting specific kinases with relevant targets remains a significant experimental frontier. The challenge of linking kinases and their substrates reflects the complexity of kinase function. For example, kinases tend to exert their biological effects through supernumerary, redundant phosphorylation, often on multiple protein complex components. Although these types of phosphorylation events are biologically significant, those kinases responsible are often difficult to identify. Recent methods for global analysis of protein phosphorylation promise to substantially accelerate efforts to map the dynamic phosphorylome. Here, we review both conventional methods to identify kinase targets and more comprehensive genomic and proteomic approaches to connect the kinome and phosphorylome.
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Affiliation(s)
- Richelle Sopko
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada
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169
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Abstract
A significant consequence of protein phosphorylation is to alter protein-protein interactions, leading to dynamic regulation of the components of protein complexes that direct many core biological processes. Recent proteomic studies have populated databases with extensive compilations of cellular phosphoproteins and phosphorylation sites and a similarly deep coverage of the subunit compositions and interactions in multiprotein complexes. However, considerably less data are available on the dynamics of phosphorylation, composition of multiprotein complexes or that define their interdependence. We describe a method to identify candidate phosphoprotein complexes by combining phosphoprotein affinity chromatography, separation by size, denaturing gel electrophoresis, protein identification by tandem mass spectrometry, and informatics analysis. Toward developing phosphoproteome profiling, we have isolated native phosphoproteins using a phosphoprotein affinity matrix, Pro-Q Diamond resin (Molecular Probes-Invitrogen). This resin quantitatively retains phosphoproteins and associated proteins from cell extracts. Pro-Q Diamond purification of a yeast whole cell extract followed by 1-D PAGE separation, proteolysis and ESI LC-MS/MS, a method we term PA-GeLC-MS/MS, yielded 108 proteins, a majority of which were known phosphoproteins. To identify proteins that were purified as parts of phosphoprotein complexes, the Pro-Q eluate was separated into two fractions by size, <100 kDa and >100 kDa, before analysis by PAGE and ESI LC-MS/MS and the component proteins queried against databases to identify protein-protein interactions. The <100 kDa fraction was enriched in phosphoproteins indicating the presence of monomeric phosphoproteins. The >100 kDa fraction contained 171 proteins of 20-80 kDa, nearly all of which participate in known protein-protein interactions. Of these 171, few are known phosphoproteins, consistent with their purification by participation in protein complexes. By comparing the results of our phosphoprotein profiling with the informational databases on phosphoproteomics, protein-protein interactions and protein complexes, we have developed an approach to examining the correlation between protein interactions and protein phosphorylation.
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Affiliation(s)
- Kolbrun Kristjansdottir
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA
- Ludwig Center for Metastasis Research, The University of Chicago, Chicago, IL 60637, USA
| | - Donald Wolfgeher
- Ludwig Center for Metastasis Research, The University of Chicago, Chicago, IL 60637, USA
| | - Nick Lucius
- De Paul University, School of Computer Science, Telecommunications and Information Systems, Chicago, IL 60604, USA.
| | - David Sigfredo Angulo
- De Paul University, School of Computer Science, Telecommunications and Information Systems, Chicago, IL 60604, USA.
| | - Stephen J. Kron
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA
- Ludwig Center for Metastasis Research, The University of Chicago, Chicago, IL 60637, USA
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170
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Van den Bergh G, Arckens L. Reducing sample complexity by RP-HPLC: beyond the tip of the protein expression iceberg. Methods Mol Biol 2008; 424:147-56. [PMID: 18369860 DOI: 10.1007/978-1-60327-064-9_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
Abstract
Because the dynamic range of most cell or tissue proteomes is enormous, separation of such complex protein samples by two-dimensional electrophoresis (2-DE) on broad pH gradients often results in the visualization of only the most abundantly expressed proteins. It is, therefore, often beneficial to first subdivide the proteome in smaller, less complex fractions before 2-DE. This enables the analysis of a larger number of proteins. One approach to prefractionate protein samples is by reversed-phase high-performance liquid chromatography (RP-HPLC), separating proteins according to their hydrophobicity. This effectively introduces a third separation dimension, increasing the spatial resolution of the experiment. Here, we will describe a procedure for separating whole protein lysates by RP-HPLC, before their analysis by 2-DE or 2-D difference gel electrophoresis.
