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van Vlimmeren AE, Voleti R, Chartier CA, Jiang Z, Karandur D, Humphries PA, Lo WL, Shah NH. The pathogenic T42A mutation in SHP2 rewires the interaction specificity of its N-terminal regulatory domain. bioRxiv 2024:2023.07.10.548257. [PMID: 37502916 PMCID: PMC10369915 DOI: 10.1101/2023.07.10.548257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Mutations in the tyrosine phosphatase SHP2 are associated with a variety of human diseases. Most mutations in SHP2 increase its basal catalytic activity by disrupting auto-inhibitory interactions between its phosphatase domain and N-terminal SH2 (phosphotyrosine recognition) domain. By contrast, some disease-associated mutations located in the ligand-binding pockets of the N- or C-terminal SH2 domains do not increase basal activity and likely exert their pathogenicity through alternative mechanisms. We lack a molecular understanding of how these SH2 mutations impact SHP2 structure, activity, and signaling. Here, we characterize five SHP2 SH2 domain ligand-binding pocket mutants through a combination of high-throughput biochemical screens, biophysical and biochemical measurements, and molecular dynamics simulations. We show that, while some of these mutations alter binding affinity to phosphorylation sites, the T42A mutation in the N-SH2 domain is unique in that it also substantially alters ligand-binding specificity, despite being 8-10 Å from the specificity-determining region of the SH2 domain. This mutation exerts its effect on sequence specificity by remodeling the phosphotyrosine binding pocket, altering the mode of engagement of both the phosphotyrosine and surrounding residues on the ligand. The functional consequence of this altered specificity is that the T42A mutant has biased sensitivity toward a subset of activating ligands and enhances downstream signaling. Our study highlights an example of a nuanced mechanism of action for a disease-associated mutation, characterized by a change in protein-protein interaction specificity that alters enzyme activation.
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Affiliation(s)
- Anne E. van Vlimmeren
- Department of Chemistry, Columbia University, New York, NY 10027
- Department of Biological Sciences, Columbia University, New York, NY 10027
| | - Rashmi Voleti
- Department of Chemistry, Columbia University, New York, NY 10027
| | | | - Ziyuan Jiang
- Department of Chemistry, Columbia University, New York, NY 10027
| | - Deepti Karandur
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232
| | - Preston A. Humphries
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Wan-Lin Lo
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Neel H. Shah
- Department of Chemistry, Columbia University, New York, NY 10027
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2
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Wu D, Fang X, Luan K, Xu Q, Lin S, Sun S, Yang J, Dong B, Manavalan B, Liao Z. Identification of SH2 domain-containing proteins and motifs prediction by a deep learning method. Comput Biol Med 2023; 162:107065. [PMID: 37267826 DOI: 10.1016/j.compbiomed.2023.107065] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 04/30/2023] [Accepted: 05/27/2023] [Indexed: 06/04/2023]
Abstract
The Src Homology 2 (SH2) domain plays an important role in the signal transmission mechanism in organisms. It mediates the protein-protein interactions based on the combination between phosphotyrosine and motifs in SH2 domain. In this study, we designed a method to identify SH2 domain-containing proteins and non-SH2 domain-containing proteins through deep learning technology. Firstly, we collected SH2 and non-SH2 domain-containing protein sequences including multiple species. We built six deep learning models through DeepBIO after data preprocessing and compared their performance. Secondly, we selected the model with the strongest comprehensive ability to conduct training and test separately again, and analyze the results visually. It was found that 288-dimensional (288D) feature could effectively identify two types of proteins. Finally, motifs analysis discovered the specific motif YKIR and revealed its function in signal transduction. In summary, we successfully identified SH2 domain and non-SH2 domain proteins through deep learning method, and obtained 288D features that perform best. In addition, we found a new motif YKIR in SH2 domain, and analyzed its function which helps to further understand the signaling mechanisms within the organism.
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Affiliation(s)
- Duanzhi Wu
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, China
| | - Xin Fang
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, China; Laboratory of Non-communicable Chronic Disease Control, Fujian Provincial Center for Disease Control and Prevention, Fuzhou, 350012, China
| | - Kai Luan
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, China
| | - Qijin Xu
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, China
| | - Shiqi Lin
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, China
| | - Shiying Sun
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, China
| | - Jiaying Yang
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, China
| | - Bingying Dong
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, China
| | - Balachandran Manavalan
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, 16419, Gyeonggi-do, Republic of Korea.
| | - Zhijun Liao
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, China.
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3
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Doggett K, Keating N, Dehkhoda F, Bidgood GM, Meza Guzman LG, Leong E, Kueh A, Nicola NA, Kershaw NJ, Babon JJ, Alexander WS, Nicholson SE. The SOCS1 KIR and SH2 domain are both required for suppression of cytokine signaling in vivo. Cytokine 2023; 165:156167. [PMID: 36934508 DOI: 10.1016/j.cyto.2023.156167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/22/2023] [Accepted: 02/24/2023] [Indexed: 03/19/2023]
Abstract
Suppressor Of Cytokine Signaling (SOCS) 1 is a critical negative regulator of cytokine signaling and required to protect against an excessive inflammatory response. Genetic deletion of Socs1 results in unrestrained cytokine signaling and neonatal lethality, characterised by an inflammatory immune infiltrate in multiple organs. Overexpression and structural studies have suggested that the SOCS1 kinase inhibitory region (KIR) and Src homology 2 (SH2) domain are important for interaction with and inhibition of the receptor-associated JAK1, JAK2 and TYK2 tyrosine kinases, which initiate downstream signaling. To investigate the role of the KIR and SH2 domain in SOCS1 function, we independently mutated key conserved residues in each domain and analysed the impact on cytokine signaling, and the in vivo impact on SOCS1 function. Mutation of the SOCS1-KIR or SH2 domain had no impact on the integrity of the SOCS box complex, however, mutation within the phosphotyrosine binding pocket of the SOCS1-SH2 domain specifically disrupted SOCS1 interaction with phosphorylated JAK1. In contrast, mutation of the KIR did not affect the interaction with JAK1, but did prevent SOCS1 inhibition of JAK1 autophosphorylation. In human and mouse cell lines, both mutants impacted the ability of SOCS1 to restrain cytokine signaling, and crucially, Socs1-R105A and Socs1-F59A mice displayed a neonatal lethality and excessive inflammatory phenotype similar to Socs1-null mice. This study defines a critical and non-redundant role for both the KIR and SH2 domain in endogenous SOCS1 function.
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Affiliation(s)
- Karen Doggett
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; Department of Medical Biology, University of Melbourne, Parkville, Australia.
| | - Narelle Keating
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Farhad Dehkhoda
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Grace M Bidgood
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Lizeth G Meza Guzman
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Evelyn Leong
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Andrew Kueh
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Nicos A Nicola
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Nadia J Kershaw
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Jeffrey J Babon
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Warren S Alexander
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Sandra E Nicholson
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; Department of Medical Biology, University of Melbourne, Parkville, Australia.
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Rios P, Kiani A, Köhn M. Measuring Protein Tyrosine Phosphatase Activity Dependent on SH2 Domain-Mediated Regulation. Methods Mol Biol 2023; 2705:351-358. [PMID: 37668983 DOI: 10.1007/978-1-0716-3393-9_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
Src-homology-2 (SH2) domains bind selectively to phosphotyrosine (pTyr) residues located in target binding proteins; therefore, they are key elements in pTyr-mediated signaling pathways. The binding of an SH2 domain to a pTyr acts as a docking mechanism that attracts proteins into signaling hubs, and in some cases, it can also regulate the catalytic activity of signaling enzymes such as protein kinases or protein phosphatases. Therefore, compounds that selectively bind SH2 domains can be potentially used to modulate the activity of such SH2 domain-containing enzymes. This chapter describes how to measure the regulation of protein tyrosine phosphatase activity through allosteric binding of peptides to SH2 domains, and uses human recombinant protein tyrosine phosphatase SHP2 (Src homology-2 domain-containing protein tyrosine phosphatase 2) purified from bacteria as a case example. The phosphatase activity against the artificial substrate DiFMUP (6, 8-Difluoro-4-Methylumbelliferyl Phosphate) is measured over time in the presence of a peptide that selectively binds and activates SHP2 at different concentrations to determine the half maximal effective concentration (EC50).
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Affiliation(s)
- Pablo Rios
- Faculty of Biology, Institute of Biology III, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Azin Kiani
- Faculty of Biology, Institute of Biology III, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
- Faculty of Chemistry and Pharmacy, University of Freiburg, Freiburg, Germany
| | - Maja Köhn
- Faculty of Biology, Institute of Biology III, University of Freiburg, Freiburg, Germany.
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.
