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Nosti AJ, Barrio LC, Calderón-Celis F, Soldado A, Encinar JR. Absolute quantification of proteins using element mass spectrometry and generic standards. J Proteomics 2022; 256:104499. [DOI: 10.1016/j.jprot.2022.104499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/21/2022] [Indexed: 10/19/2022]
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2
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Driller JH, Lützkendorf J, Depner H, Siebert M, Kuropka B, Weise C, Piao C, Petzoldt AG, Lehmann M, Stelzl U, Zahedi R, Sickmann A, Freund C, Sigrist SJ, Wahl MC. Phosphorylation of the Bruchpilot N-terminus in Drosophila unlocks axonal transport of active zone building blocks. J Cell Sci 2019; 132:jcs.225151. [PMID: 30745339 DOI: 10.1242/jcs.225151] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 01/24/2019] [Indexed: 01/31/2023] Open
Abstract
Protein scaffolds at presynaptic active zone membranes control information transfer at synapses. For scaffold biogenesis and maintenance, scaffold components must be safely transported along axons. A spectrum of kinases has been suggested to control transport of scaffold components, but direct kinase-substrate relationships and operational principles steering phosphorylation-dependent active zone protein transport are presently unknown. Here, we show that extensive phosphorylation of a 150-residue unstructured region at the N-terminus of the highly elongated Bruchpilot (BRP) active zone protein is crucial for ordered active zone precursor transport in Drosophila Point mutations that block SRPK79D kinase-mediated phosphorylation of the BRP N-terminus interfered with axonal transport, leading to BRP-positive axonal aggregates that also contain additional active zone scaffold proteins. Axonal aggregates formed only in the presence of non-phosphorylatable BRP isoforms containing the SRPK79D-targeted N-terminal stretch. We assume that specific active zone proteins are pre-assembled in transport packages and are thus co-transported as functional scaffold building blocks. Our results suggest that transient post-translational modification of a discrete unstructured domain of the master scaffold component BRP blocks oligomerization of these building blocks during their long-range transport.
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Affiliation(s)
- Jan H Driller
- Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 6, D-14195 Berlin, Germany
| | - Janine Lützkendorf
- Laboratory of Genetics, Institute of Biology, Freie Universität Berlin, Takustraße 6, D-14195 Berlin, Germany
| | - Harald Depner
- Laboratory of Genetics, Institute of Biology, Freie Universität Berlin, Takustraße 6, D-14195 Berlin, Germany
| | - Matthias Siebert
- Laboratory of Genetics, Institute of Biology, Freie Universität Berlin, Takustraße 6, D-14195 Berlin, Germany
| | - Benno Kuropka
- Laboratory of Protein Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, D-14195 Berlin, Germany
| | - Christoph Weise
- Laboratory of Protein Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, D-14195 Berlin, Germany
| | - Chengji Piao
- Laboratory of Genetics, Institute of Biology, Freie Universität Berlin, Takustraße 6, D-14195 Berlin, Germany
| | - Astrid G Petzoldt
- Laboratory of Genetics, Institute of Biology, Freie Universität Berlin, Takustraße 6, D-14195 Berlin, Germany.,NeuroCure Cluster of Excellence, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Martin Lehmann
- Cellular Imaging, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Roessle-Straße 10, D-13125 Berlin, Germany
| | - Ulrich Stelzl
- Pharmaceutical Chemistry, Institute of Pharmaceutical Sciences, University of Graz, Universitätsplatz 1/I, A-8010 Graz, Austria
| | - René Zahedi
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Bunsen-Kirchhoff-Straße 11, D-44139 Dortmund, Germany
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Bunsen-Kirchhoff-Straße 11, D-44139 Dortmund, Germany
| | - Christian Freund
- Laboratory of Protein Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, D-14195 Berlin, Germany
| | - Stephan J Sigrist
- Laboratory of Genetics, Institute of Biology, Freie Universität Berlin, Takustraße 6, D-14195 Berlin, Germany .,NeuroCure Cluster of Excellence, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Markus C Wahl
- Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 6, D-14195 Berlin, Germany .,Macromolecular Crystallography, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Straße 15, D-12489 Berlin, Germany
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3
