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Foltz L, Palacios-Moreno J, Mayfield M, Kinch S, Dillon J, Syrenne J, Levy T, Grimes M. PAG1 directs SRC-family kinase intracellular localization to mediate receptor tyrosine kinase-induced differentiation. Mol Biol Cell 2020; 31:2269-2282. [PMID: 32726167 PMCID: PMC7550700 DOI: 10.1091/mbc.e20-02-0135] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
All receptor tyrosine kinases (RTKs) activate similar downstream signaling pathways through a common set of effectors, yet it is not fully understood how different receptors elicit distinct cellular responses to cause cell proliferation, differentiation, or other cell fates. We tested the hypothesis that regulation of SRC family kinase (SFK) signaling by the scaffold protein, PAG1, influences cell fate decisions following RTK activation. We generated a neuroblastoma cell line expressing a PAG1 fragment that lacks the membrane-spanning domain (PAG1TM-) and localized to the cytoplasm. PAG1TM- cells exhibited higher amounts of active SFKs and increased growth rate. PAG1TM- cells were unresponsive to TRKA and RET signaling, two RTKs that induce neuronal differentiation, but retained responses to EGFR and KIT. Under differentiation conditions, PAG1TM- cells continued to proliferate and did not extend neurites or increase β-III tubulin expression. FYN and LYN were sequestered in multivesicular bodies (MVBs), and dramatically more FYN and LYN were in the lumen of MVBs in PAG1TM- cells. In particular, activated FYN was sequestered in PAG1TM- cells, suggesting that disruption of FYN localization led to the observed defects in differentiation. The results demonstrate that PAG1 directs SFK intracellular localization to control activity and to mediate signaling by RTKs that induce neuronal differentiation.
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Affiliation(s)
- Lauren Foltz
- Division of Biological Sciences, Center for Biomolecular Structure and Dynamics, and Center for Structural and Functional Neuroscience, University of Montana, Missoula, MT 59812
| | | | - Makenzie Mayfield
- Division of Biological Sciences, Center for Biomolecular Structure and Dynamics, and Center for Structural and Functional Neuroscience, University of Montana, Missoula, MT 59812
| | - Shelby Kinch
- Division of Biological Sciences, Center for Biomolecular Structure and Dynamics, and Center for Structural and Functional Neuroscience, University of Montana, Missoula, MT 59812
| | - Jordan Dillon
- Division of Biological Sciences, Center for Biomolecular Structure and Dynamics, and Center for Structural and Functional Neuroscience, University of Montana, Missoula, MT 59812
| | - Jed Syrenne
- Division of Biological Sciences, Center for Biomolecular Structure and Dynamics, and Center for Structural and Functional Neuroscience, University of Montana, Missoula, MT 59812
| | - Tyler Levy
- Cell Signaling Technology, Danvers, MA 01923
| | - Mark Grimes
- Division of Biological Sciences, Center for Biomolecular Structure and Dynamics, and Center for Structural and Functional Neuroscience, University of Montana, Missoula, MT 59812
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2
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Beyond the Cell Surface: Targeting Intracellular Negative Regulators to Enhance T cell Anti-Tumor Activity. Int J Mol Sci 2019; 20:ijms20235821. [PMID: 31756921 PMCID: PMC6929154 DOI: 10.3390/ijms20235821] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 11/04/2019] [Accepted: 11/07/2019] [Indexed: 02/07/2023] Open
Abstract
It is well established that extracellular proteins that negatively regulate T cell function, such as Cytotoxic T-Lymphocyte-Associated protein 4 (CTLA-4) and Programmed Cell Death protein 1 (PD-1), can be effectively targeted to enhance cancer immunotherapies and Chimeric Antigen Receptor T cells (CAR-T cells). Intracellular proteins that inhibit T cell receptor (TCR) signal transduction, though less well studied, are also potentially useful therapeutic targets to enhance T cell activity against tumor. Four major classes of enzymes that attenuate TCR signaling include E3 ubiquitin kinases such as the Casitas B-lineage lymphoma proteins (Cbl-b and c-Cbl), and Itchy (Itch), inhibitory tyrosine phosphatases, such as Src homology region 2 domain-containing phosphatases (SHP-1 and SHP-2), inhibitory protein kinases, such as C-terminal Src kinase (Csk), and inhibitory lipid kinases such as Src homology 2 (SH2) domain-containing inositol polyphosphate 5-phosphatase (SHIP) and Diacylglycerol kinases (DGKs). This review describes the mechanism of action of eighteen intracellular inhibitory regulatory proteins in T cells within these four classes, and assesses their potential value as clinical targets to enhance the anti-tumor activity of endogenous T cells and CAR-T cells.