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5
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Sámano-Sánchez H, Gibson TJ, Chemes LB. Using Linear Motif Database Resources to Identify SH2 Domain Binders. Methods Mol Biol 2023; 2705:153-197. [PMID: 37668974 DOI: 10.1007/978-1-0716-3393-9_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
The SH2-binding phosphotyrosine class of short linear motifs (SLiMs) are key conditional regulatory elements, particularly in signaling protein complexes beneath the cell's plasma membrane. In addition to transmitting cellular signaling information, they can also play roles in cellular hijack by invasive pathogens. Researchers can take advantage of bioinformatics tools and resources to predict the motifs at conserved phosphotyrosine residues in regions of intrinsically disordered protein. A candidate SH2-binding motif can be established and assigned to one or more of the SH2 domain subgroups. It is, however, not so straightforward to predict which SH2 domains are capable of binding the given candidate. This is largely due to the cooperative nature of the binding amino acids which enables poorer binding residues to be tolerated when the other residues are optimal. High-throughput peptide arrays are powerful tools used to derive SH2 domain-binding specificity, but they are unable to capture these cooperative effects and also suffer from other shortcomings. Tissue and cell type expression can help to restrict the list of available interactors: for example, some well-studied SH2 domain proteins are only present in the immune cell lineages. In this article, we provide a table of motif patterns and four bioinformatics strategies that introduce a range of tools that can be used in motif hunting in cellular and pathogen proteins. Experimental followup is essential to determine which SH2 domain/motif-containing proteins are the actual functional partners.
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Affiliation(s)
- Hugo Sámano-Sánchez
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Zhejiang University School of Medicine, International Campus, Zhejiang University, Haining, China
- Biomedical Sciences, Edinburgh Medical School, The University of Edinburgh, Edinburgh, UK
| | - Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Lucía B Chemes
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, Argentina.
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, San Martín, Argentina.
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6
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Xiao T, Zhang M, Ji H. Synthesis and Biochemical Evaluation of Monocarboxylic GRB2 SH2 Domain Inhibitors. Methods Mol Biol 2023; 2705:269-290. [PMID: 37668980 DOI: 10.1007/978-1-0716-3393-9_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
This protocol discloses the synthesis of monocarboxylic inhibitors with a macrocyclic peptide scaffold to bind with the GRB2 SH2 domain and disrupt the protein-protein interactions (PPIs) between GRB2 and phosphotyrosine-containing proteins.
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Affiliation(s)
- Tao Xiao
- Drug Discovery Department, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
- Departments of Oncologic Sciences and Chemistry, University of South Florida, Tampa, FL, USA
| | - Min Zhang
- Drug Discovery Department, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
- Departments of Oncologic Sciences and Chemistry, University of South Florida, Tampa, FL, USA
| | - Haitao Ji
- Drug Discovery Department, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA.
- Departments of Oncologic Sciences and Chemistry, University of South Florida, Tampa, FL, USA.
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7
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de Araujo ED, Orlova A, Ashraf QF, Moriggl R, Gunning PT. Inhibitor Library Screening of SH2 Domains Through Denaturation-Based Assays. Methods Mol Biol 2023; 2705:213-223. [PMID: 37668976 DOI: 10.1007/978-1-0716-3393-9_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
Screening of inhibitor libraries for candidate ligands is an important step in the drug discovery process. Thermal denaturation-based screening strategies are built on the premise that a protein-ligand complex has an altered stability profile compared to the protein alone. As such, these assays provide an accessible and rapid methodology for stratifying ligands that directly engage with the protein target of interest. Here, we describe three denaturation-based strategies for examining protein-inhibitor binding, in the context of SH2 domains. This includes conventional dye-based Thermal Shift Assays (TSA), nonconventional labeled ligand-based TSA, and Cellular Thermal Shift Assays (CETSA). Conventional dye-based TSA reports on the fluorescence of an external hydrophobic dye as it interacts with heat-exposed nonpolar protein surfaces as the temperature is incrementally increased. By contrast, nonconventional-labeled ligand TSA involves a fluorescence-tagged probe (phosphopeptide for SH2 domains) that is quenched as it dissociates from the protein during the denaturation process. CETSA involves monitoring the presence of the protein via Western blotting as the temperature is increased. In all three approaches, performing the assay in the presence of a candidate ligand can alter the melting profile of the protein. These assays offer primary screening tools to examine SH2 domain inhibitors libraries with varying chemical motifs, and a subset of the advantages and limitations of each approach is also discussed.
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Affiliation(s)
- Elvin D de Araujo
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Anna Orlova
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, Austria
| | - Qirat F Ashraf
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | - Richard Moriggl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, Austria
| | - Patrick T Gunning
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada.
- Department of Chemistry, University of Toronto, Toronto, ON, Canada.
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8
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Stiegler AL, Boggon TJ. Structure Determination of SH2-Phosphopeptide Complexes by X-Ray Crystallography: The Example of p120RasGAP. Methods Mol Biol 2023; 2705:77-89. [PMID: 37668970 DOI: 10.1007/978-1-0716-3393-9_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
The p120RasGAP protein contains two Src homology 2 (SH2) domains, each with phosphotyrosine-binding activity. We describe the crystallization of the isolated and purified p120RasGAP SH2 domains with phosphopeptides derived from a binding partner protein, p190RhoGAP. Purified recombinant SH2 domain protein is mixed with synthetic phosphopeptide at a stoichiometric ratio to form the complex in vitro. Crystallization is then achieved by the hanging drop vapor diffusion method over specific reservoir solutions that yield single macromolecular co-crystals containing SH2 domain protein and phosphopeptide. This protocol yields suitable crystals for X-ray diffraction studies, and our recent X-ray crystallography studies of the two SH2 domains of p120RasGAP demonstrate that the N-terminal SH2 domain binds phosphopeptide in a canonical interaction. In contrast, the C-terminal SH2 domain binds phosphopeptide via a unique atypical binding mode. The crystallographic studies for p120RasGAP illustrate that although the three-dimensional structure of SH2 domains and the molecular details of their binding to phosphotyrosine peptides are well defined, careful structural analysis can continue to yield new molecular-level insights.
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Affiliation(s)
- Amy L Stiegler
- Department of Pharmacology, Yale University, New Haven, CT, USA
| | - Titus J Boggon
- Department of Pharmacology, Yale University, New Haven, CT, USA.
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
- Yale Cancer Center, Yale University, New Haven, CT, USA.
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9
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Li K, Meza Guzman LG, Whitehead L, Leong E, Kueh A, Alexander WS, Kershaw NJ, Babon JJ, Doggett K, Nicholson SE. SOCS2 regulation of growth hormone signaling requires a canonical interaction with phosphotyrosine. Biosci Rep 2022; 42:BSR20221683. [PMID: 36398696 DOI: 10.1042/BSR20221683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 10/21/2022] [Accepted: 10/26/2022] [Indexed: 11/19/2022] Open
Abstract
Suppressor of cytokine signaling (SOCS) 2 is the critical negative regulator of growth hormone (GH) and prolactin signaling. Mice lacking SOCS2 display gigantism with increased body weight and length, and an enhanced response to GH treatment. Here, we characterized mice carrying a germ-line R96C mutation within the SOCS2-SH2 domain, which disrupts the ability of SOCS2 to interact with tyrosine-phosphorylated targets. Socs2R96C/R96C mice displayed a similar increase in growth as previously observed in SOCS2 null (Socs2-/-) mice, with a proportional increase in body and organ weight, and bone length. Embryonic fibroblasts isolated from Socs2R96C/R96C and Socs2-/- mice also showed a comparable increase in phosphorylation of STAT5 following GH stimulation, indicating the critical role of phosphotyrosine binding in SOCS2 function.
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10
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Stiegler AL, Vish KJ, Boggon TJ. Tandem engagement of phosphotyrosines by the dual SH2 domains of p120RasGAP. Structure 2022; 30:1603-1614.e5. [PMID: 36417908 PMCID: PMC9722645 DOI: 10.1016/j.str.2022.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/22/2022] [Accepted: 10/27/2022] [Indexed: 11/23/2022]
Abstract
p120RasGAP is a multidomain GTPase-activating protein for Ras. The presence of two Src homology 2 domains in an SH2-SH3-SH2 module raises the possibility that p120RasGAP simultaneously binds dual phosphotyrosine residues in target proteins. One known binding partner with two proximal phosphotyrosines is p190RhoGAP, a GTPase-activating protein for Rho GTPases. Here, we present the crystal structure of the p120RasGAP SH2-SH3-SH2 module bound to a doubly tyrosine-phosphorylated p190RhoGAP peptide, revealing simultaneous phosphotyrosine recognition by the SH2 domains. The compact arrangement places the SH2 domains in close proximity resembling an SH2 domain tandem and exposed SH3 domain. Affinity measurements support synergistic binding, while solution scattering reveals that dual phosphotyrosine binding induces compaction of this region. Our studies reflect a binding mode that limits conformational flexibility within the SH2-SH3-SH2 cassette and relies on the spacing and sequence surrounding the two phosphotyrosines, potentially representing a selectivity mechanism for downstream signaling events.
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Affiliation(s)
- Amy L Stiegler
- Department of Pharmacology, Yale University, New Haven, CT, USA
| | - Kimberly J Vish
- Department of Pharmacology, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Titus J Boggon
- Department of Pharmacology, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Yale Cancer Center, Yale University, New Haven, CT, USA.
