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Wu L, He Y, Hu Y, Lu H, Cao Z, Yi X, Wang J. Real-time surface plasmon resonance monitoring of site-specific phosphorylation of p53 protein and its interaction with MDM2 protein. Analyst 2019; 144:6033-6040. [DOI: 10.1039/c9an01121h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Real-time monitoring of site-specific phosphorylation of p53 protein and its binding to MDM2 is conducted using dual-channel surface plasmon resonance (SPR).
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Affiliation(s)
- Ling Wu
- College of Chemistry and Chemical Engineering
- Central South University
- Changsha
- P. R. China 410083
| | - Yuhan He
- College of Chemistry and Chemical Engineering
- Central South University
- Changsha
- P. R. China 410083
| | - Yuqing Hu
- College of Chemistry and Chemical Engineering
- Central South University
- Changsha
- P. R. China 410083
| | - Hanwen Lu
- College of Chemistry and Chemical Engineering
- Central South University
- Changsha
- P. R. China 410083
| | - Zhong Cao
- Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation
- School of Chemistry and Biological Engineering
- Changsha University of Science and Technology
- Changsha
- P. R. China 410114
| | - Xinyao Yi
- College of Chemistry and Chemical Engineering
- Central South University
- Changsha
- P. R. China 410083
| | - Jianxiu Wang
- College of Chemistry and Chemical Engineering
- Central South University
- Changsha
- P. R. China 410083
- Key Laboratory of Hunan Province for Water Environment and Agriculture Product Safety
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Shi C, Deng C. Immobilized metal ion affinity chromatography ZipTip pipette tip with polydopamine modification and Ti 4+ immobilization for selective enrichment and isolation of phosphopeptides. Talanta 2015; 143:464-468. [DOI: 10.1016/j.talanta.2015.05.039] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/14/2015] [Accepted: 05/18/2015] [Indexed: 12/22/2022]
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Heukeshoven J, März A, Warnecke G, Deppert W, Tolstonog GV. Recombinant p53 displays heterogeneity during isoelectric focusing. Electrophoresis 2012; 33:2818-27. [DOI: 10.1002/elps.201200205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Jochen Heukeshoven
- Heinrich-Pette-Institute; Leibniz Institute for Experimental Virology; Hamburg; Germany
| | - Annette März
- Heinrich-Pette-Institute; Leibniz Institute for Experimental Virology; Hamburg; Germany
| | - Gabriele Warnecke
- Heinrich-Pette-Institute; Leibniz Institute for Experimental Virology; Hamburg; Germany
| | - Wolfgang Deppert
- Heinrich-Pette-Institute; Leibniz Institute for Experimental Virology; Hamburg; Germany
| | - Genrich V. Tolstonog
- Heinrich-Pette-Institute; Leibniz Institute for Experimental Virology; Hamburg; Germany
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Shah B, Kozlowski RL, Han J, Borchers CH. Emerging mass spectrometry-based technologies for analyses of chromatin changes: analysis of histones and histone modifications. Methods Mol Biol 2011; 773:259-303. [PMID: 21898261 DOI: 10.1007/978-1-61779-231-1_16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Mass spectrometry (MS) is rapidly becoming an indispensable tool for the analysis of posttranslational modifications (PTMs) of proteins, and particularly histone PTMs that regulate physiological processes. The more traditional bottom-up approach of searching for modifications on peptides rather than intact proteins (top-down) has proven useful for finding phosphorylation, acetylation, and ubiquitination sites. With the use of modern instrumentation and various MS-based techniques, peptides and their PTMs can be characterized in a high-throughput manner while still maintaining high sensitivity and specificity. In complement to bottom-up MS, recent advances in MS technology, such as high-field Fourier transform ion cyclotron resonance (FTICR)-mass spectrometry, have permitted the study of intact proteins and their modifications. On-line and off-line protein separation instruments coupled to FTICR-MS allow the characterization of PTMs previously undetectable with bottom-up approaches. The use of unique fragmentation techniques in FTICR-MS provides a viable option for the study of labile modifications. In this chapter, we provide a detailed description of the analytical tools - mass spectrometry in particular - that are used to characterize modifications on peptides and proteins. We also examine the applicability of these mass spectrometric techniques to the study of PTMs on histones via both the bottom-up and top-down proteomics approaches.