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171
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Li Y, Xu X, Qi D, Deng C, Yang P, Zhang X. Novel Fe3O4@TiO2 Core−Shell Microspheres for Selective Enrichment of Phosphopeptides in Phosphoproteome Analysis. J Proteome Res 2008; 7:2526-38. [DOI: 10.1021/pr700582z] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yan Li
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Xiuqing Xu
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Dawei Qi
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Chunhui Deng
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Pengyuan Yang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Xiangmin Zhang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
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172
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Britton DJ, Scott GK, Schilling B, Atsriku C, Held JM, Gibson BW, Benz CC, Baldwin MA. A novel serine phosphorylation site detected in the N-terminal domain of estrogen receptor isolated from human breast cancer cells. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2008; 19:729-740. [PMID: 18367407 PMCID: PMC7456516 DOI: 10.1016/j.jasms.2008.02.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2007] [Revised: 02/19/2008] [Accepted: 02/19/2008] [Indexed: 05/26/2023]
Abstract
Activated estrogen receptor (ERalpha) plays a critical role in breast cancer development and is a major target for drug treatment. Serine phosphorylation within the N-terminal domain (NTD) contributes to ERalpha activation and may also cause drug resistance. Previous biochemical identification of phosphorylated ERalpha residues was limited to protein artificially overexpressed in transfected cell lines. We report mass spectrometric methods that have allowed the identification of a new site within the NTD of ERalpha isolated from cultured human breast cancer cells. Immunoprecipitation, trypsin digestion, and analysis by nano-LC-ESI-MS/MS (Q-STAR, MDS Sciex) and vMALDI-MS(n) (Finnigan LTQ, Thermo-Electron) identified peptides containing 8 of 14 serine residues within the NTD, one being partially phosphorylated Ser-167, known but not previously reported by MS. Chymotrypsin digestion revealed other known sites at Ser-102/104/106 and 118. Tandem methods developed for the peptide containing Ser-118 and the use of hypothesis-driven experiments--i.e., the assumption that an intact phosphopeptide showing no molecular ion might yield fragment ions including loss of phosphoric acid in vMALDI-MS/MS--allowed the identification of a novel site at Ser-154. Quantitation by selected reaction monitoring demonstrated 6-fold and 2.5-fold increases in Ser-154 phosphorylation in estradiol- and EGF-treated cells, respectively, compared to controls, confirmed by immunoblotting with a novel rabbit polyclonal antibody. Thus, the protein isolation and MS strategies described here can facilitate discovery of novel phosphorylation sites within low abundance, clinically important cancer targets like ERalpha, and may thereby contribute to our understanding of the role of phosphorylation in the development of breast cancer.
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Affiliation(s)
- David J Britton
- Buck Institute for Age Research, Novato, California 94945, USA
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173
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Temporini C, Calleri E, Massolini G, Caccialanza G. Integrated analytical strategies for the study of phosphorylation and glycosylation in proteins. MASS SPECTROMETRY REVIEWS 2008; 27:207-236. [PMID: 18335498 DOI: 10.1002/mas.20164] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The post-translational modification (PTM) of proteins is a common biological mechanism for regulating protein localization, function, and turnover. The direct analysis of modifications is required because they are not coded by genes, and thus are not predictable. Different MS-based proteomic strategies are used for the analysis of PTMs, such as phosphorylation and glycosylation, and are composed of a structural simplification step of the protein followed by specific isolation step to extract the classes of modified peptides (also called "sub-proteomes") before mass spectrometry. This specific isolation step is necessary because PTMs occur at a sub-stoichiometric level and signal suppression of the modified fractions in the mass spectrometer occurs in the presence of the more-abundant non-modified counterpart. The request of innovative analytical strategies in PTM studies is the capability to localize the modification sites, give detailed structural information on the modification, and determine the isoform composition with increased selectivity, sensitivity, and throughput. This review focuses on the description of recent integrated analytical systems proposed for the analysis of PTMs in proteins, and their application to profile the glycoproteome and the phosphoproteome in biological samples. Comments on the difficulties and usefulness of the analytical strategies are given.
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Affiliation(s)
- Caterina Temporini
- Department of Pharmaceutical Chemistry, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy.
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174
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Yang W, Steen H, Freeman MR. Proteomic approaches to the analysis of multiprotein signaling complexes. Proteomics 2008; 8:832-51. [PMID: 18297654 DOI: 10.1002/pmic.200700650] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Signal transduction is one of the most active fields in modern biomedical research. Increasing evidence has shown that signaling proteins associate with each other in characteristic ways to form large signaling complexes. These diverse structures operate to boost signaling efficiency, ensure specificity and increase sensitivity of the biochemical circuitry. Traditional methods of protein analysis are inadequate to fully characterize and understand these structures, which are intricate, contain many components and are highly dynamic. Instead, proteomics technologies are currently being applied to investigate the nature and composition of multimeric signaling complexes. This review presents commonly used and potential proteomic methods of analyzing diverse protein complexes along with a discussion and a brief evaluation of alternative approaches. Challenges associated with proteomic analysis of signaling complexes are also discussed.
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Affiliation(s)
- Wei Yang
- The Urological Diseases Research Center, Department of Urology, Children's Hospital Boston, Boston, MA 02115, USA
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175
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Coiras M, Camafeita E, López-Huertas MR, Calvo E, López JA, Alcamí J. Application of proteomics technology for analyzing the interactions between host cells and intracellular infectious agents. Proteomics 2008; 8:852-73. [PMID: 18297655 PMCID: PMC7167661 DOI: 10.1002/pmic.200700664] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Host–pathogen interactions involve protein expression changes within both the host and the pathogen. An understanding of the nature of these interactions provides insight into metabolic processes and critical regulatory events of the host cell as well as into the mechanisms of pathogenesis by infectious microorganisms. Pathogen exposure induces changes in host proteins at many functional levels including cell signaling pathways, protein degradation, cytokines and growth factor production, phagocytosis, apoptosis, and cytoskeletal rearrangement. Since proteins are responsible for the cell biological functions, pathogens have evolved to manipulate the host cell proteome to achieve optimal replication. Intracellular pathogens can also change their proteome to adapt to the host cell and escape from immune surveillance, or can incorporate cellular proteins to invade other cells. Given that the interactions of intracellular infectious agents with host cells are mainly at the protein level, proteomics is the most suitable tool for investigating these interactions. Proteomics is the systematic analysis of proteins, particularly their interactions, modifications, localization and functions, that permits the study of the association between pathogens with their host cells as well as complex interactions such as the host–vector–pathogen interplay. A review on the most relevant proteomic applications used in the study of host–pathogen interactions is presented.