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11
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Berg A, Gräber M, Schmutzler S, Hoffmann R, Berg T. A High-Throughput Fluorescence Polarization-Based Assay for the SH2 Domain of STAT4. Methods Protoc 2022; 5. [PMID: 36548135 DOI: 10.3390/mps5060093] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/14/2022] [Accepted: 11/17/2022] [Indexed: 11/25/2022] Open
Abstract
The signal transducer and activation of transcription (STAT) proteins are a family of Src homology 2 (SH2) domain-containing transcription factors. The family member STAT4 is a mediator of IL-12 signalling and has been implicated in the pathogenesis of multiple autoimmune diseases. The activity of STAT4 requires binding of phosphotyrosine-containing motifs to its SH2 domain. Selective inhibitors of the STAT4 SH2 domain have not been published to date. Here, we present a fluorescence polarization-based assay for the identification of inhibitors of the STAT4 SH2 domain. The assay is based on the interaction between the STAT4 SH2 domain and the fluorophore-labelled peptide 5-carboxyfluorescein-GpYLPQNID (Kd = 34 ± 4 nM). The assay is stable with respect to DMSO concentrations of up to 10% and incubation times of at least 8 h. The Z'-value of 0.85 ± 0.01 indicates that the assay is suited for use in high-throughput screening campaigns aimed at identifying new therapeutic modalities for the treatment of autoimmune diseases.
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12
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Wang Z, Shan Y, Wang R, Zhou H, Hu R, Li Y, Zhu J, Yang Y, Liu M. Structural Insights into the Binding Propensity of Human SHIP2 SH2 to Oncogenic CagA Isoforms from Helicobacter pylori. Int J Mol Sci 2022; 23. [PMID: 36232599 DOI: 10.3390/ijms231911299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/20/2022] [Accepted: 09/20/2022] [Indexed: 11/30/2022] Open
Abstract
SHIP2 is a multi-domain inositol 5-phosphatase binding to a variety of phosphotyrosine (pY)-containing proteins through its SH2 domain, so as to regulate various cell signaling pathways by modulating the phosphatidylinositol level in the plasma membrane. Unfavorably, Helicobacter pylori can hijack SHIP2 through the CagA protein to induce gastric cell carcinogenesis. To date, the interaction between SHIP2 and CagA was not analyzed from a structural point of view. Here, the binding of SHIP2-SH2 with Tyr-phosphorylated peptides from four EPIYA motifs (A/B/C/D) in CagA was studied using NMR spectroscopy. The results showed that EPIYA-C and -D bind to a similar interface of SHIP2-SH2, including a pY-binding pocket and a hydrophobic pocket, to achieve high affinity, while EPIYA-A and -B bind to a smaller interface of SHIP2-SH2 with weak affinity. By summarizing the interface and affinity of SHIP2-SH2 for CagA EPIYA-A/B/C/D, c-MET and FcgR2B ITIM, it was proposed that, potentially, SHIP2-SH2 has a selective preference for L > I > V for the aliphatic residues at the pY+3 position in its ligand. This study reveals the rule of the ligand sequence bound by SHIP2-SH2 and the mechanism by which CagA protein hijacks SHIP2, which will help design a peptide inhibitor against SHIP2-SH2.
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Chen JL, Barr JY, Zuk JJ, Gorman JV, Colgan JD. Reciprocal SH2-SH3 Domain Contacts between ITK Molecules Limit T Cell Receptor Signaling in Th2-type CD4 + T Cells. Immunol Invest 2022; 51:1612-1629. [PMID: 34844506 DOI: 10.1080/08820139.2021.2007262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The nonreceptor tyrosine kinase ITK is a key component of the T cell receptor (TCR) signaling pathway and is required for cytokine production by CD4+ T cells that have differentiated into Th2 cells. Structural and biochemical studies suggest that contacts between the SH2 and SH3 domains of ITK mediate intermolecular self-association, forming a structure that restrains ITK activity by interfering with interactions between ITK and other components of the TCR signaling pathway. Wild-type (WT) ITK and a panel of ITK mutants containing amino acid substitutions in the SH2 and SH3 domains were tested for self-association and for binding to the adaptor protein SLP76, a key ligand for the ITK SH2 domain. WT and ITK mutants were also expressed in Itk-deficient CD4+ T cells via retroviral-mediated gene delivery to analyze their ability to support TCR signaling and cytokine production by Th2 cells. Specific amino acid substitutions in the ITK SH2 or SH3 domains impaired self-association, with the greatest effects being seen when both intermolecular SH2-SH3 domain contacts were disrupted. Two of the SH2 domain substitutions tested reduced ITK self-association but had no effect on binding to SLP-76. When their function was analyzed in Th2 cells, ITK proteins with diminished self-association activity supported greater IL-4 production and calcium flux in response to TCR stimulation compared to WT ITK. Our findings indicate that intermolecular contacts between ITK molecules can restrain the amplitude of TCR signaling, suggesting ITK is a limiting factor for responses by CD4+ T cells.
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Affiliation(s)
- Ji-Long Chen
- Department of Internal Medicine, Roy J. And Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Jennifer Y Barr
- Department of Anatomy and Cell Biology, Roy J. And Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Jonathan J Zuk
- The Molecular Medicine Graduate Program, Roy J. And Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Jacob V Gorman
- The Immunology Graduate Program, Roy J. And Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - John D Colgan
- Department of Internal Medicine, Roy J. And Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA.,Department of Anatomy and Cell Biology, Roy J. And Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA.,The Molecular Medicine Graduate Program, Roy J. And Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA.,The Immunology Graduate Program, Roy J. And Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
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14
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Tang Q, Fang J, Lai W, Hu Y, Liu C, Hu X, Song C, Cheng T, Liu R, Huang X. Hippo pathway monomerizes STAT3 to regulate prostate cancer growth. Cancer Sci 2022; 113:2753-2762. [PMID: 35722967 PMCID: PMC9357639 DOI: 10.1111/cas.15463] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 04/25/2022] [Accepted: 06/09/2022] [Indexed: 02/05/2023] Open
Abstract
Prostate cancer ranks among the most commonly diagnosed malignancies for men, and has become a non-negligible threat for public health. Interplay between inflammatory factors and cancer cells renders inflammatory tissue environment as a predisposing condition for cancer development. The Hippo pathway is a conserved signaling pathway across multiple species during evolution that regulates tissue homeostasis and organ development. Nevertheless, whether Hippo pathway regulates cancer-related inflammatory factors remain elusive. Here we show that high cell density-mediated activation of Hippo pathway blunts STAT3 activity in prostate cancer cells. Hippo pathway component MST2 kinase phosphorylates STAT3 at T622, which is located in the SH2 domain of STAT3. This phosphorylation blocks SH2 domain in one STAT3 molecule to bind with the phosphorylated Y705 site in another STAT3 molecule, which further counteracts IL6-induced STAT3 dimerization and activation. Expression of a non-phosphoryable STAT3 T622A mutant enhances STAT3 activity and IL6 expression at high cell density, and promotes tumor growth in mice xenograft model. Our findings demonstrate that STAT3 is a novel phosphorylation substrate for MST2, and thereby highlight a regulatory cascade underlying the crosstalk between inflammation and Hippo pathway in prostate cancer cells.
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Affiliation(s)
- Qingfeng Tang
- Department of Urology, Xindu district People's hospital of Chengdu, Chengdu, 610500, China
| | - Jing Fang
- Department of Nephrology, The sixth people's hospital of Chengdu, Chengdu, 610051, China
| | - Weiqi Lai
- Department of Urology, Xindu district People's hospital of Chengdu, Chengdu, 610500, China
| | - Yu Hu
- Department of Urology, Xindu district People's hospital of Chengdu, Chengdu, 610500, China
| | - Chengwan Liu
- Department of Urology, Xindu district People's hospital of Chengdu, Chengdu, 610500, China
| | - Xiaobo Hu
- Department of Urology, Xindu district People's hospital of Chengdu, Chengdu, 610500, China
| | - Caiyong Song
- Department of Urology, Xindu district People's hospital of Chengdu, Chengdu, 610500, China
| | - Tianmu Cheng
- Department of Urology, Xindu district People's hospital of Chengdu, Chengdu, 610500, China
| | - Rui Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, P. R. China
| | - Xiaoke Huang
- Department of Urology, Xindu district People's hospital of Chengdu, Chengdu, 610500, China
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15
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Sturre NP, Colson RN, Shah N, Watson GM, Yang X, Wilce MCJ, Price JT, Wilce JA. Enhancing the Bioactivity of Bicyclic Peptides Targeted to Grb7-SH2 by Restoring Cell Permeability. Biomedicines 2022; 10:1145. [PMID: 35625882 PMCID: PMC9138261 DOI: 10.3390/biomedicines10051145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 05/14/2022] [Accepted: 05/14/2022] [Indexed: 11/17/2022] Open
Abstract
The development of peptide inhibitors against intracellular targets depends upon the dual challenge of achieving a high affinity and specificity for the target and maintaining cellular permeability for biological activity. Previous efforts to develop bicyclic peptides targeted to the Grb7 signalling protein implicated in HER2+ve cancer progression have resulted in improved affinity. However, these same peptides demonstrated a lowered activity due to their decreased ability to penetrate cell membranes. Here, we report the testing of a new series of bicyclic G7 peptides designed to possess improved bioactivity. We discovered that the incorporation of two amino acids (Phe-Pro, Phe-Trp or Phe-Arg) within the bicyclic peptide framework maintains an enhanced binding affinity for the Grb7-SH2 domain compared to that of the first-generation monocyclic peptide G7-18NATE. Structure determination using X-ray crystallography revealed that the mode of binding by the expanded bicyclic G7 peptide is analogous to that of G7-18NATE. Interestingly, while the bicyclic peptide containing Phe-Trp did not display the highest affinity for Grb7-SH2 in the series, it was the most potent inhibitor of HER2+ve SKBR3 breast cancer cell migration when coupled to Penetratin. Together, this demonstrates that peptide flexibility as well as the amino acid tryptophan can play important roles in the uptake of peptides into the cell.
