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Dual Specificity PDZ- and 14-3-3-Binding Motifs: A Structural and Interactomics Study. Structure 2020; 28:747-759.e3. [DOI: 10.1016/j.str.2020.03.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/12/2020] [Accepted: 03/20/2020] [Indexed: 12/22/2022]
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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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Gógl G, Biri-Kovács B, Póti ÁL, Vadászi H, Szeder B, Bodor A, Schlosser G, Ács A, Turiák L, Buday L, Alexa A, Nyitray L, Reményi A. Dynamic control of RSK complexes by phosphoswitch-based regulation. FEBS J 2017; 285:46-71. [PMID: 29083550 DOI: 10.1111/febs.14311] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 10/18/2017] [Accepted: 10/25/2017] [Indexed: 12/19/2022]
Abstract
Assembly and disassembly of protein-protein complexes needs to be dynamically controlled and phosphoswitches based on linear motifs are crucial in this process. Extracellular signal-regulated kinase 2 (ERK2) recognizes a linear-binding motif at the C-terminal tail (CTT) of ribosomal S6 kinase 1 (RSK1), leading to phosphorylation and subsequent activation of RSK1. The CTT also contains a classical PDZ domain-binding motif which binds RSK substrates (e.g. MAGI-1). We show that autophosphorylation of the disordered CTT promotes the formation of an intramolecular charge clamp, which efficiently masks critical residues and indirectly hinders ERK binding. Thus, RSK1 CTT operates as an autoregulated phosphoswitch: its phosphorylation at specific sites affects its protein-binding capacity and its conformational dynamics. These biochemical feedbacks, which form the structural basis for the rapid dissociation of ERK2-RSK1 and RSK1-PDZ substrate complexes under sustained epidermal growth factor (EGF) stimulation, were structurally characterized and validated in living cells. Overall, conformational changes induced by phosphorylation in disordered regions of protein kinases, coupled to allosteric events occurring in the kinase domain cores, may provide mechanisms that contribute to the emergence of complex signaling activities. In addition, we show that phosphoswitches based on linear motifs can be functionally classified as ON and OFF protein-protein interaction switches or dimmers, depending on the specific positioning of phosphorylation target sites in relation to functional linear-binding motifs. Moreover, interaction of phosphorylated residues with positively charged residues in disordered regions is likely to be a common mechanism of phosphoregulation. DATABASE Structural data are available in the PDB database under the accession numbers 5N7D, 5N7F and 5N7G. NMR spectral assignation data are available in the BMRB database under the accession numbers 27213 and 27214.
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Affiliation(s)
- Gergő Gógl
- Department of Biochemistry, ELTE Eötvös Loránd University, Budapest, Hungary.,Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Beáta Biri-Kovács
- Department of Biochemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Ádám L Póti
- Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Henrietta Vadászi
- Department of Biochemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Bálint Szeder
- Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Andrea Bodor
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Gitta Schlosser
- MTA-ELTE Research Group of Peptide Chemistry, Hungarian Academy of Sciences, ELTE Eötvös Loránd University, Budapest, Hungary
| | - András Ács
- MS Proteomics Research Group, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Lilla Turiák
- MS Proteomics Research Group, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - László Buday
- Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Anita Alexa
- Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - László Nyitray
- Department of Biochemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Attila Reményi
- Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
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Buncherd H, Roseboom W, Chokchaichamnankit D, Sawangareetrakul P, Phongdara A, Srisomsap C, de Jong L, Svasti J. β-Elimination coupled with strong cation-exchange chromatography for phosphopeptide analysis. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:1695-1704. [PMID: 28328035 DOI: 10.1002/rcm.7606] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Revised: 05/10/2016] [Accepted: 05/12/2016] [Indexed: 06/06/2023]
Abstract
RATIONALE Since the last decade, mass spectrometry (MS) has become an essential technique for phosphoprotein analysis. Formidable analytical challenges of MS for phosphoprotein study are both the low abundance of phosphopeptides and the lack of an unambiguous diagnostic fragment ion for identification of phospho residues. These challenges can be met by a charge-based isolation of β-elimination products after tryptic digestion using diagonal strong cation-exchange chromatography. METHODS β-Elimination combined with diagonal strong cation-exchange chromatography (BE/2SCX) was used for the enrichment of phosphorylated peptides prior to a mass spectrometric analysis by liquid chromatography/ion trap tandem mass spectrometry (MS/MS). Bovine α-casein (≥70% purity) was used as a model protein. RESULTS Conditions for β-elimination were optimized to maximize the efficiency of the reaction. With a β-elimination, all four model phosphopeptides from enolase (yeast) were correctly identified. The application of the BE/2SCX enrichment strategy for the analysis of β-elimination products of α-casein (bovine) allowed the identification of 11 phosphorylated products. CONCLUSIONS The introduction of a BE/2SCX-based enrichment step prior to LC/MS/MS analysis of β-elimination products facilitates the identification of phosphopeptides. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Hansuk Buncherd
- Faculty of Medical Technology, Prince of Songkla University, Hatyai, Songkhla, 90110, Thailand
