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Bobone S, Storti C, Calligari P, Stella L. Fluorescence Anisotropy and Polarization in the Characterization of Biomolecular Association Processes and Their Application to Study SH2 Domain Binding Affinity. Methods Mol Biol 2023; 2705:93-112. [PMID: 37668971 DOI: 10.1007/978-1-0716-3393-9_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
Fluorescence anisotropy (or polarization) is a powerful technique to study biomolecular association processes, by following the rotational motions of one of the two partners in the interaction, labeled with a fluorophore. It can be used to determine dissociation constants in solution, down to nM values, and unlabeled ligands can be characterized, too, by using competition experiments. In this chapter, we introduce the basic principles of the technique, compare it with other experimental approaches, and discuss the experimental details with specific examples regarding SH2 domain/phosphopeptide association processes. The experimental protocols to be used in binding experiments and displacement studies are described, as well as the caveats to be considered in performing accurate measurements.
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Affiliation(s)
- Sara Bobone
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome, Italy
| | - Claudia Storti
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome, Italy
| | - Paolo Calligari
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome, Italy
| | - Lorenzo Stella
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome, Italy.
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2
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Norouzi M, Panfilov S, Pardee K. High-Efficiency Protection of Linear DNA in Cell-Free Extracts from Escherichia coli and Vibrio natriegens. ACS Synth Biol 2021; 10:1615-1624. [PMID: 34161082 DOI: 10.1021/acssynbio.1c00110] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The field of cell-free synthetic biology is an emerging branch of engineered biology that allows for rapid prototyping of biological designs and, in its own right, is becoming a venue for the in vitro operation of gene circuit-based sensors and biomanufacturing. To date, the related DNA encoded tools that operate in cell-free reactions have primarily relied on plasmid DNA inputs, as linear templates are highly susceptible to degradation by exonucleases present in cell-free extracts. This incompatibility has precluded significant throughput, time and cost benefits that could be gained with the use of linear DNA in the cell-free expression workflow. Here to tackle this limitation, we report that terminal incorporation of Ter binding sites for the DNA-binding protein Tus enables highly efficient protection of linear expression templates encoding mCherry and deGFP. In Escherichia coli extracts, our method compares favorably with the previously reported GamS-mediated protection scheme. Importantly, we extend the Tus-Ter system to Vibrio natriegens extracts, and demonstrate that this simple and easily implemented method can enable an unprecedented plasmid-level expression from linear templates in this emerging chassis organism.
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Affiliation(s)
- Masoud Norouzi
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Sabina Panfilov
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Keith Pardee
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, Ontario M5S 3G8, Canada
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Sadoine M, Cerminara M, Kempf N, Gerrits M, Fitter J, Katranidis A. Selective Double-Labeling of Cell-Free Synthesized Proteins for More Accurate smFRET Studies. Anal Chem 2017; 89:11278-11285. [DOI: 10.1021/acs.analchem.7b01639] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mayuri Sadoine
- Forschungszentrum
Jülich, Institute of Complex Systems ICS-5, 52425 Jülich, Germany
| | - Michele Cerminara
- Forschungszentrum
Jülich, Institute of Complex Systems ICS-5, 52425 Jülich, Germany
| | - Noémie Kempf
- Forschungszentrum
Jülich, Institute of Complex Systems ICS-5, 52425 Jülich, Germany
| | | | - Jörg Fitter
- Forschungszentrum
Jülich, Institute of Complex Systems ICS-5, 52425 Jülich, Germany
- 1. Physikalisches
Institut (IA), RWTH Aachen, 52062 Aachen, Germany
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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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Shu K, Noguchi T, Honda K, Kondoh Y, Osada H, Ohno H, Fujii N, Oishi S. Synthesis of the Src SH2 domain and its application in bioassays for mirror-image screening. RSC Adv 2017. [DOI: 10.1039/c7ra07445j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Mirror-image screening systems for Src SH2 domain inhibitors were established using a synthetic Src SH2 domain.