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Affiliation(s)
- Natasha P. Sturre
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Wellington Road, Clayton, VIC 3800, Australia; (N.P.S.); (R.N.C.); (N.S.); (G.M.W.); (X.Y.); (M.C.J.W.); (J.T.P.)
| | - Rhys N. Colson
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Wellington Road, Clayton, VIC 3800, Australia; (N.P.S.); (R.N.C.); (N.S.); (G.M.W.); (X.Y.); (M.C.J.W.); (J.T.P.)
| | - Neelam Shah
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Wellington Road, Clayton, VIC 3800, Australia; (N.P.S.); (R.N.C.); (N.S.); (G.M.W.); (X.Y.); (M.C.J.W.); (J.T.P.)
| | - Gabrielle M. Watson
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Wellington Road, Clayton, VIC 3800, Australia; (N.P.S.); (R.N.C.); (N.S.); (G.M.W.); (X.Y.); (M.C.J.W.); (J.T.P.)
| | - Xue Yang
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Wellington Road, Clayton, VIC 3800, Australia; (N.P.S.); (R.N.C.); (N.S.); (G.M.W.); (X.Y.); (M.C.J.W.); (J.T.P.)
| | - Matthew C. J. Wilce
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Wellington Road, Clayton, VIC 3800, Australia; (N.P.S.); (R.N.C.); (N.S.); (G.M.W.); (X.Y.); (M.C.J.W.); (J.T.P.)
| | - John T. Price
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Wellington Road, Clayton, VIC 3800, Australia; (N.P.S.); (R.N.C.); (N.S.); (G.M.W.); (X.Y.); (M.C.J.W.); (J.T.P.)
- Institute for Health and Sport, Victoria University, Melbourne, VIC 8001, Australia
| | - Jacqueline A. Wilce
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Wellington Road, Clayton, VIC 3800, Australia; (N.P.S.); (R.N.C.); (N.S.); (G.M.W.); (X.Y.); (M.C.J.W.); (J.T.P.)
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Abstract
The non-catalytic region of tyrosine kinase (Nck) family of adaptors, consisting of Nck1 and Nck2, contributes to selectivity and specificity in the flow of cellular information by recruiting components of signaling networks. Known to play key roles in cytoskeletal remodeling, Nck adaptors modulate host cell-pathogen interactions, immune cell receptor activation, cell adhesion and motility, and intercellular junctions in kidney podocytes. Genetic inactivation of both members of the Nck family results in embryonic lethality; however, viability of mice lacking either one of these adaptors suggests partial functional redundancy. In this Cell Science at a Glance and the accompanying poster, we highlight the molecular organization and functions of the Nck family, focusing on key interactions and pathways, regulation of cellular processes, development, homeostasis and pathogenesis, as well as emerging and non-redundant functions of Nck1 compared to those of Nck2. This article thus aims to provide a timely perspective on the biology of Nck adaptors and their potential as therapeutic targets.
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Affiliation(s)
- Briana C. Bywaters
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 7783, USA
| | - Gonzalo M. Rivera
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 7783, USA
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17
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Landau LJB, Fam BSDO, Yépez Y, Caldas-Garcia GB, Pissinatti A, Falótico T, Reales G, Schüler-Faccini L, Sortica VA, Bortolini MC. Evolutionary analysis of the anti-viral STAT2 gene of primates and rodents: Signature of different stages of an arms race. Infect Genet Evol 2021; 95:105030. [PMID: 34384937 DOI: 10.1016/j.meegid.2021.105030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/24/2021] [Accepted: 08/06/2021] [Indexed: 02/04/2023]
Abstract
STAT2 plays a strategic role in defending viral infection through the signaling cascade involving the immune system initiated after type I interferon release. Many flaviviruses target the inactivation or degradation of STAT2 as a strategy to impair this host's line of defense. Primates are natural reservoirs for a range of disease-causing flaviviruses (e.g., Zika, Dengue, and Yellow Fever virus), while rodents appear less susceptible. We analyzed the STAT2 coding sequence of 28 Rodentia species and 49 Primates species. Original data from 19 Platyrrhini species were sequenced for the SH2 domain of STAT2 and included in the analysis. STAT2 has many sites whose variation can be explained by positive selection, measurement by two methods (PALM indicated 12, MEME 61). Both evolutionary tests significantly marked sites 127, 731, 739, 766, and 780. SH2 is under evolutionary constraint but presents episodic positive selection events within Rodentia: in one of them, a moderately radical change (serine > arginine) at position 638 is found in Peromyscus species, and can be implicated in the difference in susceptibility to flaviviruses within Rodentia. Some other positively selected sites are functional such as 5, 95, 203, 251, 782, and 829. Sites 251 and 287 regulate the signaling mediated by the JAK-STAT2 pathway, while 782 and 829 create a stable tertiary structure of STAT2, facilitating its connection with transcriptional co-activators. Only three positively selected sites, 5, 95, and 203, are recognized members who act on the interface between STAT2 and flaviviruses NS5 protein. We suggested that due to the higher evolutionary rate, rodents are, at this moment, taking some advantage in the battle against infections for some well-known Flaviviridae, in particular when compared to primates. Our results point to dynamics that fit with a molecular evolutionary scenario shaped by a thought-provoking virus-host arms race.
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Affiliation(s)
- Luane Jandira Bueno Landau
- Laboratório de Evolução Humana e Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Bibiana Sampaio de Oliveira Fam
- Laboratório de Evolução Humana e Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Yuri Yépez
- Laboratório de Evolução Humana e Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Gabriela Barreto Caldas-Garcia
- Laboratório de Evolução Humana e Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Alcides Pissinatti
- Rio de Janeiro's Primatology Center (RJPC - INEA), Rio de Janeiro, RJ, Brazil
| | - Tiago Falótico
- School of Arts, Sciences and Humanities, University of São Paulo, São Paulo, SP, Brazil
| | - Guillermo Reales
- Laboratório de Evolução Humana e Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil; Instituto Nacional de Genética Médica Populacional, Serviço de Genética Médica, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Lavínia Schüler-Faccini
- Instituto Nacional de Genética Médica Populacional, Serviço de Genética Médica, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Vinicius Albuquerque Sortica
- Laboratório de Evolução Humana e Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Maria Cátira Bortolini
- Laboratório de Evolução Humana e Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.
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18
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Oleksak P, Psotka M, Vancurova M, Sapega O, Bieblova J, Reinis M, Rysanek D, Mikyskova R, Chalupova K, Malinak D, Svobodova J, Andrys R, Rehulkova H, Skopek V, Ngoc Lam P, Bartek J, Hodny Z, Musilek K. Design, synthesis, and in vitro evaluation of BP-1-102 analogs with modified hydrophobic fragments for STAT3 inhibition. J Enzyme Inhib Med Chem 2021; 36:410-424. [PMID: 33440995 PMCID: PMC7808747 DOI: 10.1080/14756366.2020.1871336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Twelve novel analogs of STAT3 inhibitor BP-1-102 were designed and synthesised with the aim to modify hydrophobic fragments of the molecules that are important for interaction with the STAT3 SH2 domain. The cytotoxic activity of the reference and novel compounds was evaluated using several human and two mouse cancer cell lines. BP-1-102 and its two analogs emerged as effective cytotoxic agents and were further tested in additional six human and two murine cancer cell lines, in all of which they manifested the cytotoxic effect in a micromolar range. Reference compound S3I-201.1066 was found ineffective in all tested cell lines, in contrast to formerly published data. The ability of selected BP-1-102 analogs to induce apoptosis and inhibition of STAT3 receptor-mediated phosphorylation was confirmed. The structure–activity relationship confirmed a demand for two hydrophobic substituents, i.e. the pentafluorophenyl moiety and another spatially bulky moiety, for effective cytotoxic activity and STAT3 inhibition.