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Affiliation(s)
- Brinda Shah
- Department of Biochemistry and Microbiology, and the University of Victoria - Genome British Columbia Protein Center, University of Victoria, Victoria, BC, Canada
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Gates MB, Tomer KB, Deterding LJ. Comparison of metal and metal oxide media for phosphopeptide enrichment prior to mass spectrometric analyses. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:1649-59. [PMID: 20634090 PMCID: PMC2982680 DOI: 10.1016/j.jasms.2010.06.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2010] [Revised: 06/08/2010] [Accepted: 06/11/2010] [Indexed: 05/15/2023]
Abstract
Several affinity resins consisting of ionic metals or metal oxides were investigated for their phosphopeptide enrichment capabilities with subsequent mass spectrometric analyses. Commercially-available enrichment metal oxide affinity chromatography (MOAC) resins using manufacturer's and/or published protocols were compared and evaluated for the most efficient and selective method that could be implemented as a standard enrichment procedure. From these comparative analyses, using a tryptic digest of casein proteins, it was determined that in our hands, two of the resins out-performed the others based on a variety of criteria, including the number of phosphorylation sites identified during MS analyses, the lower numbers of nonspecifically bound peptides observed, and the limits of detection. Applicability of these enrichment resins to a complex biological mixture was investigated. For this work, a mixture of avian histones was digested, subjected to titanium dioxide phosphopeptide enrichment, and analyzed by mass spectrometry. Eight phosphorylated tryptic peptides were observed following enrichment and subsequent LC/MS/MS analyses. Of note, seven of the eight phosphopeptides were not observed without titanium dioxide enrichment. From these analyses, four sites of phosphorylation were unequivocally determined, two of which have not been reported previously. Four additional phosphopeptides were observed; however, the site of phosphorylation could not be distinguished but was localized to one of two possible amino acids. These methods should aid in the investigation of proteins post-translationally modified with phosphate, especially those present at low concentrations as was demonstrated by successful enrichment at the femtomole level.
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Affiliation(s)
| | | | - Leesa J. Deterding
- Correspondence: Dr. Leesa Deterding, NIH, NIEHS, Laboratory of Structural Biology, Phone: (919)-541-3009, Fax: (919)-541-0220,
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Atha DH, Manne U, Grizzle WE, Wagner PD, Srivastava S, Reipa V. Standards for immunohistochemical imaging: a protein reference device for biomarker quantitation. J Histochem Cytochem 2010; 58:1005-14. [PMID: 20805583 DOI: 10.1369/jhc.2010.956342] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We are developing a reference device to be used in the validation of immunohistochemical imaging of biomarkers by microscopy. The prototype device consists of p53 protein immobilized at various concentrations on a glass slide. The device is designed as a reference control to be used with assays that incorporate commercially available anti-p53 antibodies. p53 protein was characterized by mass spectrometry and covalently immobilized through amide linkage to the (3-aminopropyl)trietoxysilane-modified glass surface. This procedure is reproducible and provides a chemically stable product in high yield. The surface-bound protein was shown to be immunoreactive by its specific interaction with anti-p53 antibody (Ab) and detection by absorbance and fluorescence spectroscopy. Also, comparison was made with microscopic images of Ab-stained tissue samples, known to stain positive for p53. Further development will be required to establish accurate surface protein concentrations in the range required for specific clinical applications.
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Affiliation(s)
- Donald H Atha
- Biochemical Science Division, National Institute of Standards and Technology, Bldg. 227, Room A243, Mail Stop 8311, 100 Bureau Drive, Gaithersburg, MD 20899-8311, USA.