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Affiliation(s)
- Mayte Coiras
- Unidad de Inmunopatología del SIDA, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
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176
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Mirza SP, Olivier M. Methods and approaches for the comprehensive characterization and quantification of cellular proteomes using mass spectrometry. Physiol Genomics 2008; 33:3-11. [PMID: 18162499 PMCID: PMC2771641 DOI: 10.1152/physiolgenomics.00292.2007] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Proteomics has been proposed as one of the key technologies in the postgenomic era. So far, however, the comprehensive analysis of cellular proteomes has been a challenge because of the dynamic nature and complexity of the multitude of proteins in cells and tissues. Various approaches have been established for the analyses of proteins in a cell at a given state, and mass spectrometry (MS) has proven to be an efficient and versatile tool. MS-based proteomics approaches have significantly improved beyond the initial identification of proteins to comprehensive characterization and quantification of proteomes and their posttranslational modifications (PTMs). Despite these advances, there is still ongoing development of new technologies to profile and analyze cellular proteomes more completely and efficiently. In this review, we focus on MS-based techniques, describe basic approaches for MS-based profiling of cellular proteomes and analysis methods to identify proteins in complex mixtures, and discuss the different approaches for quantitative proteome analysis. Finally, we briefly discuss novel developments for the analysis of PTMs. Altered levels of PTM, sometimes in the absence of protein expression changes, are often linked to cellular responses and disease states, and the comprehensive analysis of cellular proteome would not be complete without the identification and quantification of the extent of PTMs of proteins.
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Affiliation(s)
- Shama P Mirza
- National Center for Proteomics Research, Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA. e-mail:
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177
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Abstract
Phosphorylation is one of the most relevant and ubiquitous post-translational modifications. Despite its relevance, the analysis of protein phosphorylation has been revealed as one of the most challenging tasks due to its highly dynamic nature and low stoichiometry. However, the development and introduction of new analytical methods are modifying rapidly and substantially this field. Especially important has been the introduction of more sensitive and specific methods for phosphoprotein and phosphopeptide purification as well as the use of more sensitive and accurate MS-based analytical methods. The integration of both approaches has enabled large-scale phosphoproteome studies to be performed, an unimaginable task few years ago. Additionally, methods originally developed for differential proteomics have been adapted making the study of the highly dynamic nature of protein phosphorylation feasible. This review aims at offering an overview on the most frequently used methods in phosphoprotein and phosphopeptide enrichment as well as on the most recent MS-based analysis strategies. Current strategies for quantitative phosphoproteomics and the study of the dynamics of protein phosphorylation are highlighted.
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Affiliation(s)
- Alberto Paradela
- Departamento de Proteómica, Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Científicas, Madrid, Spain.
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178
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Barnes NY, Shi J, Yajima H, Thinakaran G, Parent AT. Steady-state increase of cAMP-response element binding protein, Rac, and PAK signaling in presenilin-deficient neurons. J Neurochem 2008; 104:1637-48. [PMID: 17996025 PMCID: PMC2598774 DOI: 10.1111/j.1471-4159.2007.05102.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Mutations in the genes encoding presenilins (PS1 and PS2) account for the majority of cases of early-onset Alzheimer's disease. PS1 and PS2 form the catalytic center of gamma-secretase, an enzyme responsible for intramembraneous proteolysis of several type I transmembrane proteins. Many gamma-secretase substrates are coupled to intracellular signaling events such as cAMP-response element binding protein and Rac1/p21-activated kinase pathways, which are associated with synaptic function. Here, we have examined the activation of these pathways in neurons lacking PS1 expression or gamma-secretase activity. We found evidence for heightened steady-state activation of cAMP-response element binding protein, Rac1, and p21-activated kinase signaling in PS-deficient neurons. Our study highlights the importance of PS-dependent proteolytic cleavage of gamma-secretase substrates in regulating neuronal signal transduction.