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Calderón-Celis F, Sugiyama N, Yamanaka M, Sakai T, Diez-Fernández S, Calvete JJ, Sanz-Medel A, Encinar JR. Enhanced Universal Quantification of Biomolecules Using Element MS and Generic Standards: Application to Intact Protein and Phosphoprotein Determination. Anal Chem 2018; 91:1105-1112. [DOI: 10.1021/acs.analchem.8b04731] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Francisco Calderón-Celis
- Department of Physical and Analytical Chemistry, University of Oviedo, Julián Clavería 8, 33006 Oviedo, Spain
| | - Naoki Sugiyama
- Agilent Technologies International Japan, Ltd., 9-1 Takakura-cho, Hachioji-shi, Tokyo 192-0033, Japan
| | - Michiko Yamanaka
- Agilent Technologies International Japan, Ltd., 9-1 Takakura-cho, Hachioji-shi, Tokyo 192-0033, Japan
| | - Tetsushi Sakai
- Agilent Technologies International Japan, Ltd., 9-1 Takakura-cho, Hachioji-shi, Tokyo 192-0033, Japan
| | - Silvia Diez-Fernández
- Department of Physical and Analytical Chemistry, University of Oviedo, Julián Clavería 8, 33006 Oviedo, Spain
| | - Juan J. Calvete
- Instituto de Biomedicina de Valencia, IBV-CSIC, Jaume Roig 11, 46010 Valencia, Spain
| | - Alfredo Sanz-Medel
- Department of Physical and Analytical Chemistry, University of Oviedo, Julián Clavería 8, 33006 Oviedo, Spain
| | - Jorge Ruiz Encinar
- Department of Physical and Analytical Chemistry, University of Oviedo, Julián Clavería 8, 33006 Oviedo, Spain
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4
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Kuropka B, Schraven B, Kliche S, Krause E, Freund C. Tyrosine-phosphorylation of the scaffold protein ADAP and its role in T cell signaling. Expert Rev Proteomics 2017; 13:545-54. [PMID: 27258783 DOI: 10.1080/14789450.2016.1187565] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
INTRODUCTION The Adhesion and Degranulation promoting Adaptor Protein (ADAP) is phosphorylated upon T cell activation and acts as a scaffold for the formation of a signaling complex that integrates molecular interactions between T cell or chemokine receptors, the actin cytoskeleton, and integrin-mediated cellular adhesion and migration. AREAS COVERED This article reviews current knowledge of the functions of the adapter protein ADAP in T cell signaling with a focus on the role of individual phosphotyrosine (pY) motifs for SH2 domain mediated interactions. The data presented was obtained from literature searches (PubMed) as well as the authors own research on the topic. Expert commentary: ADAP can be regarded as a paradigmatic example of how tyrosine phosphorylation sites serve as dynamic interaction hubs. Molecular crowding at unstructured and redundant sites (pY595, pY651) is contrasted by more specific interactions enabled by the three-dimensional environment of a particular phosphotyrosine motif (pY571).
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Affiliation(s)
- Benno Kuropka
- a Freie Universität Berlin, Institut für Chemie und Biochemie, Protein Biochemistry Group , Berlin , Germany.,b Mass Spectrometry Group, Leibniz-Institut für Molekulare Pharmakologie , Berlin , Germany
| | - Burkhart Schraven
- c Institute of Molecular and Clinical Immunology , Otto-von-Guericke-University , Magdeburg , Germany.,d Department of Immune Control , Helmholtz Center for Infection Research (HZI) , Braunschweig , Germany
| | - Stefanie Kliche
- c Institute of Molecular and Clinical Immunology , Otto-von-Guericke-University , Magdeburg , Germany
| | - Eberhard Krause
- b Mass Spectrometry Group, Leibniz-Institut für Molekulare Pharmakologie , Berlin , Germany
| | - Christian Freund
- a Freie Universität Berlin, Institut für Chemie und Biochemie, Protein Biochemistry Group , Berlin , Germany
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5
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Kuropka B, Witte A, Sticht J, Waldt N, Majkut P, Hackenberger CPR, Schraven B, Krause E, Kliche S, Freund C. Analysis of Phosphorylation-dependent Protein Interactions of Adhesion and Degranulation Promoting Adaptor Protein (ADAP) Reveals Novel Interaction Partners Required for Chemokine-directed T cell Migration. Mol Cell Proteomics 2015; 14:2961-72. [PMID: 26246585 DOI: 10.1074/mcp.m115.048249] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Indexed: 11/06/2022] Open
Abstract