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Affiliation(s)
- Patrik Oleksak
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Miroslav Psotka
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Marketa Vancurova
- Department of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Olena Sapega
- Laboratory of Immunological and Tumour Models, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jana Bieblova
- Laboratory of Immunological and Tumour Models, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Milan Reinis
- Laboratory of Immunological and Tumour Models, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - David Rysanek
- Department of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Romana Mikyskova
- Laboratory of Immunological and Tumour Models, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Katarina Chalupova
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - David Malinak
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Jana Svobodova
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Rudolf Andrys
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Helena Rehulkova
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Vojtech Skopek
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Pham Ngoc Lam
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Jiri Bartek
- Department of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic.,Genome Integrity Unit, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Zdenek Hodny
- Department of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Kamil Musilek
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
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Sipeki S, Koprivanacz K, Takács T, Kurilla A, László L, Vas V, Buday L. Novel Roles of SH2 and SH3 Domains in Lipid Binding. Cells 2021; 10:1191. [PMID: 34068055 DOI: 10.3390/cells10051191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/10/2021] [Accepted: 05/11/2021] [Indexed: 01/07/2023] Open
Abstract
Signal transduction, the ability of cells to perceive information from the surroundings and alter behavior in response, is an essential property of life. Studies on tyrosine kinase action fundamentally changed our concept of cellular regulation. The induced assembly of subcellular hubs via the recognition of local protein or lipid modifications by modular protein interactions is now a central paradigm in signaling. Such molecular interactions are mediated by specific protein interaction domains. The first such domain identified was the SH2 domain, which was postulated to be a reader capable of finding and binding protein partners displaying phosphorylated tyrosine side chains. The SH3 domain was found to be involved in the formation of stable protein sub-complexes by constitutively attaching to proline-rich surfaces on its binding partners. The SH2 and SH3 domains have thus served as the prototypes for a diverse collection of interaction domains that recognize not only proteins but also lipids, nucleic acids, and small molecules. It has also been found that particular SH2 and SH3 domains themselves might also bind to and rely on lipids to modulate complex assembly. Some lipid-binding properties of SH2 and SH3 domains are reviewed here.
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Ge L, Wu B, Zhang Y, Wang J, Zhao H, Wang J. Biochemical and NMR characterization of the interactions of Vav2- SH2 domain with lipids and the EphA2 juxtamembrane region on membrane. Biochem J 2020; 477:3791-801. [PMID: 32897354 DOI: 10.1042/BCJ20200300] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 09/05/2020] [Accepted: 09/07/2020] [Indexed: 12/21/2022]
Abstract
Vav2 is a ubiquitous guanine nucleotide exchange factor (GEF) for Rho family GTPases that is involved in regulating a wide range of biological processes. It interacts with several tyrosine-phosphorylated cell surface receptors, including the Eph family receptors, through its SH2 domain. The interaction of Vav2 with EphA2 is crucial for EphA2-mediated tumor angiogenesis. Here we show that Vav2-SH2 domain is a lipid-binding module that can recognize PI(4,5)P2 and PI(3,4,5)P3 lipids weakly but specifically. The specific lipid-binding site in Vav2-SH2 domain was identified by NMR chemical shift perturbation experiments using the head groups of PI(4,5)P2 and PI(3,4,5)P3, both of which bind to Vav2-SH2 with millimolar binding affinities. In addition, the interaction between Vav2-SH2 and the phosphorylated juxtamembrane region (JM) of EphA2 (Y594 phosphorylated) was investigated using NMR techniques. Furthermore, by using a nickel-lipid containing peptide-based nanodiscs system, we studied the binding of Vav2-SH2 to the phosphorylated JM region of EphA2 on lipid membrane and uncovered a role of membrane environment in modulating this protein-protein recognition.
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21
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Mayoral-Varo V, Sánchez-Bailón MP, Calcabrini A, García-Hernández M, Frezza V, Martín ME, González VM, Martín-Pérez J. The Relevance of the SH2 Domain for c-Src Functionality in Triple-Negative Breast Cancer Cells. Cancers (Basel) 2021; 13:cancers13030462. [PMID: 33530373 PMCID: PMC7865352 DOI: 10.3390/cancers13030462] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/15/2021] [Accepted: 01/19/2021] [Indexed: 02/05/2023] Open
Abstract
The role of Src family kinases (SFKs) in human tumors has been always associated with tyrosine kinase activity and much less attention has been given to the SH2 and SH3 adapter domains. Here, we studied the role of the c-Src-SH2 domain in triple-negative breast cancer (TNBC). To this end, SUM159PT and MDA-MB-231 human cell lines were employed as model systems. These cells conditionally expressed, under tetracycline control (Tet-On system), a c-Src variant with point-inactivating mutation of the SH2 adapter domain (R175L). The expression of this mutant reduced the self-renewal capability of the enriched population of breast cancer stem cells (BCSCs), demonstrating the importance of the SH2 adapter domain of c-Src in the mammary gland carcinogenesis. In addition, the analysis of anchorage-independent growth, proliferation, migration, and invasiveness, all processes associated with tumorigenesis, showed that the SH2 domain of c-Src plays a very relevant role in their regulation. Furthermore, the transfection of two different aptamers directed to SH2-c-Src in both SUM159PT and MDA-MB-231 cells induced inhibition of their proliferation, migration, and invasiveness, strengthening the hypothesis that this domain is highly involved in TNBC tumorigenesis. Therefore, the SH2 domain of c-Src could be a promising therapeutic target and combined treatments with inhibitors of c-Src kinase enzymatic activity may represent a new therapeutic strategy for patients with TNBC, whose prognosis is currently very negative.
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Affiliation(s)
- Víctor Mayoral-Varo
- Instituto de Investigaciones Biomédicas A, Sols/Dpto. Bioquímica (CSIC/UAM), Arturo Duperier 4, 28029 Madrid, Spain; (V.M.-V.); (M.P.S.-B.); (A.C.)
| | - María Pilar Sánchez-Bailón
- Instituto de Investigaciones Biomédicas A, Sols/Dpto. Bioquímica (CSIC/UAM), Arturo Duperier 4, 28029 Madrid, Spain; (V.M.-V.); (M.P.S.-B.); (A.C.)
- Max Delbrück Center for Molecular Medicine (MDC), Robert-Rössle-Str. 10, 13092 Berlin, Germany
| | - Annarica Calcabrini
- Instituto de Investigaciones Biomédicas A, Sols/Dpto. Bioquímica (CSIC/UAM), Arturo Duperier 4, 28029 Madrid, Spain; (V.M.-V.); (M.P.S.-B.); (A.C.)
- National Center for Drug Research and Evaluation, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Marta García-Hernández
- Grupo de Aptámeros, Servicio Bioquímica-Investigación, IRYCIS-Hospital Ramón y Cajal. Ctra. Colmenar Viejo km 9100, 28034 Madrid, Spain; (M.G.-H.); (V.F.); (M.E.M.); (V.M.G.)
| | - Valerio Frezza
- Grupo de Aptámeros, Servicio Bioquímica-Investigación, IRYCIS-Hospital Ramón y Cajal. Ctra. Colmenar Viejo km 9100, 28034 Madrid, Spain; (M.G.-H.); (V.F.); (M.E.M.); (V.M.G.)
| | - María Elena Martín
- Grupo de Aptámeros, Servicio Bioquímica-Investigación, IRYCIS-Hospital Ramón y Cajal. Ctra. Colmenar Viejo km 9100, 28034 Madrid, Spain; (M.G.-H.); (V.F.); (M.E.M.); (V.M.G.)
| | - Víctor M. González
- Grupo de Aptámeros, Servicio Bioquímica-Investigación, IRYCIS-Hospital Ramón y Cajal. Ctra. Colmenar Viejo km 9100, 28034 Madrid, Spain; (M.G.-H.); (V.F.); (M.E.M.); (V.M.G.)
| | - Jorge Martín-Pérez
- Instituto de Investigaciones Biomédicas A, Sols/Dpto. Bioquímica (CSIC/UAM), Arturo Duperier 4, 28029 Madrid, Spain; (V.M.-V.); (M.P.S.-B.); (A.C.)
- Instituto de Investigaciones Sanitarias del Hospital La Paz (IdiPAZ), Paseo de la Castellana 261, 28046 Madrid, Spain
- Correspondence: or ; Tel.: +34-91-585-4416; Fax: +34-91-585-4401
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Staudt RP, Alvarado JJ, Emert-Sedlak LA, Shi H, Shu ST, Wales TE, Engen JR, Smithgall TE. Structure, function, and inhibitor targeting of HIV-1 Nef-effector kinase complexes. J Biol Chem 2020; 295:15158-15171. [PMID: 32862141 DOI: 10.1074/jbc.rev120.012317] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/28/2020] [Indexed: 11/06/2022] Open
Abstract
Antiretroviral therapy has revolutionized the treatment of AIDS, turning a deadly disease into a manageable chronic condition. Life-long treatment is required because existing drugs do not eradicate HIV-infected cells. The emergence of drug-resistant viral strains and uncertain vaccine prospects highlight the pressing need for new therapeutic approaches with the potential to clear the virus. The HIV-1 accessory protein Nef is essential for viral pathogenesis, making it a promising target for antiretroviral drug discovery. Nef enhances viral replication and promotes immune escape of HIV-infected cells but lacks intrinsic enzymatic activity. Instead, Nef works through diverse interactions with host cell proteins primarily related to kinase signaling pathways and endosomal trafficking. This review emphasizes the structure, function, and biological relevance of Nef interactions with host cell protein-tyrosine kinases in the broader context of Nef functions related to enhancement of the viral life cycle and immune escape. Drug discovery targeting Nef-mediated kinase activation has allowed identification of promising inhibitors of multiple Nef functions. Pharmacological inhibitors of Nef-induced MHC-I down-regulation restore the adaptive immune response to HIV-infected cells in vitro and have the potential to enhance immune recognition of latent viral reservoirs as part of a strategy for HIV clearance.
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Affiliation(s)
- Ryan P Staudt
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - John J Alvarado
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Lori A Emert-Sedlak
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Haibin Shi
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Sherry T Shu
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, USA
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, USA
| | - Thomas E Smithgall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.