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Affiliation(s)
- Natalie Y. Barnes
- Department of Neurobiology, University of Chicago, Chicago, Illinois, USA
| | - Jun Shi
- Department of Neurobiology, University of Chicago, Chicago, Illinois, USA
| | - Hiroshi Yajima
- Department of Neurobiology, University of Chicago, Chicago, Illinois, USA
| | - Gopal Thinakaran
- Department of Neurobiology, University of Chicago, Chicago, Illinois, USA
- Department of Neurology, University of Chicago, Chicago, Illinois, USA
| | - Angèle T. Parent
- Department of Neurobiology, University of Chicago, Chicago, Illinois, USA
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179
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Mohammed S, Kraiczek K, Pinkse MWH, Lemeer S, Benschop JJ, Heck AJR. Chip-Based Enrichment and NanoLC−MS/MS Analysis of Phosphopeptides from Whole Lysates. J Proteome Res 2008; 7:1565-71. [DOI: 10.1021/pr700635a] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Shabaz Mohammed
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, and Agilent Technologies R&D and Marketing GmbH & Company KG, Hewlett-Packard-Strasse 8, 76337 Waldbronn, Germany
| | - Karsten Kraiczek
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, and Agilent Technologies R&D and Marketing GmbH & Company KG, Hewlett-Packard-Strasse 8, 76337 Waldbronn, Germany
| | - Martijn W. H. Pinkse
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, and Agilent Technologies R&D and Marketing GmbH & Company KG, Hewlett-Packard-Strasse 8, 76337 Waldbronn, Germany
| | - Simone Lemeer
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, and Agilent Technologies R&D and Marketing GmbH & Company KG, Hewlett-Packard-Strasse 8, 76337 Waldbronn, Germany
| | - Joris J. Benschop
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, and Agilent Technologies R&D and Marketing GmbH & Company KG, Hewlett-Packard-Strasse 8, 76337 Waldbronn, Germany
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, and Agilent Technologies R&D and Marketing GmbH & Company KG, Hewlett-Packard-Strasse 8, 76337 Waldbronn, Germany
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180
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Li Y, Qi D, Deng C, Yang P, Zhang X. Cerium Ion-Chelated Magnetic Silica Microspheres for Enrichment and Direct Determination of Phosphopeptides by Matrix-Assisted Laser Desorption Ionization Mass Spectrometry. J Proteome Res 2008; 7:1767-77. [DOI: 10.1021/pr070385l] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yan Li
- Department of Chemistry & Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Dawei Qi
- Department of Chemistry & Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Chunhui Deng
- Department of Chemistry & Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Pengyuan Yang
- Department of Chemistry & Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Xiangmin Zhang
- Department of Chemistry & Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
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181
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Temporini C, Dolcini L, Abee A, Calleri E, Galliano M, Caccialanza G, Massolini G. Development of an integrated chromatographic system for on-line digestion and characterization of phosphorylated proteins. J Chromatogr A 2008; 1183:65-75. [PMID: 18255078 DOI: 10.1016/j.chroma.2007.12.091] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2007] [Revised: 11/29/2007] [Accepted: 12/31/2007] [Indexed: 10/22/2022]
Abstract
The development of an integrated chromatographic system for complete phosphoprotein analysis is described. The digestion of phosphoproteins with trypsin- or pronase-based monolithic bioreactors is carried out on-line with selective enrichment on a TiO(2) trap and separation of the produced phosphopeptides by reversed-phase liquid chromatography-multiple mass spectrometry (RPLC/MS(n)). A detailed study on the selective extraction of peptides with different degrees of phosphorylation on TiO(2) cartridges is discussed. This analytical strategy has been optimized using beta-casein as a standard phosphoprotein, and then applied to the identification of phosphorylation sites in insulin-like grow factor-binding protein 1 (IGFBP-1) isolated from amniotic fluid.
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Affiliation(s)
- C Temporini
- Dipartimento di Chimica Farmaceutica, Università di Pavia, Via Taramelli 12, Pavia, Italy.
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182
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Sugimoto I, Li Z, Sakamoto Y, Ito S, Hashimoto E. Mass-spectrometric identification of proteins detected in forskolin-stimulated Xenopus laevis oocytes using antibody against phospho-(Ser/Thr) cAMP-dependent protein kinase substrate. ACTA ACUST UNITED AC 2008; 28:231-8. [PMID: 18000335 DOI: 10.2220/biomedres.28.231] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In order to study the phosphorylated proteins in the resting Xenopus laevis oocytes, the proteins detected by Western blotting using phospho-(Ser/Thr) PKA substrate antibody (PKA substrate antibody) in forskolin-stimulated oocytes were purified and identified by mass spectrometry. Several proteins (ribosomal S6 protein, elongation factor-2 (EF-2), poly A binding protein, releasing factor 1) were identified, and the phosphorylation of EF-2 was further studied. Partially purified Xenopus EF-2 (xEF-2) was phosphorylated by PKA in vitro and this phosphorylation was detected by Western blotting using PKA substrate antibody. The phosphorylation of Thr-57 in xEF-2 (corresponding to Thr-56 of the mammalian enzyme) was detected in the partially purified xEF-2 from the resting oocytes, but this xEF-2 did not react with the PKA substrate antibody. These results suggest that Thr-57 in xEF-2 was phosphorylated, but xEF-2 does not seem to be phosphorylated by PKA in resting oocytes although PKA can phosphorylate xEF-2 in vitro and probably in forskolin-treated oocytes.
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Affiliation(s)
- Isamu Sugimoto
- Division of Pathological Biochemistry, Department of Biomedical Sciences, School of Life Sciences, Faculty of Medicine, Tottori University, Nishi-cho, Yonago
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183
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Palumbo AM, Tepe JJ, Reid GE. Mechanistic Insights into the Multistage Gas-Phase Fragmentation Behavior of Phosphoserine- and Phosphothreonine-Containing Peptides. J Proteome Res 2008; 7:771-9. [DOI: 10.1021/pr0705136] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Amanda M. Palumbo
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Jetze J. Tepe
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Gavin E. Reid
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
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184
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Abstract
Immunoprecipitation (IP) uses the specificity of antibodies to isolate target proteins (antigens) out of complex sample mixtures. Three different approaches for performing IP will be discussed; traditional (classical) method, oriented affinity method and direct affinity method. The traditional method of incubating the IP antibody with the sample and sequentially binding to Protein A or G agarose beads (resin) facilitates the most efficient target antigen recovery. However, this approach results in the target protein becoming contaminated with the IP antibody that can interfere with downstream analyses. The orientated affinity method uses Protein A or G beads to serve as an anchor to which the IP antibody is crosslinked thereby preventing the antibody from co-eluting with the target protein. Similarly, the direct affinity method also immobilizes the IP antibody except in this case it is directly attached to a chemically activated support. Both methods prevent co-elution of the IP antibody enabling reuse of the immunomatrix. All three approaches have unique advantages and can also be used for co-immunoprecipitation to study protein:protein interactions and investigate the functional proteome.