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Ilic K, Auer B, Mlinac-Jerkovic K, Herrera-Molina R. Neuronal Signaling by Thy-1 in Nanodomains With Specific Ganglioside Composition: Shall We Open the Door to a New Complexity? Front Cell Dev Biol 2019; 7:27. [PMID: 30899760 PMCID: PMC6416198 DOI: 10.3389/fcell.2019.00027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 02/15/2019] [Indexed: 01/06/2023] Open
Abstract
Thy-1 is a small membrane glycoprotein and member of the immunoglobulin superfamily of cell adhesion molecules. It is abundantly expressed in many cell types including neurons and is anchored to the outer membrane leaflet via a glycosyl phosphatidylinositol tail. Thy-1 displays a number of interesting properties such as fast lateral diffusion, which allows it to get in and out of membrane nanodomains with different lipid composition. Thy-1 displays a broad expression in different cell types and plays confirmed roles in cell development, adhesion and differentiation. Here, we explored the functions of Thy-1 in neuronal signaling, initiated by extracellular binding of αVβ3 integrin, may strongly dependent on the lipid content of the cell membrane. Also, we assort literature suggesting the association of Thy-1 with specific components of lipid rafts such as sialic acid containing glycosphingolipids, called gangliosides. Furthermore, we argue that Thy-1 positioning in nanodomains may be influenced by gangliosides. We propose that the traditional conception of Thy-1 localization in rafts should be reconsidered and evaluated in detail based on the potential diversity of neuronal nanodomains.
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Affiliation(s)
- Katarina Ilic
- Croatian Institute for Brain Research, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Benedikt Auer
- Laboratory of Neuronal and Synaptic Signals, Department of Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology, Magdeburg, Germany
| | - Kristina Mlinac-Jerkovic
- Croatian Institute for Brain Research, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Rodrigo Herrera-Molina
- Laboratory of Neuronal and Synaptic Signals, Department of Neurochemistry and Molecular Biology, Leibniz Institute for Neurobiology, Magdeburg, Germany.,Centro Integrativo de Biología y Química Aplicada, Universidad Bernardo O'Higgins, Santiago, Chile
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4
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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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5
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The proline-rich region of 18.5 kDa myelin basic protein binds to the SH3-domain of Fyn tyrosine kinase with the aid of an upstream segment to form a dynamic complex in vitro. Biosci Rep 2014; 34:e00157. [PMID: 25343306 PMCID: PMC4266924 DOI: 10.1042/bsr20140149] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The intrinsically disordered 18.5 kDa classic isoform of MBP (myelin basic protein) interacts with Fyn kinase during oligodendrocyte development and myelination. It does so primarily via a central proline-rich SH3 (Src homology 3) ligand (T92–R104, murine 18.5 kDa MBP sequence numbering) that is part of a molecular switch due to its high degree of conservation and modification by MAP (mitogen-activated protein) and other kinases, especially at residues T92 and T95. Here, we show using co-transfection experiments of an early developmental oligodendroglial cell line (N19) that an MBP segment upstream of the primary ligand is involved in MBP–Fyn–SH3 association in cellula. Using solution NMR spectroscopy in vitro, we define this segment to comprise MBP residues (T62–L68), and demonstrate further that residues (V83–P93) are the predominant SH3-target, assessed by the degree of chemical shift change upon titration. We show by chemical shift index analysis that there is no formation of local poly-proline type II structure in the proline-rich segment upon binding, and by NOE (nuclear Overhauser effect) and relaxation measurements that MBP remains dynamic even while complexed with Fyn–SH3. The association is a new example first of a non-canonical SH3-domain interaction and second of a fuzzy MBP complex. MBP interacts with Fyn kinase during oligodendrocyte development and myelination. We show that there is no binding-induced PPII formation in the primary ligand segment, and that a region upstream is required for in vitro interaction.
