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Thawornpan P, Thanapongpichat S, Tun AW, Phongdara A, de Jong L, Buncherd H. Fly-ash as a low-cost material for isolation of phosphoproteins. CHEMOSPHERE 2018; 213:124-132. [PMID: 30216812 DOI: 10.1016/j.chemosphere.2018.08.150] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 08/27/2018] [Accepted: 08/29/2018] [Indexed: 06/08/2023]
Abstract
Metal oxide affinity chromatography (MOAC) is one of the most commonly used techniques for selective isolation phosphoproteins and phosphopeptides. This technique is capable of capturing the phosphorylated biomolecules through the affinity of the phosphoryl group for metal oxides/hydroxides. Fly-ash (FA), a by-product of coal-combustion power plants, is primarily composed of oxides of silicon and metals, among which iron and titanium. A number of studies have demonstrated the potential of these metal oxides for phosphoprotein and phosphopeptide enrichment. FA is annually produced over hundred million tons worldwide and generally considered as hazardous waste. It is thus of great importance to enhance its utilization. Here we present the first demonstration of the utility of FA as a low-cost MOAC material for the enrichment of phosphoproteins. With an FA-microcolumn, phosphoproteins can be successfully sequestered from other proteins. FA-microcolumns are shown to be simple, cheap and selective devices for phosphoprotein enrichment from a small volume of mixtures.
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Affiliation(s)
- Pongsakorn Thawornpan
- Department of Molecular Biotechnology and Bioinformatics, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | | | - Aung Win Tun
- Faculty of Graduate Studies, Mahidol University, Thailand
| | - Amornrat Phongdara
- Faculty of Medical Technology, Prince of Songkla University, Songkhla, Thailand; Center for Genomics and Bioinformatics Research, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Luitzen de Jong
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1090 GE Amsterdam, the Netherlands
| | - Hansuk Buncherd
- Faculty of Medical Technology, Prince of Songkla University, Songkhla, Thailand.
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Komulainen E, Zdrojewska J, Freemantle E, Mohammad H, Kulesskaya N, Deshpande P, Marchisella F, Mysore R, Hollos P, Michelsen KA, Mågard M, Rauvala H, James P, Coffey ET. JNK1 controls dendritic field size in L2/3 and L5 of the motor cortex, constrains soma size, and influences fine motor coordination. Front Cell Neurosci 2014; 8:272. [PMID: 25309320 PMCID: PMC4162472 DOI: 10.3389/fncel.2014.00272] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 08/20/2014] [Indexed: 11/23/2022] Open
Abstract
Genetic anomalies on the JNK pathway confer susceptibility to autism spectrum disorders, schizophrenia, and intellectual disability. The mechanism whereby a gain or loss of function in JNK signaling predisposes to these prevalent dendrite disorders, with associated motor dysfunction, remains unclear. Here we find that JNK1 regulates the dendritic field of L2/3 and L5 pyramidal neurons of the mouse motor cortex (M1), the main excitatory pathway controlling voluntary movement. In Jnk1-/- mice, basal dendrite branching of L5 pyramidal neurons is increased in M1, as is cell soma size, whereas in L2/3, dendritic arborization is decreased. We show that JNK1 phosphorylates rat HMW-MAP2 on T1619, T1622, and T1625 (Uniprot P15146) corresponding to mouse T1617, T1620, T1623, to create a binding motif, that is critical for MAP2 interaction with and stabilization of microtubules, and dendrite growth control. Targeted expression in M1 of GFP-HMW-MAP2 that is pseudo-phosphorylated on T1619, T1622, and T1625 increases dendrite complexity in L2/3 indicating that JNK1 phosphorylation of HMW-MAP2 regulates the dendritic field. Consistent with the morphological changes observed in L2/3 and L5, Jnk1-/- mice exhibit deficits in limb placement and motor coordination, while stride length is reduced in older animals. In summary, JNK1 phosphorylates HMW-MAP2 to increase its stabilization of microtubules while at the same time controlling dendritic fields in the main excitatory pathway of M1. Moreover, JNK1 contributes to normal functioning of fine motor coordination. We report for the first time, a quantitative Sholl analysis of dendrite architecture, and of motor behavior in Jnk1-/- mice. Our results illustrate the molecular and behavioral consequences of interrupted JNK1 signaling and provide new ground for mechanistic understanding of those prevalent neuropyschiatric disorders where genetic disruption of the JNK pathway is central.