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185
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Liu J, Cai Y, Wang J, Zhou Q, Yang B, Lu Z, Jiao L, Zhang D, Sui S, Jiang Y, Ying W, Qian X. Phosphoproteome profile of human liver Chang's cell based on 2-DE with fluorescence staining and MALDI-TOF/TOF-MS. Electrophoresis 2007; 28:4348-58. [DOI: 10.1002/elps.200600696] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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186
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Abstract
Phosphorylation, the most intensively studied and common PTM on proteins, is a complex biological phenomenon. Its complexity manifests itself in the large numbers of proteins that attach it, remove it and recognise it as a protein code. Since the first report of protein phosphorylation on vitellin 100 years ago, a wide variety of biochemical and analytical chemical approaches have been developed to enrich and detect protein phosphorylation. The last 5 years have witnessed a renaissance in methodologies capable of characterising protein phosphorylation on a proteome-scale. These technological advances have allowed identification of hundreds to thousands of phosphorylation sites in a proteome and have resulted in a profound paradigm shift. For the first time, using quantitative MS, the topology and significance of global phosphorylation networks may be investigated, marking a new era of cell signalling research. This review addresses recent technological advances in the purification of phosphorylated proteins and peptides and current MS-based strategies used to qualitatively and quantitatively probe these enriched phosphoproteomes. In addition, we review the application of complementary array-based technologies to derive signalling networks from kinase-substrate interactions and discuss future challenges in the field.
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Affiliation(s)
- Mark O Collins
- Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.
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187
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Abstract
Plasma membrane proteins serve essential functions for cells, interacting with both cellular and extracellular components, structures and signaling molecules. Additionally, plasma membrane proteins comprise more than two-thirds of the known protein targets for existing drugs. Consequently, defining membrane proteomes is crucial to understanding the role of plasma membranes in fundamental biological processes and for finding new targets for action in drug development. MS-based identification methods combined with chromatographic and traditional cell-biology techniques are powerful tools for proteomic mapping of proteins from organelles. However, the separation and identification of plasma membrane proteins remains a challenge for proteomic technology because of their hydrophobicity and microheterogeneity. Creative approaches to solve these problems and potential pitfalls will be discussed. Finally, a representative overview of the impressive achievements in this field will also be given.
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Affiliation(s)
- Djuro Josic
- Department of Medicine, Brown Medical School, Providence, RI, USA.
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188
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Thingholm TE, Jørgensen TJD, Jensen ON, Larsen MR. Highly selective enrichment of phosphorylated peptides using titanium dioxide. Nat Protoc 2007; 1:1929-35. [PMID: 17487178 DOI: 10.1038/nprot.2006.185] [Citation(s) in RCA: 483] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The characterization of phosphorylated proteins is a challenging analytical task since many of the proteins targeted for phosphorylation are low in abundance and phosphorylation is typically substoichiometric. Highly efficient enrichment procedures are therefore required. Here we describe a protocol for selective phosphopeptide enrichment using titanium dioxide (TiO2) chromatography. The selectivity toward phosphopeptides is obtained by loading the sample in a 2,5-dihydroxybenzoic acid (DHB) or phthalic acid solution containing acetonitrile and trifluoroacetic acid (TFA) onto a TiO2 micro-column. Although phosphopeptide enrichment can be achieved by using TFA and acetonitrile alone, the selectivity is dramatically enhanced by adding DHB or phthalic acid since these compounds, in conjunction with the low pH caused by TFA, prevent binding of nonphosphorylated peptides to TiO2. Using an alkaline solution (pH > or = 10.5) both monophosphorylated and multiphosphorylated peptides are eluted from the TiO2 beads. This highly efficient method for purification of phosphopeptides is well suited for the characterization of phosphoproteins from both in vitro and in vivo studies in combination with mass spectrometry (MS). It is a very easy and fast method. The entire protocol requires less than 15 min per sample if the buffers have been prepared in advance (not including lyophilization).
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Affiliation(s)
- Tine E Thingholm
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark
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189
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Nice EC, Rothacker J, Weinstock J, Lim L, Catimel B. Use of multidimensional separation protocols for the purification of trace components in complex biological samples for proteomics analysis. J Chromatogr A 2007; 1168:190-210; discussion 189. [PMID: 17597136 DOI: 10.1016/j.chroma.2007.06.015] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2007] [Revised: 06/06/2007] [Accepted: 06/07/2007] [Indexed: 01/09/2023]
Abstract
The routine detection of low abundance components in complex samples for detailed proteomics analysis continues to be a challenge. Whilst the potential of multidimensional chromatographic fractionation for this purpose has been proposed for some years, and was used effectively for the purification to homogeneity of trace components in bulk biological samples for N-terminal sequence analysis, its practical application in the proteomics arena is still limited. This article reviews some of the recent data using these approaches, including the use of microaffinity purification as part of multidimensional protocols for downstream proteomics analysis.
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Affiliation(s)
- E C Nice
- Protein Biosensing and Epithelial Laboratories, Ludwig Institute for Cancer Research, Melbourne Tumour Biology Branch, P.O. Royal Melbourne Hospital, Parkville, Vic. 3050, Australia.