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MALDI/MS Comparison of Fe-NTA Immobilized Metal Affinity Chromatography and Commercially-Available Metal Oxide Affinity Resins for Phosphopeptide Enrichment. ACTA ACUST UNITED AC 2008. [DOI: 10.1007/978-1-4020-8811-7_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
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Hsieh HC, Sheu C, Shi FK, Li DT. Development of a titanium dioxide nanoparticle pipette-tip for the selective enrichment of phosphorylated peptides. J Chromatogr A 2007; 1165:128-35. [PMID: 17714720 DOI: 10.1016/j.chroma.2007.08.012] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2007] [Revised: 08/01/2007] [Accepted: 08/02/2007] [Indexed: 11/29/2022]
Abstract
The selective enrichment of specific proteins or peptides on micropipette tips prior to mass spectrometry analysis, which can minimize non-specific interferences as well as sample loss, has been an important issue in current proteomics field. In this paper, we have developed an easy-to-use phosphopeptide-selective pipette tip in which titanium dioxide nanoparticles were embedded in monolithic structure photopolymerized from ethylene glycol dimethacrylate. The simple and convenient fabrication was feasible in a commercial polypropylene pipette tip. Phosphorylated peptides were isolated from non-phosphopeptides by TiO(2) nanoparticle and eluted by 100 mM ammonium phosphate (pH 8.5), which was compatible with 2,5-dihydroxybenzoic acid (DHB)/1% phosphoric acid matrix and allowed for direct analysis of the elution fraction by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) without the necessity of desalting pretreatment. Tryptic digested alpha-casein and beta-casein spiked into bovine serum albumin (BSA) nonphosphorylated peptides (molar ratio 1:1:10) were used to assess the selectivity of TiO(2) tips. The effect of 50 mM ammonium hydrogencarbonate, pH 8 in 50% acetonitrile used as a wash buffer in reduction of nonspecific bound peptide to TiO(2) tip was dramatic. Almost all non-phosphopeptides were not detected by MALDI-MS analysis. The lowest detectable amount of phosphopeptide was estimated at low femtomole level. The easy-to-use TiO(2)-embeded tips operated in combination with the modified wash and elution conditions enable an efficient phosphopeptide enrichment for mass spectrometric analysis.
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Affiliation(s)
- Hui-Ching Hsieh
- Life Science Business Unit, C SUN MFG. LTD., 7F-9, No. 79, Hsin Tai Wu Rd., Sec. 1, Hsi-Chin, Taipei Hsien, Taiwan
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D'Ambrosio C, Salzano AM, Arena S, Renzone G, Scaloni A. Analytical methodologies for the detection and structural characterization of phosphorylated proteins. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 849:163-80. [PMID: 16891166 DOI: 10.1016/j.jchromb.2006.06.033] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2006] [Accepted: 06/28/2006] [Indexed: 01/12/2023]
Abstract
Phosphorylation of proteins is a frequent post-translational modification affecting a great number of fundamental cellular functions in living organisms. Because of its key role in many biological processes, much effort has been spent over the time on the development of analytical methodologies for characterizing phosphoproteins. In the past decade, mass spectrometry-based techniques have emerged as a viable alternative to more traditional methods of phosphorylation analysis, providing accurate information for a purified protein on the number of the occurring phosphate groups and their exact localization on the polypeptide sequence. This review summarizes the analytical methodologies currently available for the analysis of protein phosphorylation, emphasizing novel mass spectrometry (MS) technologies and dedicated biochemical procedures that have been recently introduced in this field. A formidable armamentarium is now available for selective enrichment, exaustive structural characterization and quantitative determination of the modification degree for phosphopeptides/phosphoproteins. These methodologies are now successfully applied to the global analysis of cellular proteome repertoire according a holistic approach, allowing the quantitative study of phosphoproteomes on a dynamic time-course basis. The enormous complexity of the protein phosphorylation pattern inside the cell and its dynamic modification will grant important challenges to future scientists, contributing significantly to deeper insights into cellular processes and cell regulation.
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Affiliation(s)
- Chiara D'Ambrosio
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, via Argine 1085, 80147 Naples, Italy
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Hunzinger C, Schrattenholz A, Poznanović S, Schwall GP, Stegmann W. Comparison of different separation technologies for proteome analyses: Isoform resolution as a prerequisite for the definition of protein biomarkers on the level of posttranslational modifications. J Chromatogr A 2006; 1123:170-81. [PMID: 16822517 DOI: 10.1016/j.chroma.2006.06.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2005] [Revised: 05/10/2006] [Accepted: 06/01/2006] [Indexed: 11/29/2022]
Abstract
In this article we evaluate methods used to reveal the molecular complexity, which is generated in biological samples by posttranslational modifications (PTM) of proteins. We show how distinct molecular differences on the level of phosphorylation sites in a single protein (ovalbumin) can be resolved with different success using 1D and 2D gel-electrophoresis and reversed-phase liquid chromatography (LC) with monolithic polystyrol-divinylbenzol (PS-DVB) columns for protein separation, and matrix-assisted laser desorption ionisation-time of flight mass spectrometry (MALDI-TOF MS) for protein identification. Phosphorylation site analysis was performed using enzymatic dephosphorylation in combination with differential peptide mass mapping. Liquid chromatography-MALDI-TOF MS coupling with subsequent on-target tryptic protein digestion turned out to be the fastest method tested but yielded low resolution for the analysis of PTM, whereas 2D gel-electrophoresis, due to its unique capability of resolving highly complex isoform pattern, turned out to be the most suitable method for this purpose. The evaluated methods complement one another and in connection with efficient technologies for differential and quantitative analysis, these approaches have the potential to reveal novel molecular details of protein biomarkers.