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Affiliation(s)
- Keitou Shu
- Graduate School of Pharmaceutical Sciences
- Kyoto University
- Kyoto 606-8501
- Japan
- Graduate School of Advanced Integrated Studies in Human Survivability
| | - Taro Noguchi
- Graduate School of Pharmaceutical Sciences
- Kyoto University
- Kyoto 606-8501
- Japan
| | - Kaori Honda
- Chemical Biology Research Group
- RIKEN Center for Sustainable Resource Science
- Saitama 351-0198
- Japan
| | - Yasumitsu Kondoh
- Chemical Biology Research Group
- RIKEN Center for Sustainable Resource Science
- Saitama 351-0198
- Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group
- RIKEN Center for Sustainable Resource Science
- Saitama 351-0198
- Japan
| | - Hiroaki Ohno
- Graduate School of Pharmaceutical Sciences
- Kyoto University
- Kyoto 606-8501
- Japan
| | - Nobutaka Fujii
- Graduate School of Pharmaceutical Sciences
- Kyoto University
- Kyoto 606-8501
- Japan
| | - Shinya Oishi
- Graduate School of Pharmaceutical Sciences
- Kyoto University
- Kyoto 606-8501
- Japan
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Gerbec ZJ, Thakar MS, Malarkannan S. The Fyn-ADAP Axis: Cytotoxicity Versus Cytokine Production in Killer Cells. Front Immunol 2015; 6:472. [PMID: 26441977 PMCID: PMC4584950 DOI: 10.3389/fimmu.2015.00472] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 08/31/2015] [Indexed: 11/13/2022] Open
Abstract
Lymphocyte signaling cascades responsible for anti-tumor cytotoxicity and inflammatory cytokine production must be tightly regulated in order to control an immune response. Disruption of these cascades can cause immune suppression as seen in a tumor microenvironment, and loss of signaling integrity can lead to autoimmunity and other forms of host-tissue damage. Therefore, understanding the distinct signaling events that exclusively control specific effector functions of “killer” lymphocytes (T and NK cells) is critical for understanding disease progression and formulating successful immunotherapy. Elucidation of divergent signaling pathways involved in receptor-mediated activation has provided insights into the independent regulation of cytotoxicity and cytokine production in lymphocytes. Specifically, the Fyn signaling axis represents a branch point for killer cell effector functions and provides a model for how cytotoxicity and cytokine production are differentially regulated. While the Fyn–PI(3)K pathway controls multiple functions, including cytotoxicity, cell development, and cytokine production, the Fyn–ADAP pathway preferentially regulates cytokine production in NK and T cells. In this review, we discuss how the structure of Fyn controls its function in lymphocytes and the role this plays in mediating two facets of lymphocyte effector function, cytotoxicity and production of inflammatory cytokines. This offers a model for using mechanistic and structural approaches to understand clinically relevant lymphocyte signaling.
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Affiliation(s)
- Zachary J Gerbec
- Laboratory of Molecular Immunology and Immunotherapy, Blood Research Institute, Medical College of Wisconsin , Milwaukee, WI , USA ; Department of Microbiology, Immunology and Molecular Genetics, Medical College of Wisconsin , Milwaukee, WI , USA
| | - Monica S Thakar
- Laboratory of Molecular Immunology and Immunotherapy, Blood Research Institute, Medical College of Wisconsin , Milwaukee, WI , USA ; Department of Pediatrics, Medical College of Wisconsin , Milwaukee, WI , USA ; Department of Medicine, Medical College of Wisconsin , Milwaukee, WI , USA
| | - Subramaniam Malarkannan
- Laboratory of Molecular Immunology and Immunotherapy, Blood Research Institute, Medical College of Wisconsin , Milwaukee, WI , USA ; Department of Microbiology, Immunology and Molecular Genetics, Medical College of Wisconsin , Milwaukee, WI , USA ; Department of Pediatrics, Medical College of Wisconsin , Milwaukee, WI , USA ; Department of Medicine, Medical College of Wisconsin , Milwaukee, WI , USA
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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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Vallée MRJ, Majkut P, Krause D, Gerrits M, Hackenberger CPR. Chemoselective Bioconjugation of Triazole Phosphonites in Aqueous Media. Chemistry 2014; 21:970-4. [DOI: 10.1002/chem.201404690] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Indexed: 11/07/2022]
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