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Van Roey K, Uyar B, Weatheritt RJ, Dinkel H, Seiler M, Budd A, Gibson TJ, Davey NE. Short Linear Motifs: Ubiquitous and Functionally Diverse Protein Interaction Modules Directing Cell Regulation. Chem Rev 2014; 114:6733-78. [DOI: 10.1021/cr400585q] [Citation(s) in RCA: 293] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Kim Van Roey
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Bora Uyar
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Robert J. Weatheritt
- MRC
Laboratory of Molecular Biology (LMB), Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Holger Dinkel
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Markus Seiler
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Aidan Budd
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Toby J. Gibson
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Norman E. Davey
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Department
of Physiology, University of California, San Francisco, San Francisco, California 94143, United States
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7
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Saitou T, Kajiwara K, Oneyama C, Suzuki T, Okada M. Roles of raft-anchored adaptor Cbp/PAG1 in spatial regulation of c-Src kinase. PLoS One 2014; 9:e93470. [PMID: 24675741 PMCID: PMC3968143 DOI: 10.1371/journal.pone.0093470] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 03/06/2014] [Indexed: 11/21/2022] Open
Abstract
The tyrosine kinase c-Src is upregulated in numerous human cancers, implying a role for c-Src in cancer progression. Previously, we have shown that sequestration of activated c-Src into lipid rafts via a transmembrane adaptor, Cbp/PAG1, efficiently suppresses c-Src-induced cell transformation in Csk-deficient cells, suggesting that the transforming activity of c-Src is spatially regulated via Cbp in lipid rafts. To dissect the molecular mechanisms of the Cbp-mediated regulation of c-Src, a combined analysis was performed that included mathematical modeling and in vitro experiments in a c-Src- or Cbp-inducible system. c-Src activity was first determined as a function of c-Src or Cbp levels, using focal adhesion kinase (FAK) as a crucial c-Src substrate. Based on these experimental data, two mathematical models were constructed, the sequestration model and the ternary model. The computational analysis showed that both models supported our proposal that raft localization of Cbp is crucial for the suppression of c-Src function, but the ternary model, which includes a ternary complex consisting of Cbp, c-Src, and FAK, also predicted that c-Src function is dependent on the lipid-raft volume. Experimental analysis revealed that c-Src activity is elevated when lipid rafts are disrupted and the ternary complex forms in non-raft membranes, indicating that the ternary model accurately represents the system. Moreover, the ternary model predicted that, if Cbp enhances the interaction between c-Src and FAK, Cbp could promote c-Src function when lipid rafts are disrupted. These findings underscore the crucial role of lipid rafts in the Cbp-mediated negative regulation of c-Src-transforming activity, and explain the positive role of Cbp in c-Src regulation under particular conditions where lipid rafts are perturbed.