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190
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Li Y, Leng T, Lin H, Deng C, Xu X, Yao N, Yang P, Zhang X. Preparation of Fe3O4@ZrO2 Core−Shell Microspheres as Affinity Probes for Selective Enrichment and Direct Determination of Phosphopeptides Using Matrix-Assisted Laser Desorption Ionization Mass Spectrometry. J Proteome Res 2007; 6:4498-510. [PMID: 17900103 DOI: 10.1021/pr070167s] [Citation(s) in RCA: 131] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Fe3O4@ZrO2 microspheres with well-defined core-shell structure were prepared and applied for the highly selective enrichment of phosphopeptides from tryptic digest product of proteins. To successfully coat iron oxide microspheres with uniform zirconia shell, magnetic Fe3O4 microspheres were first synthesized via a solvothermal reaction, followed by being coated with a thin layer of carbon by polymerization and carbonization of glucose through hydrothermal reaction. Finally, with the use of the Fe3O4@C microspheres as templates, zirconium isopropoxide was prehydrolyzed and absorbed onto the microspheres and eventually converted into zirconia by calcinations. The as-prepared Fe3O4@ZrO2 core-shell microspheres were used as affinity probes to selectively concentrate phosphopeptides from tryptic digest of beta-casein, casein, and five protein mixtures to exemplify their selective enrichment ability of phosphopeptides from complex protein samples. In only 0.5 min, phosphopeptides sufficient for characterization by MALDI-MS could be enriched by the Fe3O4@ZrO2 microspheres. The results demonstrate that Fe3O4@ZrO2 microspheres have the excellent selective enrichment capacity for phosphopeptides from complex samples. The performance of the Fe3O4@ZrO2 microspheres was further compared with commercial IMAC beads for the enrichment of peptides originating from tryptic digestion of beta-casein and bovine serum albumin (BSA) with a molar ratio of 1:50, and the results proved a stronger selective ability of Fe3O4@ZrO2 microspheres over IMAC beads. Finally, the Fe3O4@ZrO2 microspheres were successfully utilized for enrichment of phosphopeptides from human blood serum without any other purification procedures.
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Affiliation(s)
- Yan Li
- Department of Chemistry and Institute of Biomedical Sciences, Fudan University, Shanghai 200433, China
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191
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Akashi T, Yamori T. A novel method for analyzing phosphoproteins using SELDI-TOF MS in combination with a series of recombinant proteins. Proteomics 2007; 7:2350-4. [PMID: 17570519 DOI: 10.1002/pmic.200700157] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A novel SELDI-TOF MS-based method for analyzing phosphoproteins was developed using a series of recombinant wild-type and mutant ribosomal P2 proteins. We demonstrated that the phosphorylation status of the overexpressed proteins in cells was easily and rapidly confirmed using this method. The ribosomal P2 protein contained two phosphorylation sites, which were sequentially phosphorylated in vivo. We also quantitatively detected the phosphoprotein by using SELDI-TOF MS.
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Affiliation(s)
- Tetsuyuki Akashi
- Division of Molecular Pharmacology, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan
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192
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Zhou H, Tian R, Ye M, Xu S, Feng S, Pan C, Jiang X, Li X, Zou H. Highly specific enrichment of phosphopeptides by zirconium dioxide nanoparticles for phosphoproteome analysis. Electrophoresis 2007; 28:2201-15. [PMID: 17539039 DOI: 10.1002/elps.200600718] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Large-scale characterization of phosphoproteins requires highly specific methods for the purification of phosphopeptides because of the low abundance of phosphoproteins and substoichiometry of phosphorylation. A phosphopeptide enrichment method using ZrO2 nanoparticles is presented. The high specificity of this approach was demonstrated by the isolation of phosphopeptides from the digests of model phosphoproteins. The strong affinity of ZrO2 nanoparticles to phosphopeptides enables the specific enrichment of phosphopeptides from a complex peptide mixture in which the abundance of phosphopeptides is two orders of magnitude lower than that of nonphosphopeptides. Superior selectivity of ZrO2 nanoparticles for the enrichment of phosphorylated peptides than that of conventional immobilized metal affinity chromatography was observed. Femtomole phosphopeptides from digestion products could be enriched by ZrO2 nanoparticles and can be well detected by MALDI mass spectrometric analysis. ZrO2 nanoparticles were further applied to selectively isolate phosphopeptides from the tryptic digestion of mouse liver lysate for phosphoproteome analysis by nanoliter LC MS/MS (nano-LC-MS/MS) and MS/MS/MS. A total of 248 defining phosphorylation sites and 140 phosphorylated peptides were identified by manual validation using a series of rigid criteria.
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Affiliation(s)
- Houjiang Zhou
- National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China
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193
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Yu LR, Issaq HJ, Veenstra TD. Phosphoproteomics for the discovery of kinases as cancer biomarkers and drug targets. Proteomics Clin Appl 2007; 1:1042-57. [DOI: 10.1002/prca.200700102] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2007] [Indexed: 12/31/2022]
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194
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Wang Y, Chen W, Wu J, Guo Y, Xia X. Highly efficient and selective enrichment of phosphopeptides using porous anodic alumina membrane for MALDI-TOF MS analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2007; 18:1387-95. [PMID: 17533135 DOI: 10.1016/j.jasms.2007.04.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2007] [Revised: 04/22/2007] [Accepted: 04/24/2007] [Indexed: 05/15/2023]
Abstract
Because of its good biocompatibility, high surface-to-volume ratio, and distinct surface electrical properties, porous anodic alumina (PAA) membrane has been used to selectively enrich phosphopeptides from a mixture of synthetic peptides and tryptic digest product of beta-casein by a direct MALDI-TOF MS analysis. As we reported previously, PAA membrane has strong incorporation ability to the phosphate anion. Herein, we describe the application of PAA membrane as a selective sampling absorbent for phosphopeptides. The PAA membrane could enrich phosphopeptides with high efficiency and selectivity; for example, the tryptic digest product of beta-casein at a concentration as low as 4 x 10(-9) M can be satisfactorily detected. Compared to that from the nonenriching peptide mixture, the MS signal of the phosphorylated peptides enriched by the PAA membrane is remarkably improved. In addition, acidic peptides have insignificant influence on the enriching process. Results show that the adsorption of phosphate anions on the PAA membrane plays a determining role in achieving highly selective enriching capacity toward phosphopeptides. The feasibility of PAA membranes as specific absorbents for phosphopeptides is also demonstrated.