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Affiliation(s)
- Emilia Komulainen
- Turku Centre for Biotechnology, Åbo Akademi University and University of Turku Turku, Finland
| | - Justyna Zdrojewska
- Turku Centre for Biotechnology, Åbo Akademi University and University of Turku Turku, Finland
| | - Erika Freemantle
- Turku Centre for Biotechnology, Åbo Akademi University and University of Turku Turku, Finland
| | - Hasan Mohammad
- Turku Centre for Biotechnology, Åbo Akademi University and University of Turku Turku, Finland
| | | | - Prasannakumar Deshpande
- Turku Centre for Biotechnology, Åbo Akademi University and University of Turku Turku, Finland
| | - Francesca Marchisella
- Turku Centre for Biotechnology, Åbo Akademi University and University of Turku Turku, Finland
| | - Raghavendra Mysore
- Turku Centre for Biotechnology, Åbo Akademi University and University of Turku Turku, Finland
| | - Patrik Hollos
- Turku Centre for Biotechnology, Åbo Akademi University and University of Turku Turku, Finland
| | | | - Mats Mågard
- Institute for Immune Technology, Medicon Village, University of Lund Lund, Sweden
| | - Heikki Rauvala
- Neuroscience Center, University of Helsinki Helsinki, Finland
| | - Peter James
- Institute for Immune Technology, Medicon Village, University of Lund Lund, Sweden
| | - Eleanor T Coffey
- Turku Centre for Biotechnology, Åbo Akademi University and University of Turku Turku, Finland
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Huang J, Qin H, Dong J, Song C, Bian Y, Dong M, Cheng K, Wang F, Sun D, Wang L, Ye M, Zou H. In situ sample processing approach (iSPA) for comprehensive quantitative phosphoproteome analysis. J Proteome Res 2014; 13:3896-904. [PMID: 25072903 DOI: 10.1021/pr500454g] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Current sample preparation protocols for quantitative phosphoproteome analysis are tedious and time-consuming. Here, a facile in situ sample processing approach (iSPA) is developed by using macroporous Ti(IV)-IMAC microspheres as the preparation "beds", where all sample preparation procedures including the enrichment of phosphoproteins, tryptic digestion of proteins, enrichment, and isotope labeling of phosphopeptides are performed in situ sequentially. As a result of the in situ processing design and the seamless procedures, extra steps for desalting and buffer exchanging, which are always required in conventional approaches, are avoided, and the sample loss and contamination could be greatly reduced. Thus, better sensitivity and accuracy for the quantitative phosphoproteome analysis were obtained. This strategy was further applied to differential phosphoproteome analysis of human liver tissues with or without hepatocellular carcinoma (HCC). In total, 8548 phosphorylation sites were confidently quantified from three replicate analyses of 0.5 mg of human liver protein extracts.