Stimulation of T cells leads to distinct changes of their adhesive and migratory properties. Signal propagation from activated receptors to integrins depends on scaffolding proteins such as the adhesion and degranulation promoting adaptor protein (ADAP)(1). Here we have comprehensively investigated the phosphotyrosine interactome of ADAP in T cells and define known and novel interaction partners of functional relevance. While most phosphosites reside in unstructured regions of the protein, thereby defining classical SH2 domain interaction sites for master regulators of T cell signaling such as SLP76, Fyn-kinase, and NCK, other binding events depend on structural context. Interaction proteomics using different ADAP constructs comprising most of the known phosphotyrosine motifs as well as the structured domains confirm that a distinct set of proteins is attracted by pY571 of ADAP, including the ζ-chain-associated protein kinase of 70 kDa (ZAP70). The interaction of ADAP and ZAP70 is inducible upon stimulation either of the T cell receptor (TCR) or by chemokine. NMR spectroscopy reveals that the N-terminal SH2 domains within a ZAP70-tandem-SH2 construct is the major site of interaction with phosphorylated ADAP-hSH3(N) and microscale thermophoresis (MST) indicates an intermediate binding affinity (Kd = 2.3 μm). Interestingly, although T cell receptor dependent events such as T cell/antigen presenting cell (APC) conjugate formation and adhesion are not affected by mutation of Y571, migration of T cells along a chemokine gradient is compromised. Thus, although most phospho-sites in ADAP are linked to T cell receptor related functions we have identified a unique phosphotyrosine that is solely required for chemokine induced T cell behavior.
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Affiliation(s)
- Benno Kuropka
- From the ‡Freie Universität Berlin, Institut für Chemie und Biochemie, Protein Biochemistry group, Thielallee 63, 14195 Berlin, Germany; §Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Amelie Witte
- ¶Otto-von-Guericke-University, Institute of Molecular and Clinical Immunology, Leipziger Strasse 44, 39120 Magdeburg, Germany
| | - Jana Sticht
- From the ‡Freie Universität Berlin, Institut für Chemie und Biochemie, Protein Biochemistry group, Thielallee 63, 14195 Berlin, Germany
| | - Natalie Waldt
- ¶Otto-von-Guericke-University, Institute of Molecular and Clinical Immunology, Leipziger Strasse 44, 39120 Magdeburg, Germany
| | - Paul Majkut
- §Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125 Berlin, Germany; ‖RiNA GmbH, Volmerstrasse 9, 12489 Berlin, Germany
| | | | - Burkhart Schraven
- ¶Otto-von-Guericke-University, Institute of Molecular and Clinical Immunology, Leipziger Strasse 44, 39120 Magdeburg, Germany; **Helmholtz Center for Infection Research (HZI), Department of Immune Control, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Eberhard Krause
- §Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125 Berlin, Germany;
| | - Stefanie Kliche
- ¶Otto-von-Guericke-University, Institute of Molecular and Clinical Immunology, Leipziger Strasse 44, 39120 Magdeburg, Germany;
| | - Christian Freund
- From the ‡Freie Universität Berlin, Institut für Chemie und Biochemie, Protein Biochemistry group, Thielallee 63, 14195 Berlin, Germany;
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6
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Quantitative and dynamic analysis of PTEN phosphorylation by NMR. Methods 2015; 77-78:82-91. [DOI: 10.1016/j.ymeth.2014.10.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 09/29/2014] [Accepted: 10/07/2014] [Indexed: 12/15/2022] Open
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7
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Küster SK, Pabst M, Zenobi R, Dittrich PS. Automatisierte Detektion von Proteinphosphorylierung durch Nanoliter-Enzymreaktionen auf Mikroarrays. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201409440] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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8
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Küster SK, Pabst M, Zenobi R, Dittrich PS. Screening for protein phosphorylation using nanoscale reactions on microdroplet arrays. Angew Chem Int Ed Engl 2014; 54:1671-5. [PMID: 25504774 DOI: 10.1002/anie.201409440] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Indexed: 12/25/2022]
Abstract
We present a novel and straightforward screening method to detect protein phosphorylations in complex protein mixtures. A proteolytic digest is separated by a conventional nanoscale liquid chromatography (nano-LC) separation and the eluate is immediately compartmentalized into microdroplets, which are spotted on a microarray MALDI plate. Subsequently, the enzyme alkaline phosphatase is applied to every second microarray spot to remove the phosphate groups from phosphorylated peptides, which results in a mass shift of n×-80 Da. The MALDI-MS scan of the microarray is then evaluated by a software algorithm to automatically identify the phosphorylated peptides by exploiting the characteristic chromatographic peak profile induced by the phosphatase treatment. This screening method does not require extensive MS/MS experiments or peak list evaluation and can be easily extended to other enzymatic or chemical reactions.