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Wagner V, Gessner G, Heiland I, Kaminski M, Hawat S, Scheffler K, Mittag M. Analysis of the phosphoproteome of Chlamydomonas reinhardtii provides new insights into various cellular pathways. EUKARYOTIC CELL 2006; 5:457-68. [PMID: 16524901 PMCID: PMC1398068 DOI: 10.1128/ec.5.3.457-468.2006] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The unicellular flagellated green alga Chlamydomonas reinhardtii has emerged as a model organism for the study of a variety of cellular processes. Posttranslational control via protein phosphorylation plays a key role in signal transduction, regulation of gene expression, and control of metabolism. Thus, analysis of the phosphoproteome of C. reinhardtii can significantly enhance our understanding of various regulatory pathways. In this study, we have grown C. reinhardtii cultures in the presence of an inhibitor of Ser/Thr phosphatases to increase the phosphoprotein pool. Phosphopeptides from these cells were enriched by immobilized metal-ion affinity chromatography and analyzed by nano-liquid chromatography-electrospray ionization-mass spectrometry (MS) with MS-MS as well as neutral-loss-triggered MS-MS-MS spectra. In this way, we were able to identify 360 phosphopeptides from 328 different phosphoproteins of C. reinhardtii, thus providing new insights into a variety of cellular processes, including metabolic and signaling pathways. Comparative analysis of the phosphoproteome also yielded new functional information on proteins controlled by redox regulation (thioredoxin target proteins) and proteins of the chloroplast 70S ribosome, the centriole, and especially the flagella, for which 32 phosphoproteins were identified. The high yield of phosphoproteins of the latter correlates well with the presence of several flagellar kinases and indicates that phosphorylation/dephosphorylation represents one of the key regulatory mechanisms of eukaryotic cilia. Our data also provide new insights into certain cilium-related mammalian diseases.
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Affiliation(s)
- Volker Wagner
- Institut für Allgemeine Botanik, Friedrich-Schiller-Universität Jena, Am Planetarium 1, 07743 Jena, Germany
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Barnouin KN, Hart SR, Thompson AJ, Okuyama M, Waterfield M, Cramer R. Enhanced phosphopeptide isolation by Fe(III)-IMAC using 1,1,1,3,3,3-hexafluoroisopropanol. Proteomics 2006; 5:4376-88. [PMID: 16294313 DOI: 10.1002/pmic.200401323] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
IMAC can be used to selectively enrich phosphopeptides from complex peptide mixtures, but co-retention of acidic peptides together with the failure to retain some phosphopeptides restricts the general utility of the method. In this study Fe(III)-IMAC was qualitatively and quantitatively assessed using a panel of phosphopeptides, both synthetic and derived from proteolysis of known phosphoproteins, to identify the causes of success and failure in the application of this technique. Here we demonstrate that, as expected, peptides with a more acidic amino acid content are generally more efficiently purified and detected by MALDI-MS after Fe(III)-IMAC than those with a more basic content. Modulating the loading buffer used for Fe(III)-IMAC significantly affects phosphopeptide binding and suggests that conformational factors that lead to steric hindrance and reduced accessibility to the phosphate are important. The use of 1,1,1,3,3,3-hexafluoroisopropanol is shown here to significantly improve Fe(III)-IMAC enrichment and subsequent detection of phosphopeptides by MALDI-MS.
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Affiliation(s)
- Karin N Barnouin
- The Ludwig Institute for Cancer Research, Proteomics Unit, UCL branch, London, UK.