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Affiliation(s)
- Yuebo Wang
- Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
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195
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Huang SY, Tsai ML, Chen GY, Wu CJ, Chen SH. A Systematic MS-Based Approach for IdentifyinginvitroSubstrates of PKA and PKG in Rat Uteri. J Proteome Res 2007; 6:2674-84. [PMID: 17564427 DOI: 10.1021/pr070134c] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein phosphorylation is an important modulator of many cellular processes, and identification of kinase substrates provides critical insights for signal transduction. However, this identification process is often difficult and many kinase substrates remain unexplored. Herein, a systematic proteomics approach solely depending on MS detection is reported for identifying substrates of PKA and PKG, which are suspected to have similar specificity determinants, in pregnant rat uteri. Instead of radioisotopes that are commonly used to couple with MS for substrate identification, this study developed an efficient in vitro kinase assay on depleted tissue homogenates to reveal substrate candidates directly by MS. To facilitate MS detection, exogenous phosphatases were added to remove intrinsic phosphorylation followed by a heating step to inactivate all enzymes. No observable interference caused by endogenous kinases or background phosphorylation was detected in the control experiment in which no kinase was externally added. A total of 61 and 12 substrate candidates were identified in vitro for PKA and PKG, respectively, and most of these identified sites contain consensus motifs of each kinase with only a few sites overlapped, indicating a good specificity. Moreover, differential phosphoproteomics analysis using stable isotope dimethyl labeling and MS was performed to detect the change of protein phosphorylation upon kinase stimulation in vivo. Four identified in vitro PKA substrates including three reported sites on HSP27 or filamin A were significantly phosphorylated in vivo, giving them high confidence as physiological substrates in pregnant rat uteri. Moreover, telokin, a known PKG substrate on S1880, and actin-binding proteins such as Arp 3, titin, and desmuslin were also identified to be in vitro PKG substrates in pregnant rat uteri. These proteins are all expected to be involved in the regulation of actin-mediated cytoskeletal remodeling.
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Affiliation(s)
- Sheng-Yu Huang
- Department of Chemistry, National Cheng Kung University, No.1, Ta-Hsueh Road, Tainan, 701, Taiwan
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196
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Li X, Kim JW, Grønborg M, Urlaub H, Lane MD, Tang QQ. Role of cdk2 in the sequential phosphorylation/activation of C/EBPbeta during adipocyte differentiation. Proc Natl Acad Sci U S A 2007; 104:11597-602. [PMID: 17601773 PMCID: PMC1913868 DOI: 10.1073/pnas.0703771104] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Upon induction of differentiation, growth-arrested (G(1) phase) 3T3-L1 preadipocytes express CCAAT/enhancer binding protein-beta (C/EBPbeta), initiating a transcriptional cascade. C/EBPbeta immediately undergoes a priming phosphorylation (on Thr(188)) by MAPK/ERK. However, the acquisition of DNA binding and transactivation capacity of C/EBPbeta is delayed until further phosphorylation (on Ser(184) or Thr(179)) by GSK3beta occurs. Phosphorylation by glycogen synthase kinase-3beta (GSK3beta) induces S phase entry and thereby mitotic clonal expansion (MCE), a requirement for terminal differentiation. Because MAPK activity is down-regulated before S phase is completed, we sought to identify the kinase that maintains C/EBPbeta in the primed phosphorylated state throughout S phase and MCE. We show here that cdk2/cyclinA, whose expression is activated at the onset of S phase, functions in this capacity. Ex vivo and in vitro experiments show that cdk2/cyclinA catalyzes this delayed priming phosphorylation. Mass spectrometric analysis revealed that cdk2/cyclinA phosphorylates C/EBPbeta on Thr(188) and is required for phosphorylation (on Ser(184) or Thr(179)) of C/EBPbeta by GSK3beta and maintenance of DNA binding activity. Suppression of cdk2 activity by RNA interference or pharmacologic inhibitor disrupts subsequent events in the differentiation program. Thus, MAPK and cdk2/cyclinA act sequentially to maintain Thr(188) of C/EBPbeta in the primed phosphorylated state during MCE and thereby progression of terminal differentiation.