| | - Winfried Roseboom
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 HX, Amsterdam, The Netherlands
| | | | | | - Amornrat Phongdara
- Center for Genomics and Bioinformatics Research, Faculty of Science, Prince of Songkla University, Hatyai, Songkhla, 90110, Thailand
| | | | - Luitzen de Jong
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 HX, Amsterdam, The Netherlands
| | - Jisnuson Svasti
- Laboratory of Biochemistry, Chulabhorn Research Institute, Bangkok, Thailand
- Applied Biological Sciences Program, Chulabhorn Graduate Institute, Bangkok, Thailand
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Matheron L, van den Toorn H, Heck AJR, Mohammed S. Characterization of Biases in Phosphopeptide Enrichment by Ti4+-Immobilized Metal Affinity Chromatography and TiO2 Using a Massive Synthetic Library and Human Cell Digests. Anal Chem 2014; 86:8312-20. [DOI: 10.1021/ac501803z] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Lucrece Matheron
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute of Pharmaceutical Sciences and The
Netherlands Proteomics Centre, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Henk van den Toorn
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute of Pharmaceutical Sciences and The
Netherlands Proteomics Centre, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute of Pharmaceutical Sciences and The
Netherlands Proteomics Centre, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Shabaz Mohammed
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute of Pharmaceutical Sciences and The
Netherlands Proteomics Centre, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, OX1 3TA, Oxford, United Kingdom
- Department
of Biochemistry, University of Oxford, South Parks Road, OX1 3QU, Oxford, United Kingdom
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Markoutsa S, Bahr U, Papasotiriou DG, Häfner AK, Karas M, Sorg BL. Sulfo-NHS-SS-biotin derivatization: A versatile tool for MALDI mass analysis of PTMs in lysine-rich proteins. Proteomics 2014; 14:659-67. [DOI: 10.1002/pmic.201300309] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 09/11/2013] [Accepted: 12/20/2013] [Indexed: 01/09/2023]
Affiliation(s)
| | - Ute Bahr
- Institute of Pharmaceutical Chemistry; Goethe-University; Frankfurt Germany
| | | | - Ann-Kathrin Häfner
- Institute of Pharmaceutical Chemistry; Goethe-University; Frankfurt Germany
| | - Michael Karas
- Institute of Pharmaceutical Chemistry; Goethe-University; Frankfurt Germany
| | - Bernd L. Sorg
- Institute of Pharmaceutical Chemistry; Goethe-University; Frankfurt Germany
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Eriksson AIK, Edwards K, Hagfeldt A, Hernández VA. Physicochemical Characterization of Phosphopeptide/Titanium Dioxide Interactions Employing the Quartz Crystal Microbalance Technique. J Phys Chem B 2013; 117:2019-25. [DOI: 10.1021/jp310161m] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
| | - Katarina Edwards
- Department of Chemistry−BMC, Uppsala University, Uppsala, Sweden
- FRIAS,
School of Soft Matter Research, University of Freiburg, Freiburg, Germany
| | - Anders Hagfeldt
- Department
of Chemistry−Ångström, Uppsala University, Uppsala, Sweden
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Matheron L, Clavier S, Diebate O, Karoyan P, Bolbach G, Guianvarc'h D, Sachon E. Improving the selectivity of the phosphoric acid β-elimination on a biotinylated phosphopeptide. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1981-1990. [PMID: 22956181 DOI: 10.1007/s13361-012-0467-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Revised: 07/16/2012] [Accepted: 08/01/2012] [Indexed: 06/01/2023]
Abstract
This study aims at improving the MALDI-TOF detection of a phosphorylated peptide containing a cysteine residue by β-elimination of H(3)PO(4) hardly enriched by classical methods. The experimental conditions were optimized on this phosphopeptide (biot-pAdd) and its nonphosphorylated counterpart (biot-Add). The major side-reactions were H(2)S elimination on the cysteine residues and H(2)O elimination on the non phosphorylated serine residue of biot-Add. The former dilutes the MALDI-TOF signal for the desired species. The latter gives a product similar to what is obtained by H(3)PO(4) elimination and should prompt to caution when working with a mixture between phosphorylated and non phosphorylated peptides. Modifications on the solvent, the reaction temperature and time, the nature, and concentration of the base were made. Major improvement of the selectivity of the reaction was observed in 30 % ACN, at room temperature for 4 h. However, these optimizations are specific to these sequences and should be performed anew for different peptides. The selectivity of the reaction towards H(3)PO(4) elimination is improved, but the persistence of side-reactions renders a previous sample fractionation necessary. In these optimized conditions, the ionization enhancement is 3-fold and the detection limits for biot-pAdd are similar to biot-Add (100 fmol).
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Affiliation(s)
- Lucrèce Matheron
- Laboratoire des Biomolécules, Université P et M Curie, UMR 7203 UPMC-CNRS-ENS, Paris, France
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Abstract
Sample preparation has historically been, and continues to be, the most challenging part of the bioanalytical workflow. Several techniques have been developed over the years to deal with the problems of recovery and matrix effects in an effort to increase the reliability and robustness of the bioanalytical method. In recent years certain techniques have come into prominence and gained acceptance in routine sample preparation, and some have shown promise in their use in a discovery environment where speed is critical and method development time is often limited. The aim of this review is to examine several of these techniques and provide examples of their use from the literature, as well as comment on their utility in current workflows.
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