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Affiliation(s)
- Takashi Saitou
- Department of Molecular Medicine for Pathogenesis, Graduate School of Medicine, Ehime University, Shitsukawa, Toon, Ehime, Japan
- * E-mail: (TS); (KK)
| | - Kentaro Kajiwara
- Department of Oncogene Research, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- * E-mail: (TS); (KK)
| | - Chitose Oneyama
- Department of Oncogene Research, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Takashi Suzuki
- Division of Mathematical Science, Department of Systems Innovation, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, Japan
- JST, CREST, Chiyoda-ku, Tokyo, Japan
| | - Masato Okada
- Department of Oncogene Research, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
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8
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Rolland D, Basrur V, Conlon K, Wolfe T, Fermin D, Nesvizhskii AI, Lim MS, Elenitoba-Johnson KSJ. Global phosphoproteomic profiling reveals distinct signatures in B-cell non-Hodgkin lymphomas. THE AMERICAN JOURNAL OF PATHOLOGY 2014; 184:1331-42. [PMID: 24667141 DOI: 10.1016/j.ajpath.2014.01.036] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 12/05/2013] [Accepted: 01/02/2014] [Indexed: 12/23/2022]
Abstract
Deregulation of signaling pathways controlled by protein phosphorylation underlies the pathogenesis of hematological malignancies; however, the extent to which deregulated phosphorylation may be involved in B-cell non-Hodgkin lymphoma (B-NHL) pathogenesis is largely unknown. To identify phosphorylation events important in B-NHLs, we performed mass spectrometry-based, label-free, semiquantitative phosphoproteomic profiling of 11 cell lines derived from three B-NHL categories: Burkitt lymphoma, follicular lymphoma, and mantle-cell lymphoma. In all, 6579 unique phosphopeptides, corresponding to 1701 unique phosphorylated proteins, were identified and quantified. The data are available via ProteomeXchange with identifier PXD000658. Hierarchical clustering highlighted distinct phosphoproteomic signatures associated with each lymphoma subtype. Interestingly, germinal center-derived B-NHL cell lines were characterized by phosphorylation of proteins involved in the B-cell receptor signaling. Of these proteins, phosphoprotein associated with glycosphingolipid-enriched microdomains 1 (PAG1) was identified with the most phosphorylated tyrosine peptides in Burkitt lymphoma and follicular lymphoma. PAG1 knockdown resulted in perturbation of the tyrosine phosphosignature of B-cell receptor signaling components. Significantly, PAG1 knockdown increased cell proliferation and response to antigen stimulation of these germinal center-derived B-NHLs. These data provide a detailed annotation of phosphorylated proteins in human lymphoid cancer. Overall, our study revealed the utility of unbiased phosphoproteome interrogation in characterizing signaling networks that may provide insights into pathogenesis mechanisms in B-cell lymphomas.
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Affiliation(s)
- Delphine Rolland
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Venkatesha Basrur
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Kevin Conlon
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Thomas Wolfe
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan; Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Damian Fermin
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan; Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Megan S Lim
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan; Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Kojo S J Elenitoba-Johnson
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan; Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan; Center for Protein Folding Disease, University of Michigan Medical School, Ann Arbor, Michigan.
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9
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Yamada E, Bastie CC. Disruption of Fyn SH3 domain interaction with a proline-rich motif in liver kinase B1 results in activation of AMP-activated protein kinase. PLoS One 2014; 9:e89604. [PMID: 24586906 PMCID: PMC3934923 DOI: 10.1371/journal.pone.0089604] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 01/22/2014] [Indexed: 11/19/2022] Open
Abstract
Fyn-deficient mice display increased AMP-activated Protein Kinase (AMPK) activity as a result of Fyn-dependent regulation of Liver Kinase B1 (LKB1) in skeletal muscle. Mutation of Fyn-specific tyrosine sites in LKB1 results in LKB1 export into the cytoplasm and increased AMPK activation site phosphorylation. This study characterizes the structural elements responsible for the physical interaction between Fyn and LKB1. Effects of point mutations in the Fyn SH2/SH3 domains and in the LKB1 proline-rich motif on 1) Fyn and LKB1 binding, 2) LKB1 subcellular localization and 3) AMPK phosphorylation were investigated in C2C12 muscle cells. Additionally, novel LKB1 proline-rich motif mimicking cell permeable peptides were generated to disrupt Fyn/LKB1 binding and investigate the consequences on AMPK activity in both C2C12 cells and mouse skeletal muscle. Mutation of either Fyn SH3 domain or the proline-rich motif of LKB1 resulted in the disruption of Fyn/LKB1 binding, re-localization of 70% of LKB1 signal in the cytoplasm and a 2-fold increase in AMPK phosphorylation. In vivo disruption of the Fyn/LKB1 interaction using LKB1 proline-rich motif mimicking cell permeable peptides recapitulated Fyn pharmacological inhibition. We have pinpointed the structural elements within Fyn and LKB1 that are responsible for their binding, demonstrating the functionality of this interaction in regulating AMPK activity.