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Fogal V, Hsieh JK, Royer C, Zhong S, Lu X. Cell cycle-dependent nuclear retention of p53 by E2F1 requires phosphorylation of p53 at Ser315. EMBO J 2005; 24:2768-82. [PMID: 16037820 PMCID: PMC1182237 DOI: 10.1038/sj.emboj.7600735] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2004] [Accepted: 06/08/2005] [Indexed: 11/08/2022] Open
Abstract
We show here that the cell cycle-dependent DNA-binding and transcriptional activity of p53 correlates with E2F expression in human primary fibroblasts. E2F1 binds and stimulates DNA-binding, transactivation and apoptotic functions of p53 but not p63 and p73. E2F1 binds residues 347-370 of p53 and enhances nuclear retention of Ser315 phosphorylated p53. This regulation of p53 by E2F1 is cell cycle dependent, as the cellular distribution of Ser315 phosphorylated p53 is associated with the periodic expression of E2F and cyclin A throughout the cell cycle. This is the first demonstration that the activities of p53 are regulated during the cell cycle by E2F/p53 interactions and that phosphorylation of p53 at Ser315 is required for this regulation.
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Affiliation(s)
- Valentina Fogal
- Ludwig Institute for Cancer Research, University College London Branch, London, UK
| | - Jung-Kuang Hsieh
- Ludwig Institute for Cancer Research, University College London Branch, London, UK
| | - Christophe Royer
- Ludwig Institute for Cancer Research, University College London Branch, London, UK
| | - Shan Zhong
- Ludwig Institute for Cancer Research, University College London Branch, London, UK
| | - Xin Lu
- Ludwig Institute for Cancer Research, University College London Branch, London, UK
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Dreyfus DH, Nagasawa M, Gelfand EW, Ghoda LY. Modulation of p53 activity by IkappaBalpha: evidence suggesting a common phylogeny between NF-kappaB and p53 transcription factors. BMC Immunol 2005; 6:12. [PMID: 15969767 PMCID: PMC1184076 DOI: 10.1186/1471-2172-6-12] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2004] [Accepted: 06/21/2005] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In this work we present evidence that the p53 tumor suppressor protein and NF-kappaB transcription factors could be related through common descent from a family of ancestral transcription factors regulating cellular proliferation and apoptosis. P53 is a homotetrameric transcription factor known to interact with the ankyrin protein 53BP2 (a fragment of the ASPP2 protein). NF-kappaB is also regulated by ankyrin proteins, the prototype of which is the IkappaB family. The DNA binding sequences of the two transcription factors are similar, sharing 8 out of 10 nucleotides. Interactions between the two proteins, both direct and indirect, have been noted previously and the two proteins play central roles in the control of proliferation and apoptosis. RESULTS Using previously published structure data, we noted a significant degree of structural alignment between p53 and NF-kappaB p65. We also determined that IkappaBalpha and p53 bind in vitro through a specific interaction in part involving the DNA binding region of p53, or a region proximal to it, and the amino terminus of IkappaBalpha independently or cooperatively with the ankyrin 3 domain of IkappaBalpha In cotransfection experiments, kappaBalpha could significantly inhibit the transcriptional activity of p53. Inhibition of p53-mediated transcription was increased by deletion of the ankyrin 2, 4, or 5 domains of IkappaBalpha Co-precipitation experiments using the stably transfected ankyrin 5 deletion mutant of kappaBalpha and endogenous wild-type p53 further support the hypothesis that p53 and IkappaBalpha can physically interact in vivo. CONCLUSION The aggregate results obtained using bacterially produced IkappaBalpha and p53 as well as reticulocyte lysate produced proteins suggest a correlation between in vitro co-precipitation in at least one of the systems and in vivo p53 inhibitory activity. These observations argue for a mechanism involving direct binding of IkappaBalpha to p53 in the inhibition of p53 transcriptional activity, analogous to the inhibition of NF-kappaB by kappaBalpha and p53 by 53BP2/ASPP2. These data furthermore suggest a role for ankyrin proteins in the regulation of p53 activity. Taken together, the NFkappaB and p53 proteins share similarities in structure, DNA binding sites and binding and regulation by ankyrin proteins in support of our hypothesis that the two proteins share common descent from an ancestral transcriptional factor.