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Affiliation(s)
- Junfeng Huang
- CAS Key Lab of Separation Sciences for Analytical Chemistry National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023, China
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Sample preparation and analytical strategies for large-scale phosphoproteomics experiments. Semin Cell Dev Biol 2012; 23:843-53. [DOI: 10.1016/j.semcdb.2012.05.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2012] [Accepted: 05/29/2012] [Indexed: 12/28/2022]
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Artemenko KA, Bergström Lind S, Elfineh L, Mayrhofer C, Zubarev RA, Bergquist J, Pettersson U. Optimization of immunoaffinity enrichment and detection: toward a comprehensive characterization of the phosphotyrosine proteome of K562 cells by liquid chromatography-mass spectrometry. Analyst 2011; 136:1971-8. [PMID: 21403953 DOI: 10.1039/c0an00649a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Phosphorylation of protein tyrosine residues regulates many cell functions and has also been proved to be involved in oncogenesis. Thus, the identification of the phosphotyrosine (pTyr) proteome of cells is a very important task. Since tyrosine phosphorylation represents only around 1% of the total human phosphoproteome, the study of pTyr proteins is rather challenging. Here we report the optimization study of the phosphotyrosine proteome using K562 cells as a model system. A substantial segment of the phosphotyrosine proteome of K562 cells was characterized by immunoaffinity enrichment with 4G10 and PYKD1 antibodies followed by LC-MS/MS analysis. 480 non-redundant pTyr peptides corresponding to 342 pTyr proteins were found. 141 pTyr peptides were not described elsewhere. The mass spectrometry approach involving high-resolving FTMS analysis of precursor ions and subsequent detection of CID fragments in a linear ion trap was considered as optimal. For detection of low abundant pTyr peptides pooling of individual immunoaffinity enrichments for one LC-MS/MS analysis was crucial. The enrichment properties of the monoclonal PYKD1 antibody were presented for the first time, also in comparison to the 4G10 antibody. PYKD1 was found to be more effective for protein enrichment (1.2 and 5% efficiency at peptide and protein level correspondingly), while 4G10 showed better results when peptide enrichment was performed (15% efficiency versus 3.6% at protein level). Substantially different subsets of the phosphoproteome were enriched by these antibodies. This finding together with previous studies demonstrates that comprehensive pTyr proteome characterization by immunoprecipitation requires multiple antibodies to be used for the affinity enrichment.
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Affiliation(s)
- Konstantin A Artemenko
- Department of Physical and Analytical Chemistry, Uppsala University, SE-751 24 Uppsala, Sweden.
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Merrick BA, Witzmann FA. The role of toxicoproteomics in assessing organ specific toxicity. EXS 2009; 99:367-400. [PMID: 19157068 DOI: 10.1007/978-3-7643-8336-7_13] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Aims of this chapter on the role of toxicoproteomics in assessing organ-specific toxicity are to define the field of toxicoproteomics, describe its development among global technologies, and show potential uses in experimental toxicological research, preclinical testing and mechanistic biological research. Disciplines within proteomics deployed in preclinical research are described as Tier I analysis, involving global protein mapping and protein profiling for differential expression, and Tier II proteomic analysis, including global methods for description of function, structure, interactions and post-translational modification of proteins. Proteomic platforms used in toxicoproteomics research are briefly reviewed. Preclinical toxicoproteomic studies with model liver and kidney toxicants are critically assessed for their contributions toward understanding pathophysiology and in biomarker discovery. Toxicoproteomics research conducted in other organs and tissues are briefly discussed as well. The final section suggests several key developments involving new approaches and research focus areas for the field of toxicoproteomics as a new tool for toxicological pathology.
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Affiliation(s)
- B Alex Merrick
- Laboratory of Respiratory Biology, National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, Durham, NC 27709, USA.
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Daulat AM, Maurice P, Jockers R. Recent methodological advances in the discovery of GPCR-associated protein complexes. Trends Pharmacol Sci 2008; 30:72-8. [PMID: 19100631 DOI: 10.1016/j.tips.2008.10.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2008] [Revised: 10/26/2008] [Accepted: 10/27/2008] [Indexed: 12/30/2022]
Abstract
Protein-interaction networks have important roles in cellular homeostasis and the generation of complexity in biological systems. G-protein-coupled receptors (GPCRs), the largest family of membrane receptors and important drug targets, are integral parts of these networks. Ligand stimulation and the dynamic interaction with GPCR-associated protein complexes (GAPCs) constitute two important regulatory mechanisms of GPCR function. Several genomic and proteomic approaches have been developed to identify GAPCs in the past. However, this task turned out to be particularly demanding owing to difficulties in preserving the complex three-dimensional GPCR structure during receptor solubilization and to inherent limitations in the use of isolated receptor domains as bait. Newly emerging methods have the potential to overcome these limitations and will certainly boost the identification of functionally relevant GAPCs to finally increase our knowledge of the regulation of GPCRs and provide novel drug targets. Here, we focus on the comparison of two complementary GAPC purification strategies, which are based on soluble GPCR subdomains and entire GPCRs.