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Affiliation(s)
- Eijiro Yamada
- Diabetes Research and Training Center, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Department of Medicine and Molecular Science, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Claire C. Bastie
- Diabetes Research and Training Center, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Division Metabolic and Vascular Health, Warwick Medical School, University of Warwick, Coventry, United Kingdom
- * E-mail:
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10
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Hrdinka M, Horejsi V. PAG - a multipurpose transmembrane adaptor protein. Oncogene 2013; 33:4881-92. [DOI: 10.1038/onc.2013.485] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 09/25/2013] [Accepted: 09/25/2013] [Indexed: 12/25/2022]
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11
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Shammas S, Rogers J, Hill S, Clarke J. Slow, reversible, coupled folding and binding of the spectrin tetramerization domain. Biophys J 2012; 103:2203-14. [PMID: 23200054 PMCID: PMC3512043 DOI: 10.1016/j.bpj.2012.10.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 10/02/2012] [Accepted: 10/10/2012] [Indexed: 11/16/2022] Open
Abstract
Many intrinsically disordered proteins (IDPs) are significantly unstructured under physiological conditions. A number of these IDPs have been shown to undergo coupled folding and binding reactions whereby they can gain structure upon association with an appropriate partner protein. In general, these systems display weaker binding affinities than do systems with association between completely structured domains, with micromolar K(d) values appearing typical. One such system is the association between α- and β-spectrin, where two partially structured, incomplete domains associate to form a fully structured, three-helix bundle, the spectrin tetramerization domain. Here, we use this model system to demonstrate a method for fitting association and dissociation kinetic traces where, using typical biophysical concentrations, the association reactions are expected to be highly reversible. We elucidate the unusually slow, two-state kinetics of spectrin assembly in solution. The advantages of studying kinetics in this regime include the potential for gaining equilibrium constants as well as rate constants, and for performing experiments with low protein concentrations. We suggest that this approach would be particularly appropriate for high-throughput mutational analysis of two-state reversible binding processes.
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Affiliation(s)
| | | | | | - J. Clarke
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
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12
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Barua D, Hlavacek WS, Lipniacki T. A computational model for early events in B cell antigen receptor signaling: analysis of the roles of Lyn and Fyn. THE JOURNAL OF IMMUNOLOGY 2012; 189:646-58. [PMID: 22711887 DOI: 10.4049/jimmunol.1102003] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BCR signaling regulates the activities and fates of B cells. BCR signaling encompasses two feedback loops emanating from Lyn and Fyn, which are Src family protein tyrosine kinases (SFKs). Positive feedback arises from SFK-mediated trans phosphorylation of BCR and receptor-bound Lyn and Fyn, which increases the kinase activities of Lyn and Fyn. Negative feedback arises from SFK-mediated cis phosphorylation of the transmembrane adapter protein PAG1, which recruits the cytosolic protein tyrosine kinase Csk to the plasma membrane, where it acts to decrease the kinase activities of Lyn and Fyn. To study the effects of the positive and negative feedback loops on the dynamical stability of BCR signaling and the relative contributions of Lyn and Fyn to BCR signaling, we consider in this study a rule-based model for early events in BCR signaling that encompasses membrane-proximal interactions of six proteins, as follows: BCR, Lyn, Fyn, Csk, PAG1, and Syk, a cytosolic protein tyrosine kinase that is activated as a result of SFK-mediated phosphorylation of BCR. The model is consistent with known effects of Lyn and Fyn deletions. We find that BCR signaling can generate a single pulse or oscillations of Syk activation depending on the strength of Ag signal and the relative levels of Lyn and Fyn. We also show that bistability can arise in Lyn- or Csk-deficient cells.