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Abstract
Fosfosal is the O-phosphorylated derivative of salicylic acid, with documented clinical use as a prodrug for the treatment of inflammatory diseases. We recently discovered that fosfosal itself inhibits the protein-protein interaction domain, the SH2 domain, of the tumor-related transcription factor STAT5b. Here, we demonstrate that fosfosal is selective for STAT5b over its close homologue STAT5a. This selectivity is mediated by the STAT5b residue Arg566, located in the SH2 domain-adjacent linker domain. Our data provide further evidence for the role of the STAT linker domain in determining the activity of small molecules against the SH2 domain. We present a refined binding model for fosfosal and STAT5b, which can serve as the basis for the development of fosfosal-based STAT5b inhibitors.
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Affiliation(s)
- Julian Gräb
- Leipzig University, Institute of Organic ChemistryJohannisallee 2904103LeipzigGermany
| | - Thorsten Berg
- Leipzig University, Institute of Organic ChemistryJohannisallee 2904103LeipzigGermany
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24
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Cerulli RA, Shehaj L, Tosic I, Jiang K, Wang J, Frank DA, Kritzer JA. Cytosolic delivery of peptidic STAT3 SH2 domain inhibitors. Bioorg Med Chem 2020; 28:115542. [PMID: 32503696 PMCID: PMC7294595 DOI: 10.1016/j.bmc.2020.115542] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 04/24/2020] [Accepted: 04/29/2020] [Indexed: 01/08/2023]
Abstract
The signal transducer and activator of transcription 3 (STAT3) protein is constitutively activated in several cancers. STAT3 activity can be blocked by inhibiting its Src Homology 2 (SH2) domain, but phosphotyrosine and its isosteres have poor bioavailability. In this work, we develop peptide-based inhibitors of STAT3-SH2 by combining chemical strategies that have proven effective for targeting other SH2 domains. These strategies include a STAT3-specific selectivity sequence, non-hydrolyzable phosphotyrosine isosteres, and a high-efficiency cell-penetrating peptide. Peptides that combined these three strategies had substantial biological stability and cytosolic delivery, as measured using highly quantitative cell-based assays. However, these peptides did not inhibit STAT3 activity in cells. By comparing in vitro binding affinity, cell penetration, and proteolytic stability, this work explores the delicate balance of factors that contribute to biological activity for peptidic inhibitors of STAT3.
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Affiliation(s)
- Robert A Cerulli
- Cell, Molecular and Developmental Biology Program, Graduate School of Biomedical Sciences, Tufts University, Boston, MA 02111, United States
| | - Livia Shehaj
- Department of Chemistry, Tufts University, Medford, MA 02155, United States
| | - Isidora Tosic
- Department of Biochemistry, Faculty of Medicine, University of Novi Sad, Novi Sad, Serbia; Dana Farber Cancer Institute, Department of Medical Oncology, Boston, MA 02215, United States
| | - Kevin Jiang
- Dana Farber Cancer Institute, Department of Medical Oncology, Boston, MA 02215, United States
| | - Jing Wang
- Department of Chemistry, Tufts University, Medford, MA 02155, United States
| | - David A Frank
- Dana Farber Cancer Institute, Department of Medical Oncology, Boston, MA 02215, United States; Brigham and Women's Hospital, Department of Medicine, Boston, MA 02115, United States; Harvard Medical School, Boston, MA 02111, United States
| | - Joshua A Kritzer
- Department of Chemistry, Tufts University, Medford, MA 02155, United States.
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25
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Marasco M, Carlomagno T. Specificity and regulation of phosphotyrosine signaling through SH2 domains. J Struct Biol X 2020; 4:100026. [PMID: 32647828 PMCID: PMC7337045 DOI: 10.1016/j.yjsbx.2020.100026] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/14/2020] [Accepted: 05/15/2020] [Indexed: 10/26/2022]
Abstract
Phosphotyrosine (pY) signaling is instrumental to numerous cellular processes. pY recognition occurs through specialized protein modules, among which the Src-homology 2 (SH2) domain is the most common. SH2 domains are small protein modules with an invariant fold, and are present in more than a hundred proteins with different function. Here we ask the question of how such a structurally conserved, small protein domain can recognize distinct phosphopeptides with the breath of binding affinity, specificity and kinetic parameters necessary for proper control of pY-dependent signaling and rapid cellular response. We review the current knowledge on structure, thermodynamics and kinetics of SH2-phosphopeptide complexes and conclude that selective phosphopeptide recognition is governed by both structure and dynamics of the SH2 domain, as well as by the kinetics of the binding events. Further studies on the thermodynamic and kinetic properties of SH2-phosphopeptide complexes, beyond their structure, are required to understand signaling regulation.
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Affiliation(s)
- Michelangelo Marasco
- Leibniz University Hannover, Institute of Organic Chemistry and Centre for Biomolecular Drug Research, Schneiderberg 38, 30167 Hannover, Germany
| | - Teresa Carlomagno
- Leibniz University Hannover, Institute of Organic Chemistry and Centre for Biomolecular Drug Research, Schneiderberg 38, 30167 Hannover, Germany.,Helmholtz Centre for Infection Research, Group of Structural Chemistry, Inhoffenstrasse 7, 38124 Braunschweig, Germany
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26
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Nishisaka F, Taniguchi K, Tsugane M, Hirata G, Takagi A, Asakawa N, Kurita A, Takahashi H, Ogo N, Shishido Y, Asai A. Antitumor activity of a novel oral signal transducer and activator of transcription 3 inhibitor YHO-1701. Cancer Sci 2020; 111:1774-1784. [PMID: 32112605 PMCID: PMC7226286 DOI: 10.1111/cas.14369] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 02/16/2020] [Accepted: 02/18/2020] [Indexed: 12/14/2022] Open
Abstract
The signal transducer and activator of transcription 3 (STAT3) signaling pathway is a key mediator of cancer cell proliferation, survival and invasion. Aberrant STAT3 has been demonstrated in various malignant cancers. YHO-1701 is a novel quinolinecarboxamide derivative generated from STX-0119. Here, we examined the effect of YHO-1701 on STAT3 and evaluated antitumor activity of YHO-1701 as a single agent and in combination. YHO-1701 inhibited STAT3-SH2 binding to phospho-Tyr peptide selectively and more potently than STX-0119 in biochemical assays. Molecular docking studies with STAT3 suggested more stable interaction of YHO-1701 with the SH2 domain. YHO-1701 exhibited approximately 10-fold stronger activity than STX-0119 in abrogating the STAT3 signaling pathway of human oral cancer cell line SAS. YHO-1701 also blocked multi-step events by inhibiting STAT3 dimerization and suppressed STAT3 promoter activity. As expected, YHO-1701 exerted strong antiproliferative activity against human cancer cell lines addicted to STAT3 signaling. Orally administered YHO-1701 showed statistically significant antitumor effects with long exposure to high levels of YHO-1701 at tumor sites in SAS xenograft models. Moreover, combination regimen with sorafenib led to significantly stronger antitumor activity. In addition, the suppression level of survivin (a downstream target) was superior for the combination as compared with monotherapy groups within tumor tissues. Thus, YHO-1701 had a favorable specificity for STAT3 and pharmacokinetics after oral treatment; it also contributed to the enhanced antitumor activity of sorafenib. The evidence presented here provides justification using for this approach in future clinical settings.
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Affiliation(s)
- Fukiko Nishisaka
- Center for Drug Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan.,Yakult Central Institute, Yakult Honsha Co., Ltd., Kunitachi, Tokyo, Japan
| | - Keisuke Taniguchi
- Yakult Central Institute, Yakult Honsha Co., Ltd., Kunitachi, Tokyo, Japan
| | - Momomi Tsugane
- Yakult Central Institute, Yakult Honsha Co., Ltd., Kunitachi, Tokyo, Japan
| | - Genya Hirata
- Yakult Central Institute, Yakult Honsha Co., Ltd., Kunitachi, Tokyo, Japan
| | - Akimitsu Takagi
- Yakult Central Institute, Yakult Honsha Co., Ltd., Kunitachi, Tokyo, Japan
| | - Naoyuki Asakawa
- Yakult Central Institute, Yakult Honsha Co., Ltd., Kunitachi, Tokyo, Japan
| | - Akinobu Kurita
- Yakult Central Institute, Yakult Honsha Co., Ltd., Kunitachi, Tokyo, Japan
| | | | - Naohisa Ogo
- Center for Drug Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Yoshiyuki Shishido
- Yakult Central Institute, Yakult Honsha Co., Ltd., Kunitachi, Tokyo, Japan
| | - Akira Asai
- Center for Drug Discovery, Graduate School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
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27
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Watson GM, Wilce JA. Direct Interaction between Calmodulin and the Grb7 RA-PH Domain. Int J Mol Sci 2020; 21:ijms21041336. [PMID: 32079204 PMCID: PMC7073000 DOI: 10.3390/ijms21041336] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/11/2020] [Accepted: 02/15/2020] [Indexed: 01/18/2023] Open
Abstract
Grb7 is a signalling adapter protein that engages activated receptor tyrosine kinases at cellular membranes to effect downstream pathways of cell migration, proliferation and survival. Grb7’s cellular location was shown to be regulated by the small calcium binding protein calmodulin (CaM). While evidence for a Grb7/CaM interaction is compelling, a direct interaction between CaM and purified Grb7 has not been demonstrated and quantitated. In this study we sought to determine this, and prepared pure full-length Grb7, as well as its RA-PH and SH2 subdomains, and tested for CaM binding using surface plasmon resonance. We report a direct interaction between full-length Grb7 and CaM that occurs in a calcium dependent manner. While no binding was observed to the SH2 domain alone, we observed a high micromolar affinity interaction between the Grb7 RA-PH domain and CaM, suggesting that the Grb7/CaM interaction is mediated through this region of Grb7. Together, our data support the model of a CaM interaction with Grb7 via its RA-PH domain.