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Affiliation(s)
- Simon K Küster
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich (Switzerland)
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9
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Pichlo M, Bungert-Plümke S, Weyand I, Seifert R, Bönigk W, Strünker T, Kashikar ND, Goodwin N, Müller A, Pelzer P, Van Q, Enderlein J, Klemm C, Krause E, Trötschel C, Poetsch A, Kremmer E, Kaupp UB, Körschen HG, Collienne U. High density and ligand affinity confer ultrasensitive signal detection by a guanylyl cyclase chemoreceptor. J Cell Biol 2014; 206:541-57. [PMID: 25135936 PMCID: PMC4137060 DOI: 10.1083/jcb.201402027] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 07/15/2014] [Indexed: 12/28/2022] Open
Abstract
Guanylyl cyclases (GCs), which synthesize the messenger cyclic guanosine 3',5'-monophosphate, control several sensory functions, such as phototransduction, chemosensation, and thermosensation, in many species from worms to mammals. The GC chemoreceptor in sea urchin sperm can decode chemoattractant concentrations with single-molecule sensitivity. The molecular and cellular underpinnings of such ultrasensitivity are not known for any eukaryotic chemoreceptor. In this paper, we show that an exquisitely high density of 3 × 10(5) GC chemoreceptors and subnanomolar ligand affinity provide a high ligand-capture efficacy and render sperm perfect absorbers. The GC activity is terminated within 150 ms by dephosphorylation steps of the receptor, which provides a means for precise control of the GC lifetime and which reduces "molecule noise." Compared with other ultrasensitive sensory systems, the 10-fold signal amplification by the GC receptor is surprisingly low. The hallmarks of this signaling mechanism provide a blueprint for chemical sensing in small compartments, such as olfactory cilia, insect antennae, or even synaptic boutons.
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Affiliation(s)
- Magdalena Pichlo
- Center of Advanced European Studies and Research, 53175 Bonn, Germany Marine Biological Laboratory, Woods Hole, MA 02543
| | - Stefanie Bungert-Plümke
- Marine Biological Laboratory, Woods Hole, MA 02543 Institute of Complex Systems (ICS-4), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Ingo Weyand
- Marine Biological Laboratory, Woods Hole, MA 02543 Institute of Complex Systems (ICS-4), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Reinhard Seifert
- Center of Advanced European Studies and Research, 53175 Bonn, Germany Marine Biological Laboratory, Woods Hole, MA 02543
| | - Wolfgang Bönigk
- Center of Advanced European Studies and Research, 53175 Bonn, Germany
| | - Timo Strünker
- Center of Advanced European Studies and Research, 53175 Bonn, Germany Marine Biological Laboratory, Woods Hole, MA 02543
| | - Nachiket Dilip Kashikar
- Center of Advanced European Studies and Research, 53175 Bonn, Germany Marine Biological Laboratory, Woods Hole, MA 02543 Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton BN1 9QG, England, UK
| | - Normann Goodwin
- Center of Advanced European Studies and Research, 53175 Bonn, Germany Marine Biological Laboratory, Woods Hole, MA 02543 Babraham Institute, Cambridge CB22 3AT, England, UK
| | - Astrid Müller
- Center of Advanced European Studies and Research, 53175 Bonn, Germany
| | - Patric Pelzer
- Marine Biological Laboratory, Woods Hole, MA 02543 Department of Functional Neuroanatomy, Institute of Anatomy and Cell Biology, Heidelberg University, 69120 Heidelberg, Germany
| | - Qui Van
- III. Physikalisches Institut, Universität Göttingen, 37077 Göttingen, Germany
| | - Jörg Enderlein
- III. Physikalisches Institut, Universität Göttingen, 37077 Göttingen, Germany
| | - Clementine Klemm
- Leibniz-Institut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | - Eberhard Krause
- Leibniz-Institut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | | | - Ansgar Poetsch
- Plant Biochemistry, Ruhr University Bochum. 44801 Bochum, Germany
| | - Elisabeth Kremmer
- Institut für Molekulare Immunologie, Helmholtz-Zentrum München, 81377 München, Germany