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Affiliation(s)
- Dipak Barua
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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13
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Lindquist S, Karitkina D, Langnaese K, Posevitz-Fejfar A, Schraven B, Xavier R, Seed B, Lindquist JA. Phosphoprotein associated with glycosphingolipid-enriched microdomains differentially modulates SRC kinase activity in brain maturation. PLoS One 2011; 6:e23978. [PMID: 21915273 PMCID: PMC3167820 DOI: 10.1371/journal.pone.0023978] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Accepted: 08/02/2011] [Indexed: 12/19/2022] Open
Abstract
Src family kinases (SFK) control multiple processes during brain development and function. We show here that the phosphoprotein associated with glycosphigolipid-enriched microdomains (PAG)/Csk binding protein (Cbp) modulates SFK activity in the brain. The timing and localization of PAG expression overlap with Fyn and Src, both of which we find associated to PAG. We demonstrate in newborn (P1) mice that PAG negatively regulates Src family kinases (SFK). P1 Pag1-/- mouse brains show decreased recruitment of Csk into lipid rafts, reduced phosphorylation of the inhibitory tyrosines within SFKs, and an increase in SFK activity of >/ = 50%. While in brain of P1 mice, PAG and Csk are highly and ubiquitously expressed, little Csk is found in adult brain suggesting altered modes of SFK regulation. In adult brain Pag1-deficiency has no effect upon Csk-distribution or inhibitory tyrosine phosphorylation, but kinase activity is now reduced (−20–30%), pointing to the development of a compensatory mechanism that may involve PSD93. The distribution of the Csk-homologous kinase CHK is not altered. Importantly, since the activities of Fyn and Src are decreased in adult Pag1-/- mice, thus presenting the reversed phenotype of P1, this provides the first in vivo evidence for a Csk-independent positive regulatory function for PAG in the brain.
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Affiliation(s)
- Sabine Lindquist
- Department of Neurology, Hannover Medical School, Hannover, Germany.
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14
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Protein stability, flexibility and function. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:969-76. [PMID: 21094283 DOI: 10.1016/j.bbapap.2010.11.005] [Citation(s) in RCA: 156] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Revised: 09/24/2010] [Accepted: 11/11/2010] [Indexed: 02/08/2023]
Abstract
Proteins rely on flexibility to respond to environmental changes, ligand binding and chemical modifications. Potentially, a perturbation that changes the flexibility of a protein may interfere with its function. Millions of mutations have been performed on thousands of proteins in quests for a delineation of the molecular details of their function. Several of these mutations interfered with the binding of a specific ligand with a concomitant effect on the stability of the protein scaffold. It has been ambiguous and not straightforward to recognize if any relationships exist between the stability of a protein and the affinity for its ligand. In this review, we present examples of proteins where changes in stability results in changes in affinity and of proteins where stability and affinity are uncorrelated. We discuss the possibility for a relationship between stability and binding. From the data presented is it clear that there are specific sites (flexibility hotspots) in proteins that are important for both binding and stability. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.
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Loza MJ, Penn RB. Regulation of T cells in airway disease by beta-agonist. Front Biosci (Schol Ed) 2010; 2:969-79. [PMID: 20515836 DOI: 10.2741/s113] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
It is widely recognized that Th2 cytokines derived from T cells play a major role in the development of allergic lung inflammation that causes most asthma. Beta-agonists are important rescue and maintenance therapies for asthma, yet our understanding of beta-agonist effects on T cell biology is surprisingly poor. Recent studies using both cell culture and more integrative models are beginning to reveal beta-agonist regulation of T cell signaling and function that may be important in the pathogenesis and treatment of asthma and possibly other inflammatory diseases. Here we provide a comprehensive review of the literature concerning beta-agonist effects on T cells, and discuss the relevance of emerging paradigms of beta-adrenergic receptor signaling to T cell function.