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28
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Badolato M, Manetti F, Garofalo A, Aiello F. Triazolopyrimidinium salts: discovery of a new class of agents for cancer therapy. Future Med Chem 2020; 12:387-402. [PMID: 32028797 DOI: 10.4155/fmc-2019-0317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Aim: The [1,2,4]triazolo[1,5-a]pyrimidine core is highly privileged in medicinal chemistry due to its versatile pharmacological activity profile. Recently, the search for novel anticancer agents has focused on [1,2,4]triazolo[1,5-a]pyrimidine derivatives. Results: Our hit functionalization has led to the discovery of new [1,2,4]triazolo[1,5-a]pyrimidinium salts with potential anticancer activity. Among a small library of molecules, compound 9 significantly inhibits cancer cell growth in a panel of in vitro models. Molecular docking studies and preliminary binding assay have displayed that 9 could directly bind the Src homology 2 (SH2) domain of STAT3 protein. Conclusion: Compound 9 is a novel promising lead compound that motivates additional evaluation of [1,2,4]triazolo[1,5-a]pyrimidinium salts as novel potential chemotherapeutics.
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29
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Gelain A, Mori M, Meneghetti F, Villa S. Signal Transducer and Activator of Transcription Protein 3 (STAT3): An Update on its Direct Inhibitors as Promising Anticancer Agents. Curr Med Chem 2019; 26:5165-5206. [PMID: 30027840 DOI: 10.2174/0929867325666180719122729] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 06/08/2018] [Accepted: 07/12/2018] [Indexed: 12/16/2022]
Abstract
BACKGROUND Since Signal Transducer and Activator of Transcription 3 (STAT3) is a transcription factor which plays an important role in multiple aspects of cancer, including progression and migration, and it is constitutively activated in various human tumors, STAT3 inhibition has emerged as a validated strategy for the treatment of several malignancies. The aim of this review is to provide an update on the identification of new promising direct inhibitors targeting STAT3 domains, as potential anticancer agents. METHODS A thorough literature search focused on recently reported STAT3 direct inhibitors was undertaken. We considered the relevant developments regarding the STAT3 domains, which have been identified as potential drug targets. RESULTS In detail, 135 peer-reviewed papers and 7 patents were cited; the inhibitors we took into account targeted the DNA binding domain (compounds were grouped into natural derivatives, small molecules, peptides, aptamers and oligonucleotides), the SH2 binding domain (natural, semi-synthetic and synthetic compounds) and specific residues, like cysteines (natural, semi-synthetic, synthetic compounds and dual inhibitors) and tyrosine 705. CONCLUSION The huge number of direct STAT3 inhibitors recently identified demonstrates a strong interest in the investigation of this target, although it represents a challenging task considering that no drug targeting this enzyme is currently available for anticancer therapy. Notably, many studies on the available inhibitors evidenced that some of them possess a dual mechanism of action.
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Affiliation(s)
- Arianna Gelain
- Dipartimento di Scienze Farmaceutiche, Universita degli Studi di Milano, via L. Mangiagalli 25, 20133 Milano, Italy
| | - Matteo Mori
- Dipartimento di Scienze Farmaceutiche, Universita degli Studi di Milano, via L. Mangiagalli 25, 20133 Milano, Italy
| | - Fiorella Meneghetti
- Dipartimento di Scienze Farmaceutiche, Universita degli Studi di Milano, via L. Mangiagalli 25, 20133 Milano, Italy
| | - Stefania Villa
- Dipartimento di Scienze Farmaceutiche, Universita degli Studi di Milano, via L. Mangiagalli 25, 20133 Milano, Italy
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30
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Bai L, Zhou H, Xu R, Zhao Y, Chinnaswamy K, McEachern D, Chen J, Yang CY, Liu Z, Wang M, Liu L, Jiang H, Wen B, Kumar P, Meagher JL, Sun D, Stuckey JA, Wang S. A Potent and Selective Small-Molecule Degrader of STAT3 Achieves Complete Tumor Regression In Vivo. Cancer Cell 2019; 36:498-511.e17. [PMID: 31715132 PMCID: PMC6880868 DOI: 10.1016/j.ccell.2019.10.002] [Citation(s) in RCA: 318] [Impact Index Per Article: 63.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 08/14/2019] [Accepted: 10/07/2019] [Indexed: 01/21/2023]
Abstract
Signal transducer and activator of transcription 3 (STAT3) is an attractive cancer therapeutic target. Here we report the discovery of SD-36, a small-molecule degrader of STAT3. SD-36 potently induces the degradation of STAT3 protein in vitro and in vivo and demonstrates high selectivity over other STAT members. Induced degradation of STAT3 results in a strong suppression of its transcription network in leukemia and lymphoma cells. SD-36 inhibits the growth of a subset of acute myeloid leukemia and anaplastic large-cell lymphoma cell lines by inducing cell-cycle arrest and/or apoptosis. SD-36 achieves complete and long-lasting tumor regression in multiple xenograft mouse models at well-tolerated dose schedules. Degradation of STAT3 protein, therefore, is a promising cancer therapeutic strategy.
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MESH Headings
- Animals
- Antineoplastic Agents/pharmacology
- Antineoplastic Agents/therapeutic use
- Apoptosis/drug effects
- Apoptosis/genetics
- Cell Cycle Checkpoints/drug effects
- Cell Cycle Checkpoints/genetics
- Cell Line, Tumor
- Cell Proliferation/drug effects
- Cell Proliferation/genetics
- Female
- Gene Expression Regulation, Neoplastic/drug effects
- Humans
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Lymphoma, Large-Cell, Anaplastic/drug therapy
- Lymphoma, Large-Cell, Anaplastic/genetics
- Lymphoma, Large-Cell, Anaplastic/pathology
- Mice
- Proteolysis/drug effects
- STAT3 Transcription Factor/antagonists & inhibitors
- STAT3 Transcription Factor/metabolism
- Tumor Burden/drug effects
- Tumor Burden/genetics
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Longchuan Bai
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Haibin Zhou
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Renqi Xu
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yujun Zhao
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Donna McEachern
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jianyong Chen
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Chao-Yie Yang
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Zhaomin Liu
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mi Wang
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Liu Liu
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hui Jiang
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Bo Wen
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - Praveen Kumar
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jennifer L Meagher
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Duxin Sun
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jeanne A Stuckey
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shaomeng Wang
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
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31
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de Araujo ED, Orlova A, Neubauer HA, Bajusz D, Seo HS, Dhe-Paganon S, Keserű GM, Moriggl R, Gunning PT. Structural Implications of STAT3 and STAT5 SH2 Domain Mutations. Cancers (Basel) 2019; 11:E1757. [PMID: 31717342 PMCID: PMC6895964 DOI: 10.3390/cancers11111757] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/02/2019] [Accepted: 11/05/2019] [Indexed: 01/13/2023] Open
Abstract
Src Homology 2 (SH2) domains arose within metazoan signaling pathways and are involved in protein regulation of multiple pleiotropic cascades. In signal transducer and activator of transcription (STAT) proteins, SH2 domain interactions are critical for molecular activation and nuclear accumulation of phosphorylated STAT dimers to drive transcription. Sequencing analysis of patient samples has revealed the SH2 domain as a hotspot in the mutational landscape of STAT proteins although the functional impact for the vast majority of these mutations remains poorly characterized. Despite several well resolved structures for SH2 domain-containing proteins, structural data regarding the distinctive STAT-type SH2 domain is limited. Here, we review the unique features of STAT-type SH2 domains in the context of all currently reported STAT3 and STAT5 SH2 domain clinical mutations. The genetic volatility of specific regions in the SH2 domain can result in either activating or deactivating mutations at the same site in the domain, underscoring the delicate evolutionary balance of wild type STAT structural motifs in maintaining precise levels of cellular activity. Understanding the molecular and biophysical impact of these disease-associated mutations can uncover convergent mechanisms of action for mutations localized within the STAT SH2 domain to facilitate the development of targeted therapeutic interventions.
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Affiliation(s)
- Elvin D. de Araujo
- Centre for Medicinal Chemistry, University of Toronto at Mississauga, Mississauga, ON L5L 1C6, Canada;
- Department of Chemical & Physical Sciences, University of Toronto at Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Anna Orlova
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, A-1210 Vienna, Austria; (A.O.); (H.A.N.); (R.M.)
| | - Heidi A. Neubauer
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, A-1210 Vienna, Austria; (A.O.); (H.A.N.); (R.M.)
| | - Dávid Bajusz
- Medicinal Chemistry Research Group, Research Center for Natural Sciences, 1117 Budapest, Hungary; (D.B.); (G.M.K.)
| | - Hyuk-Soo Seo
- Department of Cancer Biology, Dana-Farber Cancer Institute, Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; (H.-S.S.); (S.D.-P.)