| | - U Benjamin Kaupp
- Center of Advanced European Studies and Research, 53175 Bonn, Germany Marine Biological Laboratory, Woods Hole, MA 02543
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10
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Gonzalez-Sanchez MB, Lanucara F, Hardman GE, Eyers CE. Gas-phase intermolecular phosphate transfer within a phosphohistidine phosphopeptide dimer. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2014; 367:28-34. [PMID: 25844054 PMCID: PMC4375673 DOI: 10.1016/j.ijms.2014.04.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 04/14/2014] [Accepted: 04/22/2014] [Indexed: 05/26/2023]
Abstract
The hydrogen bonds and electrostatic interactions that form between the protonated side chain of a basic residue and the negatively charged phosphate of a phosphopeptide can play crucial roles in governing their dissociation pathways under low-energy collision-induced dissociation (CID). Understanding how phosphoramidate (i.e. phosphohistidine, phospholysine and phosphoarginine), rather than phosphomonoester-containing peptides behave during CID is paramount in investigation of these problematic species by tandem mass spectrometry. To this end, a synthetic peptide containing either phosphohistidine (pHis) or phospholysine (pLys) was analyzed by ESI-MS using a Paul-type ion trap (AmaZon, Bruker) and by traveling wave ion mobility-mass spectrometry (Synapt G2-Si, Waters). Analysis of the products of low-energy CID demonstrated formation of a doubly 'phosphorylated' product ion arising from intermolecular gas-phase phosphate transfer within a phosphopeptide dimer. The results are explained by the formation of a homodimeric phosphohistidine (pHis) peptide non-covalent complex (NCX), likely stabilized by the electrostatic interaction between the pHis phosphate group and the protonated C-terminal lysine residue of the peptide. To the best of our knowledge this is the first report of intermolecular gas-phase phosphate transfer from one phosphopeptide to another, leading to a doubly phosphorylated peptide product ion.
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Affiliation(s)
- Maria-Belen Gonzalez-Sanchez
- Michael Barber Centre for Mass Spectrometry, School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Francesco Lanucara
- Michael Barber Centre for Mass Spectrometry, School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - Gemma E. Hardman
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - Claire E. Eyers
- Michael Barber Centre for Mass Spectrometry, School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
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11
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Boehm ME, Hahn B, Lehmann WD. One-source peptide/phosphopeptide ratio standards for accurate and site-specific determination of the degree of phosphorylation. Methods Mol Biol 2014; 1156:367-78. [PMID: 24792001 DOI: 10.1007/978-1-4939-0685-7_24] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Reversible protein phosphorylation is a key mediator for intracellular signal transduction. Here we describe an innovative method for the production of pairs of peptide standards designed for quantitative mass spectrometry. These standard pairs can be used for site-specific analysis of the degree of phosphorylation of proteins in a bottom-up approach. The method starts from an isotopically labeled phosphopeptide analogue of the analyte phosphopeptide and ends up with a labeled peptide/phosphopeptide ratio standard in which the molar ratio between the phosphorylated and the unphosphorylated form is exactly defined. The signals of the ratio standard are used to standardize the corresponding analyte signals. This compensates for differences in LC recovery or ionization efficiency between the phosphorylated and unphosphorylated forms. The method can also be extended to quantitative analysis of multisite phosphorylation in a single peptide, which is exemplified for the presence of two phosphorylation sites. Peptide/phosphopeptide ratio standards exhibit high ratio accuracy, since ratio adjustment is performed by volumetric operations only.