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Affiliation(s)
- David H Dreyfus
- Division of Basic Sciences, Department of Pediatrics, National Jewish Medical Research Center, Denver, CO 80262 USA
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - Masayuki Nagasawa
- Division of Basic Sciences, Department of Pediatrics, National Jewish Medical Research Center, Denver, CO 80262 USA
- Departments of Pediatrics and Developmental Biology, Postgraduate School, Tokyo Medical and Dental University, Tokyo, Japan
| | - Erwin W Gelfand
- Division of Basic Sciences, Department of Pediatrics, National Jewish Medical Research Center, Denver, CO 80262 USA
| | - Lucy Y Ghoda
- The Webb-Waring Institute for Cancer, Aging, and Antioxidant Research and the Department of Medicine, the University of Colorado at Denver and Health Sciences Center, Denver CO 80262 USA; To whom correspondence should be addressed at The Webb-Waring Institute, UCDHSC, Box C321, 4200 East Ninth Ave., Denver, CO 80262 USA
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Barrier M, Mirkes PE. Proteomics in developmental toxicology. Reprod Toxicol 2005; 19:291-304. [PMID: 15686865 DOI: 10.1016/j.reprotox.2004.09.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2004] [Revised: 07/26/2004] [Accepted: 09/03/2004] [Indexed: 10/26/2022]
Abstract
The objective of this presentation is to review the major proteomic technologies available to developmental toxicologists and, when possible, to provide examples of how various proteomic technologies have been used in developmental toxicology or toxicology in general. The field of proteomics is too broad for us to go into great depth about each technology, so we have attempted to provide brief overviews supplemented with many references that cover the subjects in more detail. Proteomics tools produce a global view of complex biological systems by examining complex protein mixtures using large-scale, high-throughput technologies. These technologies speed up the process of protein separation, quantification, and identification. As an important complement to genomics, proteomics allows for the examination of the entire complement of proteins in an organism, tissue, or cell-type. Current proteomics technologies not only identify protein expression, but also post-translational modifications and protein interactions. The field of proteomics is expanding rapidly to provide greater volume and quality of protein information to help understand the multifaceted nature of biological systems.
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Affiliation(s)
- Marianne Barrier
- Birth Defects Research Laboratory, Division of Genetics and Developmental Medicine, Department of Pediatrics, University of Washington, Box 356320, 1959 NE Pacific Street, Seattle, WA 98195, USA
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Vaghefi H, Neet KE. Deacetylation of p53 after nerve growth factor treatment in PC12 cells as a post-translational modification mechanism of neurotrophin-induced tumor suppressor activation. Oncogene 2004; 23:8078-87. [PMID: 15361854 DOI: 10.1038/sj.onc.1207953] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The tumor suppressor protein p53 is a transcription factor that regulates the response to cellular insults such as DNA damage and growth factor withdrawal. Transcriptional activity of p53 requires post-translational modification by phosphorylation and acetylation. This study used site-specific antibodies to demonstrate that nerve growth factor (NGF) treatment of PC12 cells results in p53 deacetylation at lysine (Lys) 382. Histone deacetylase (HDAC) activity, measured by a direct fluorescent assay, was increased after NGF treatment and peaked before p53 deacetylation. Inhibition of HDAC by trichostatin blocked the deacetylation of p53 and its transcriptional activity toward a reporter gene construct. Comparison of PC12 with PC12 cells containing a temperature-sensitive, dominant-negative construct showed that p53 deacetylation required functional p53. Inhibitors of MAP kinase that block p53 transactivation and inhibitors of TrkA receptor also abolished HDAC activation, indicating that deacetylation of p53 is an NGF-dependent post-translational mechanism of p53 activation. Finally, NGF or serum withdrawal did not lead to p53 deacetylation. A model is proposed in which the acetylation status of Lys 382 of p53 discriminates between cell cycle arrest and apoptosis.