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Affiliation(s)
- Xi Li
- *Department of Biological Chemistry, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205
- Key Laboratory of Molecular Medicine, Ministry of Education and Institutes of Biomedical Sciences, Shanghai Medical School, Fudan University, Shanghai 200032, People's Republic of China
| | - Jae Woo Kim
- *Department of Biological Chemistry, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205
- Department of Biochemistry and Molecular Biology, Medical Research Center for Chronic Metabolic Disease, Yonsei University College of Medicine, Brain Korea 21 Project for Medical Sciences, Yonsei University, Seoul 120-752, Korea; and
| | - Mads Grønborg
- Department of Neurobiology, Max Planck Institute of Biophysical Chemistry, Am Fassberg 11, 37077 Gottingen, Germany
| | - Henning Urlaub
- Department of Neurobiology, Max Planck Institute of Biophysical Chemistry, Am Fassberg 11, 37077 Gottingen, Germany
| | - M. Daniel Lane
- *Department of Biological Chemistry, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205
- To whom correspondence should be addressed. E-mail:
| | - Qi-Qun Tang
- *Department of Biological Chemistry, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205
- Key Laboratory of Molecular Medicine, Ministry of Education and Institutes of Biomedical Sciences, Shanghai Medical School, Fudan University, Shanghai 200032, People's Republic of China
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197
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Agnetti G, Kane LA, Guarnieri C, Caldarera CM, Van Eyk JE. Proteomic technologies in the study of kinases: novel tools for the investigation of PKC in the heart. Pharmacol Res 2007; 55:511-22. [PMID: 17548206 PMCID: PMC2693016 DOI: 10.1016/j.phrs.2007.04.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2006] [Revised: 02/28/2007] [Accepted: 04/16/2007] [Indexed: 01/18/2023]
Abstract
Recent developments in the field of protein separation allows for the analysis of qualitative and quantitative global protein changes in a particular state of a biological system. Due to the enormous number of proteins potentially present in a cell, sub-fractionation and the enrichment of specific organelles are emerging as a necessary step to allow a more comprehensive representation of the protein content. The proteomic studies demonstrate that a key to understand the mechanisms underlying physiological or pathological phenotypes lies, at least in part, in post-translational modifications (PTMs), including phosphorylation of proteins. Rapid improvements in proteomic characterization of amino acid modifications are further expanding our comprehension of the importance of these mechanisms. The present review will provide an overview of technologies available for the study of a proteome, including tools to assess changes in protein quantity (abundance) as well as in quality (PTM forms). Examples of the recent application of these technologies and strategies in the field of kinase signalling will be provided with particular attention on the role of PKC in the heart. Studies of PKC-mediated phosphorylation of cytoskeletal, myofilament and mitochondrial proteins in the heart have provided great insight into the phenotypes of heart failure, hypertrophy and cardioprotection. Proteomics studies of the mitochondria have provided novel evidences for kinase signalling cascades localized to the mitochondria, some of which are known to involve various isoforms of PKC. Proteomics technologies allow for the identification of the different PTM forms of specific proteins and this information is likely to provide insight into the determinants of morphological as well as metabolic mal-adaptations, both in the heart and other tissues.
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198
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Schumacher JA, Crockett DK, Elenitoba-Johnson KSJ, Lim MS. Evaluation of enrichment techniques for mass spectrometry: identification of tyrosine phosphoproteins in cancer cells. J Mol Diagn 2007; 9:169-77. [PMID: 17384208 PMCID: PMC1867451 DOI: 10.2353/jmoldx.2007.060031] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Phosphorylation of tyrosine residues by protein tyrosine kinases mediates numerous cellular processes. Deregulated tyrosine phosphorylation underlies constitutive activation of signaling pathways leading to oncogenesis. Analytical techniques for evaluation of the global phosphoproteome level are challenging and can be improved on to enhance yields. Here, we evaluated several approaches to enrich for tyrosine phosphoproteins in cancer cells for subsequent liquid chromatography-tandem mass spectrometry analysis using lysates from SU-DHL-1 cells, which express the nucleophosmin-anaplastic lymphoma kinase tyrosine kinase as a model system. Cells were grown in the presence or absence of the phosphatase inhibitor sodium orthovanadate, and tyrosine phosphoproteins were subsequently enriched by immunoprecipitation or immunoaffinity chromatography and protein identification performed by liquid chromatography-tandem mass spectrometry. Our results show that sodium orthovanadate improves enrichment and thus detection of tyrosine phosphoproteins. Immunoprecipitation of tyrosine phosphoproteins using two different antiphosphotyrosine antibodies increased the number of protein identifications. Finally, peptides from proteins enriched by immunoprecipitation were more abundant (n=338) than those enriched by immunoaffinity chromatography (n=138), and relatively few proteins were found in common (n=43). Our data demonstrate the utility of an enrichment strategy for the mass spectrometry-based identification of tyrosine phosphoproteins and show the advantage of complementary techniques for greater protein identification.
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Affiliation(s)
- Jonathan A Schumacher
- Associated Regional and University Pathologists (ARUP), Institute for Clinical and Experimental Pathology, University of Utah, Salt Lake City, Utah, USA
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199
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Affiliation(s)
- Keith D Green
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
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200
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Schmidt SR, Schweikart F, Andersson ME. Current methods for phosphoprotein isolation and enrichment. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 849:154-62. [PMID: 17035107 DOI: 10.1016/j.jchromb.2006.09.016] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2006] [Revised: 08/24/2006] [Accepted: 09/08/2006] [Indexed: 11/30/2022]
Abstract
The phosphorylation of proteins is a central paradigm of signal transduction. The substitution of neutral hydroxyl groups of serine, threonine and tyrosine with a negatively charged phosphate group alters the physicochemical and immunogenic properties of the protein, which then can be used to isolate these isoforms. In the last decades several different techniques were applied, attempting to selectively enrich protein populations with this post-translational modification. This review aims to give an overview on the arsenal of available methods to extract phosphoproteins focusing on chromatographic approaches.
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Affiliation(s)
- Stefan R Schmidt
- Global Protein Science and Supply, AstraZeneca R&D Södertälje, SE-15185 Södertälje, Sweden.
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