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Affiliation(s)
- Avais M Daulat
- Institut Cochin, Université Paris Descartes, Centre National de la Recherche Scientifique (UMR 8104), Department of Cell Biology, F-75014 Paris, France
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Tang W, Deng Z, Oses-Prieto JA, Suzuki N, Zhu S, Zhang X, Burlingame AL, Wang ZY. Proteomics studies of brassinosteroid signal transduction using prefractionation and two-dimensional DIGE. Mol Cell Proteomics 2008; 7:728-38. [PMID: 18182375 DOI: 10.1074/mcp.m700358-mcp200] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Signal transduction involves posttranslational modifications and protein-protein interactions, which can be studied by proteomics. In Arabidopsis, the steroid hormone (brassinosteroid (BR)) binds to the extracellular domain of a receptor kinase (BRI1) to initiate a phosphorylation/dephosphorylation cascade that controls gene expression and plant growth. Here we detected early BR signaling events and identified early response proteins using prefractionation and two-dimensional (2-D) DIGE. Proteomic changes induced rapidly by BR treatments were detected in phosphoprotein and plasma membrane (PM) fractions by 2-D DIGE but not in total protein extracts. LC-MS/MS analysis of gel spots identified 19 BR-regulated PM proteins and six proteins from phosphoprotein fractions. These include the BAK1 receptor kinase and BZR1 transcription factor of the BR signaling pathway. Both proteins showed spot shifts consistent with BR-regulated phosphorylation. In addition, in vivo phosphorylation sites were identified for BZR1, two tetratricopeptide repeat proteins, and a phosphoenolpyruvate carboxykinase (PCK1). Overexpression of a novel BR-induced PM protein (DREPP) partially suppressed the phenotypes of a BR-deficient mutant, demonstrating its important function in BR responses. Our study demonstrates that prefractionation coupled with 2-D DIGE is a powerful approach for studying signal transduction.
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Affiliation(s)
- Wenqiang Tang
- Department of Plant Biology, Carnegie Institution of Washington, Stanford, California 94305, USA
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Abstract
Our knowledge of the complex synaptic proteome and its relationship to physiological or pathological conditions is rapidly expanding. This has been greatly accelerated by the application of various evolving proteomic techniques, enabling more efficient protein resolution, more accurate protein identification, and more comprehensive characterization of proteins undergoing quantitative and qualitative changes. More recently, the combination of the classical subcellular fractionation techniques for the isolation of synaptosomes from the brain with the various proteomic analyses has facilitated this effort. This has resulted from the enrichment of many low abundant proteins comprising the fundamental structure and molecular machinery of brain neurotransmission and neuroplasticity. The analysis of various subproteomes obtained from the synapse, such as synaptic vesicles, synaptic membranes, presynaptic particles, synaptodendrosomes, and postsynaptic densities (PSD) holds great promise for improving our understanding of the temporal and spatial processes that coordinate synaptic proteins in closely related complexes under both normal and diseased states. This chapter will summarize a selection of recent studies that have drawn upon established and emerging proteomic technologies, along with fractionation techniques that are essential to the isolation and analysis of specific synaptic components, in an effort to understand the complexity and plasticity of the synapse proteome.
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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: 59] [Impact Index Per Article: 3.5] [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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