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Affiliation(s)
- Houman Vaghefi
- Department of Biochemistry and Molecular Biology, Rosalind Franklin University of Medicine and Science (formerly Finch University of Health Sciences), The Chicago Medical School, 3333 Green Bay Rd., North Chicago, IL 60064, USA
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Veenstra TD. Proteome analysis of posttranslational modifications. ADVANCES IN PROTEIN CHEMISTRY 2004; 65:161-94. [PMID: 12964369 DOI: 10.1016/s0065-3233(03)01019-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Affiliation(s)
- Timothy D Veenstra
- SAIC-Frederick Inc., National Cancer Institute at Frederick, Frederick, Maryland 21702, USA
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Vaghefi H, Hughes AL, Neet KE. Nerve growth factor withdrawal-mediated apoptosis in naive and differentiated PC12 cells through p53/caspase-3-dependent and -independent pathways. J Biol Chem 2004; 279:15604-14. [PMID: 14739302 DOI: 10.1074/jbc.m311500200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Programmed cell death is regulated in response to a variety of stimuli, including the tumor suppressor protein p53, that can mediate cell cycle arrest through p21/Waf1 and apoptosis through the Bcl-2/Bax equilibrium and caspases. Neuronal cell apoptosis has been reported to require p53, whereas other data suggest that neuronal cell death may be independent of p53. Comparison of wild type PC12 to a temperature-sensitive PC12 cell line that depresses the normal function of p53 has permitted investigation of the importance of p53 in a variety of cell functions. This study examined the role of p53 in trophic factor withdrawal-mediated apoptosis in both naïve and differentiated PC12 cells. Our data show that as PC12 cells differentiate they are more poised to undergo apoptosis than their undifferentiated counterparts. Survival assays with XTT (sodium 3'-1-(phenylaminocarbonyl)-3,4-tetrazolium-bis(4-methoxy-6-nitro)benzene sulfonic acid) and TUNEL (terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling) demonstrated that lack of p53 is initially protective against apoptosis. The window of protection is about 20 h for naïve and 36 h for differentiated cells. Apoptosis involved caspases 3, 6, and 9. However, caspase 3 activation was absent in cells lacking p53, concomitant with the delayed apoptosis. When the expression of caspase 3 was silenced with interference RNA, wild type PC12 cells revealed a morphology and biochemistry similar to PC12[p53ts] cells, indicating that caspase 3 accounts for the observed delay in apoptosis in p53 dysfunction. These results suggest that p53 is important, but not essential, in factor withdrawal-mediated apoptosis. Parallel pathways of caspase-mediated apoptosis are activated later in the absence of functional p53.
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Affiliation(s)
- Houman Vaghefi
- Department of Biochemistry and Molecular Biology, The Rosalind Franklin University of Medicine and Science, The Chicago Medical School, North Chicago, Illinois 60064, USA.
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Bruno ME, Borchers CH, Dial JM, Walker NJ, Hartis JE, Wetmore BA, Carl Barrett JC, Tomer KB, Merrick BA. Effects of TCDD upon IkappaB and IKK subunits localized in microsomes by proteomics. Arch Biochem Biophys 2002; 406:153-64. [PMID: 12361703 DOI: 10.1016/s0003-9861(02)00452-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Biochemical studies have shown that microsomes represent an important subcellular fraction for determining 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) effects. Proteomic analysis by two-dimensional gel-mass spectrometry of liver microsomes was undertaken to gain new insight into the actions of TCDD in male and female rats. Proteomic analysis showed TCDD induced several xenobiotic metabolism enzymes as well as a protein at 90kDa identified by mass spectrometry as IkappaB kinase beta/IKK2. This observation led to the discovery of other NF-kappaB binding proteins and kinases in microsomes and effects by TCDD. Western blotting for IKK and IkappaB family members in microsomes showed a distinct pattern from cytosol. IKK1 and IKK2 were both present in microsomes and were catalytically active although, unlike cytosol, IKKgamma/NEMO was not detectable. TCDD exposure produced an elevation in cytosolic and microsomal IKK activity of both genders. The NF-kappaB binding proteins IkappaBbeta and IkappaBgamma were prevalent in microsomes, while IkappaBalpha and IkappaB epsilon proteins were absent. TCDD treatment produced hyperphosphorylation of microsomal IkappaBbeta in both sexes with females being most sensitive. In cytosol, IkappaBalpha, IkappaBbeta, and IkappaB epsilon, but not IkappaBgamma, were clearly observed but were not changed by TCDD. Overall, proteomic analysis indicated the presence of NF-kappaB pathway members in microsomes, selectively altered by dioxin, which may influence immune and inflammatory responses within the liver.
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Affiliation(s)
- Maribel E Bruno
- Proteomics Group, National Center for Toxicogenomics, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
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Abstract
Centrosome duplication is under precise control and occurs only once in a normal mammalian cell cycle. Disruption of this process causes centrosome amplification, unequal segregation of chromosomes and, ultimately, tumorigenesis. Recent studies indicate that breast cancer suppressor gene 1 (BRCA1) plays an important role in regulating centrosome duplication. BRCA1 is located in the centrosome and binds to gamma-tubulin. It interacts with a variety of proteins that regulate centrosome duplication, including BRCA2, CDK2-Cyclin A, CDK2-Cyclin E, Gadd45, p21, p53 and Rb. Furthermore, targeted disruption of murine BRCA1 results in centrosome amplification, suggesting that BRCA1 serves as a negative regulator for centrosome duplication. This review will examine these data and discuss possible relationships between BRCA1 and its interacting proteins in centrosome duplication.