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Affiliation(s)
- Matthew J Loza
- Department of Medicine, Division of Pulmonary and Critical Care Medicine University of Maryland School of Medicine, Baltimore, MD 21201, USA
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Tiwari R, Parang K. Protein conjugates of SH3-domain ligands and ATP-competitive inhibitors as bivalent inhibitors of protein kinases. Chembiochem 2010; 10:2445-8. [PMID: 19731277 DOI: 10.1002/cbic.200900462] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Rakesh Tiwari
- Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, 41 Lower College Road, Kingston, RI 02881, USA
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Kinetic advantage of intrinsically disordered proteins in coupled folding-binding process: a critical assessment of the "fly-casting" mechanism. J Mol Biol 2009; 393:1143-59. [PMID: 19747922 DOI: 10.1016/j.jmb.2009.09.010] [Citation(s) in RCA: 212] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2009] [Revised: 06/29/2009] [Accepted: 09/04/2009] [Indexed: 11/20/2022]
Abstract
Intrinsically disordered proteins (IDPs) are recognized to play important roles in many biological functions such as transcription and translation regulation, cellular signal transduction, protein phosphorylation, and molecular assemblies. The coupling of folding with binding through a "fly-casting" mechanism has been proposed to account for the fast binding kinetics of IDPs. In this article, experimental data from the literature were collated to verify the kinetic advantages of IDPs, while molecular simulations were performed to clarify the origin of the kinetic advantages. The phosphorylated KID-kinase-inducible domain interacting domain (KIX) complex was used as an example in the simulations. By modifying a coarse-grained model with a native-centric Gō-like potential, we were able to continuously tune the degree of disorder of the phosphorylated KID domain and thus investigate the intrinsic role of chain flexibility in binding kinetics. The simulations show that the "fly-casting" effect is not only due to the greater capture radii of IDPs. The coupling of folding with binding of IDPs leads to a significant reduction in binding free-energy barrier. Such a reduction accelerates the binding process. Although the greater capture radius has been regarded as the main factor in promoting the binding rate of IDPs, we found that this parameter will also lead to the slower translational diffusion of IDPs when compared with ordered proteins. As a result, the capture rate of IDPs was found to be slower than that of ordered proteins. The main origin of the faster binding for IDPs are the fewer encounter times required before the formation of the final binding complex. The roles of the interchain native contacts fraction (Q(b)) and the mass-center distance (DeltaR) as reaction coordinates are also discussed.
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Demers JP, Mittermaier A. Binding mechanism of an SH3 domain studied by NMR and ITC. J Am Chem Soc 2009; 131:4355-67. [PMID: 19267471 DOI: 10.1021/ja808255d] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Complexes between Src-homology 3 domains and proline-rich target peptides can have lifetimes on the order of milliseconds, making them too short-lived for kinetic characterization by conventional methods. Nuclear magnetic resonance (NMR) dynamics experiments are ideally suited to study such rapid binding equilibria, and additionally provide information on partly bound intermediate states. We used NMR together with isothermal titration calorimetry (ITC) to characterize the interaction of the SH3 domain from the Fyn tyrosine kinase with a 12-residue peptide at temperatures between 10 and 50 degrees C. NMR data at all temperatures are consistent with an effectively two-state binding reaction, such that any intermediates are either very weakly populated or exchange extremely rapidly with the free or bound forms. Dissociation rate constants, determined by CPMG and ZZ-exchange NMR experiments, range from k(off)(10 degrees C) = 4.5 s(-1) to k(off)(50 degrees C) = 331 s(-1). ITC data at all temperatures follow a simple two-state interaction model. Binding is favored enthalpically, with a dissociation enthalpy, DeltaH(D)(30 degrees C) = 15.4 kcal mol(-1), and disfavored entropically, with a dissociation entropy, DeltaS(D)(30 degrees C) = 20.0 cal mol(-1) K(-1). The free protein and peptide have significantly higher heat capacity than the bound complex, DeltaC(p) = 352 cal mol(-1) K(-1), which is consistent with the largely hydrophobic character of the binding interface. An Eyring plot of k(off) values gives an activation enthalpy of dissociation, DeltaH(D)(double dagger)(30 degrees C) = 19.3 kcal mol(-1) and exhibits slight curvature consistent with the ITC-derived value of DeltaC(p). The curvature suggests that nonpolar residues of the hydrophobic interface are solvated in the transition state for dissociation. Association rate constants were calculated as k(on) = k(off)/K(D), and range from k(on)(10 degrees C) = 1.03 x 10(8) M(-1) s(-1) to k(on)(50 degrees C) = 2.0 x 10(8) M(-1) s(-1), with an apparent activation enthalpy, DeltaH(A)(double dagger) = 3.4 kcal mol(-1). Both the magnitudes and temperature dependence of k(on) values are consistent with a diffusion-limited association mechanism. The combination of NMR and ITC data sheds light on how the Fyn tyrosine kinase is activated by binding to proline-rich targets, and represents a powerful approach for characterizing transient protein/ligand interactions.
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Affiliation(s)
- Jean-Philippe Demers
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, Canada, H3A 2K6
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