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Affiliation(s)
- Martin E Boehm
- Molecular Structure Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
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12
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Winter DL, Paulin D, Mericskay M, Li Z. Posttranslational modifications of desmin and their implication in biological processes and pathologies. Histochem Cell Biol 2013; 141:1-16. [DOI: 10.1007/s00418-013-1148-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2013] [Indexed: 11/29/2022]
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13
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Theillet FX, Rose HM, Liokatis S, Binolfi A, Thongwichian R, Stuiver M, Selenko P. Site-specific NMR mapping and time-resolved monitoring of serine and threonine phosphorylation in reconstituted kinase reactions and mammalian cell extracts. Nat Protoc 2013; 8:1416-32. [PMID: 23807285 DOI: 10.1038/nprot.2013.083] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We outline NMR protocols for site-specific mapping and time-resolved monitoring of protein phosphorylation reactions using purified kinases and mammalian cell extracts. These approaches are particularly amenable to intrinsically disordered proteins and unfolded, regulatory protein domains. We present examples for the ¹⁵N isotope-labeled N-terminal transactivation domain of human p53, which is either sequentially reacted with recombinant enzymes or directly added to mammalian cell extracts and phosphorylated by endogenous kinases. Phosphorylation reactions with purified enzymes are set up in minutes, whereas NMR samples in cell extracts are prepared within 1 h. Time-resolved NMR measurements are performed over minutes to hours depending on the activities of the probed kinases. Phosphorylation is quantitatively monitored with consecutive 2D ¹H-¹⁵N band-selective optimized-flip-angle short-transient (SOFAST)-heteronuclear multiple-quantum (HMQC) NMR experiments, which provide atomic-resolution insights into the phosphorylation levels of individual substrate residues and time-dependent changes thereof, thereby offering unique advantages over western blotting and mass spectrometry.
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Affiliation(s)
- Francois-Xavier Theillet
- In-Cell NMR Laboratory, Department of NMR-supported Structural Biology, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Berlin, Germany
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14
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Tezel G. A proteomics view of the molecular mechanisms and biomarkers of glaucomatous neurodegeneration. Prog Retin Eye Res 2013; 35:18-43. [PMID: 23396249 DOI: 10.1016/j.preteyeres.2013.01.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 01/25/2013] [Accepted: 01/28/2013] [Indexed: 02/07/2023]
Abstract
Despite improving understanding of glaucoma, key molecular players of neurodegeneration that can be targeted for treatment of glaucoma, or molecular biomarkers that can be useful for clinical testing, remain unclear. Proteomics technology offers a powerful toolbox to accomplish these important goals of the glaucoma research and is increasingly being applied to identify molecular mechanisms and biomarkers of glaucoma. Recent studies of glaucoma using proteomics analysis techniques have resulted in the lists of differentially expressed proteins in human glaucoma and animal models. The global analysis of protein expression in glaucoma has been followed by cell-specific proteome analysis of retinal ganglion cells and astrocytes. The proteomics data have also guided targeted studies to identify post-translational modifications and protein-protein interactions during glaucomatous neurodegeneration. In addition, recent applications of proteomics have provided a number of potential biomarker candidates. Proteomics technology holds great promise to move glaucoma research forward toward new treatment strategies and biomarker discovery. By reviewing the major proteomics approaches and their applications in the field of glaucoma, this article highlights the power of proteomics in translational and clinical research related to glaucoma and also provides a framework for future research to functionally test the importance of specific molecular pathways and validate candidate biomarkers.
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Affiliation(s)
- Gülgün Tezel
- Department of Ophthalmology & Visual Sciences, University of Louisville School of Medicine, Louisville, KY, USA.
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15
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Cordier F, Chaffotte A, Terrien E, Préhaud C, Theillet FX, Delepierre M, Lafon M, Buc H, Wolff N. Ordered Phosphorylation Events in Two Independent Cascades of the PTEN C-tail Revealed by NMR. J Am Chem Soc 2012; 134:20533-43. [DOI: 10.1021/ja310214g] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
| | | | - Elouan Terrien
- CNRS, UMR3528, F-75015 Paris, France
- Cellule Pasteur UPMC, University of Pierre and Marie Curie, rue du Dr Roux,
75015 Paris, France
| | | | | | | | | | - Henri Buc
- Institut Pasteur,
F-75015 Paris, France
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