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Affiliation(s)
- Chu-Xia Deng
- Genetics of Development and Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 10/9N105, 10 Center Drive, Bethesda, Maryland, MD 20892, USA.
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Rusconi F, Guillonneau F, Praseuth D. Contributions of mass spectrometry in the study of nucleic acid-binding proteins and of nucleic acid-protein interactions. MASS SPECTROMETRY REVIEWS 2002; 21:305-348. [PMID: 12645088 DOI: 10.1002/mas.10036] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Nucleic-acid-protein (NA-P) interactions play essential roles in a variety of biological processes-gene expression regulation, DNA repair, chromatin structure regulation, transcription regulation, RNA processing, and translation-to cite only a few. Such biological processes involve a broad spectrum of NA-P interactions as well as protein-protein (P-P) interactions. These interactions are dynamic, in terms of the chemical composition of the complexes involved and in terms of their mere existence, which may be restricted to a given cell-cycle phase. In this review, the contributions of mass spectrometry (MS) to the deciphering of these intricate networked interactions are described along with the numerous applications in which it has proven useful. Such applications include, for example, the identification of the partners involved in NA-P or P-P complexes, the identification of post-translational modifications that (may) regulate such complexes' activities, or even the precise molecular mapping of the interaction sites in the NA-P complex. From a biological standpoint, we felt that it was worth the reader's time to be as informative as possible about the functional significance of the analytical methods reviewed herein. From a technical standpoint, because mass spectrometry without proper sample preparation would serve no purpose, each application described in this review is detailed by duly emphasizing the sample preparation-whenever this step is considered innovative-that led to significant analytical achievements.
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Affiliation(s)
- Filippo Rusconi
- UMR CNRS 8646, U INSERM 565, USM MNHN 0503-43, rue Cuvier, F-75231, Paris Cedex 05, France
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Abstract
Cyclin dependent kinase 5 (Cdk5) is a proline-direct protein kinase that is most active in the CNS, and has been implicated as a contributing factor in certain neurodegenerative diseases. Further, there is evidence to suggest that Cdk5 may facilitate the progression of apoptosis. However, the mechanisms involved have not been elucidated. The tumor suppressor protein p53, a transcription factor that is regulated by phosphorylation, increases the expression of genes that control growth arrest or cell death. To understand how Cdk5 could facilitate apoptosis, the effects of Cdk5 on p53 activity were examined. In the present study it is shown that in apoptotic PC12 cells the levels of p53 and Cdk5 increase concomitantly. Further, Cdk5/p25 effectively phosphorylates recombinant p53 in vitro. Transient transfection of Cdk5/p25 into cells results in an increase in p53 levels, as well as the expression of the p53-responsive genes p21 and Bax. Furthermore, evidence is provided that increased Cdk5 activity increases p53 transcriptional activity significantly, suggesting that p53 is modulated in situ by Cdk5. This is the first demonstration that p53 is a substrate of Cdk5, and that Cdk5 can modulate p53 levels and activity.
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Affiliation(s)
- Jianwen Zhang
- Department of Psychiatry and Neurobiology, University of Alabama at Birmingham, 35294-0017, USA
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Affiliation(s)
- Yehia Mechref
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
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Abstract
Phosphorylation on serine, threonine and tyrosine residues is an extremely important modulator of protein function. Therefore, there is a great need for methods capable of accurately elucidating sites of phosphorylation. Although full characterization of phosphoproteins remains a formidable analytical challenge, mass spectrometry has emerged as an increasingly viable tool for this task. This review summarizes the methodologies currently available for the analysis of phosphoproteins by mass spectrometry, including enrichment of compounds of interest using immobilized metal affinity chromatography and chemical tagging techniques, detection of phosphopeptides using mass mapping and precursor ion scans, localization of phosphorylation sites by peptide sequencing, and quantitation of phosphorylation by the introduction of mass tags. Despite the variety of powerful analytical methods that are now available, complete characterization of the phosphorylation state of a protein isolated in small quantities from a biological sample remains far from routine.
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Affiliation(s)
- D T McLachlin
- The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.
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Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2001; 36:838-848. [PMID: 11473409 DOI: 10.1002/jms.94] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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