- Department of Biological Chemistry, Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Sirano Dhe-Paganon
- Department of Cancer Biology, Dana-Farber Cancer Institute, Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; (H.-S.S.); (S.D.-P.)
- Department of Biological Chemistry, Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - György M. Keserű
- Medicinal Chemistry Research Group, Research Center for Natural Sciences, 1117 Budapest, Hungary; (D.B.); (G.M.K.)
| | - Richard Moriggl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, A-1210 Vienna, Austria; (A.O.); (H.A.N.); (R.M.)
| | - Patrick T. Gunning
- Centre for Medicinal Chemistry, University of Toronto at Mississauga, Mississauga, ON L5L 1C6, Canada;
- Department of Chemical & Physical Sciences, University of Toronto at Mississauga, Mississauga, ON L5L 1C6, Canada
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32
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Kim BH, Lee H, Song Y, Park JS, Gadhe CG, Choi J, Lee CG, Pae AN, Kim S, Ye SK. Development of Oxadiazole-Based ODZ10117 as a Small-Molecule Inhibitor of STAT3 for Targeted Cancer Therapy. J Clin Med 2019; 8:jcm8111847. [PMID: 31684051 PMCID: PMC6912340 DOI: 10.3390/jcm8111847] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 10/24/2019] [Accepted: 10/30/2019] [Indexed: 12/15/2022] Open
Abstract
Persistently activated STAT3 is a promising target for a new class of anticancer drug development and cancer therapy, as it is associated with tumor initiation, progression, malignancy, drug resistance, cancer stem cell properties, and recurrence. Here, we discovered 3-(2,4-dichloro-phenoxymethyl)-5-trichloromethyl-[1,2,4]oxadiazole (ODZ10117) as a small-molecule inhibitor of STAT3 to be used in STAT3-targeted cancer therapy. ODZ10117 targeted the SH2 domain of STAT3 regardless of other STAT family proteins and upstream regulators of STAT3, leading to inhibition of the tyrosine phosphorylation, dimerization, nuclear translocation, and transcriptional activity of STAT3. The inhibitory effect of ODZ10117 on STAT3 was stronger than the known STAT3 inhibitors such as S3I-201, STA-21, and nifuroxazide. ODZ10117 suppressed the migration and invasion, induced apoptosis, reduced tumor growth and lung metastasis, and extended the survival rate in both in vitro and in vivo models of breast cancer. Overall, we demonstrated that ODZ10117 is a novel STAT3 inhibitor and may be a promising agent for the development of anticancer drugs.
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Affiliation(s)
- Byung-Hak Kim
- Department of Pharmacology and Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea.
- Biomedical Science Project (BK21PLUS), Seoul National University College of Medicine, Seoul 03080, Korea.
- CYTUS H&B Corporation, Cheongju 28159, Korea.
| | - Haeri Lee
- Department of Pharmacology and Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea.
- Biomedical Science Project (BK21PLUS), Seoul National University College of Medicine, Seoul 03080, Korea.
| | - Yeonghun Song
- College of Pharmacy, Seoul National University, Seoul 08826, Korea.
| | - Joon-Suk Park
- Laboratory Animal Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu 41061, Korea.
| | - Changdev G Gadhe
- Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology, Seoul 02792, Korea.
| | - Jiwon Choi
- Department of Pharmacology and Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea.
| | | | - Ae Nim Pae
- Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology, Seoul 02792, Korea.
- Division of Bio-Medical Science &Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Korea.
| | - Sanghee Kim
- College of Pharmacy, Seoul National University, Seoul 08826, Korea.
| | - Sang-Kyu Ye
- Department of Pharmacology and Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Korea.
- Biomedical Science Project (BK21PLUS), Seoul National University College of Medicine, Seoul 03080, Korea.
- Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul 03080, Korea.
- Neuro-Immune Information Storage Network Research Center, Seoul National University College of Medicine, Seoul 03080, Korea.
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33
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Sanches K, Caruso ÍP, Almeida FCL, Melo FA. NMR assignment of free 1H, 15N and 13C-Grb2- SH2 domain. Biomol NMR Assign 2019; 13:295-298. [PMID: 31028611 DOI: 10.1007/s12104-019-09894-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 04/23/2019] [Indexed: 06/09/2023]
Abstract
Growth factor receptor-bound protein 2 (Grb2) is an adaptor protein composed of three domains, an N-terminal SH3 (nSH3), SH2 and a C-terminal SH3 (cSH3) domains. This multi-domain protein has been reported to be a key factor in many signaling pathways related to controlling cell survival, differentiation, and growth. The Grb2-SH2 domain has been a focus for the study of the interaction with peptides and small molecules to act as inhibitors in uncontrolled cell growth, and consequently inhibit tumor proliferation. Here we describe the almost complete assignment of the free SH2 domain at pH 7. This work prepares the ground for further structural studies, backbone dynamics, mapping of interactions and drug screening and development. TalosN secondary structure prediction showed great similarity with the available structures in the PDB.
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Affiliation(s)
- Karoline Sanches
- Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, São Paulo State University (UNESP), São José Do Rio Preto, São Paulo, Brazil
| | - Ícaro P Caruso
- Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, São Paulo State University (UNESP), São José Do Rio Preto, São Paulo, Brazil
- Institute of Medical Biochemistry (IBqM) and National Center of Nuclear Magnetic Resonance (CNRMN), Center for Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fábio C L Almeida
- Institute of Medical Biochemistry (IBqM) and National Center of Nuclear Magnetic Resonance (CNRMN), Center for Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Fernando A Melo
- Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, São Paulo State University (UNESP), São José Do Rio Preto, São Paulo, Brazil.
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Abstract
Phosphorylation events modify bacterial and archaeal proteomes, imparting cells with rapid and reversible responses to specific environmental stimuli or niches. Phosphorylated proteins are generally modified at one or more serine, threonine, or tyrosine residues. Within the last ten years, increasing numbers of global phosphoproteomic surveys of prokaryote species have revealed an abundance of tyrosine-phosphorylated proteins. In some cases, novel phosphorylation-dependent regulatory paradigms for cell division, gene transcription, and protein translation have been identified, suggesting that a wide scope of prokaryotic physiology remains to be characterized. Recent observations of bacterial proteins with putative phosphotyrosine binding pockets or Src homology 2 (SH2)-like domains suggest the presence of phosphotyrosine-dependent protein interaction networks. Here in this minireview, we focus on protein tyrosine phosphorylation, a posttranslational modification once thought to be rare in prokaryotes but which has emerged as an important regulatory facet in microbial biology.
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35
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Matsuura Y. High-resolution structural analysis shows how different crystallographic environments can induce alternative modes of binding of a phosphotyrosine peptide to the SH2 domain of Fer tyrosine kinase. Protein Sci 2019; 28:2011-2019. [PMID: 31441171 DOI: 10.1002/pro.3713] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 08/16/2019] [Accepted: 08/20/2019] [Indexed: 11/08/2022]
Abstract
Fes and Fes-related (Fer) protein tyrosine kinases (PTKs) comprise a subfamily of nonreceptor tyrosine kinases characterized by a unique multidomain structure composed of an N-terminal Fer/CIP4 homology-Bin/Amphiphysin/Rvs (F-BAR) domain, a central Src homology 2 (SH2) domain, and a C-terminal PTK domain. Fer is ubiquitously expressed, and upregulation of Fer has been implicated in various human cancers. The PTK activity of Fes has been shown to be positively regulated by the binding of phosphotyrosine-containing ligands to the SH2 domain. Here, the X-ray crystal structure of human Fer SH2 domain bound to a phosphopeptide that has D-E-pY-E-N-V-D sequence is reported at 1.37 å resolution. The asymmetric unit (ASU) contains six Fer-phosphopeptide complexes, and the structure reveals three distinct binding modes for the same phosphopeptide. At four out of the six binding sites in the ASU, the phosphopeptide binds to Fer SH2 domain in a type I β-turn conformation, and this could be the optimal binding mode of this phosphopeptide. At the other two binding sites in the ASU, it appears that spatial proximity of neighboring SH2 domains in the crystal induces alternative modes of binding of this phosphopeptide.
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Affiliation(s)
- Yoshiyuki Matsuura
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan.,Structural Biology Research Center, Graduate School of Science, Nagoya University, Nagoya, Japan
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36
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Ehm PAH, Lange F, Hentschel C, Jepsen A, Glück M, Nelson N, Bettin B, de Bruyn Kops C, Kirchmair J, Nalaskowski M, Jücker M. Analysis of the FLVR motif of SHIP1 and its importance for the protein stability of SH2 containing signaling proteins. Cell Signal 2019; 63:109380. [PMID: 31377397 DOI: 10.1016/j.cellsig.2019.109380] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 07/26/2019] [Accepted: 07/29/2019] [Indexed: 12/31/2022]
Abstract
Binding of proteins with SH2 domains to tyrosine-phosphorylated signaling proteins is a key mechanism for transmission of biological signals within the cell. Characterization of dysregulated proteins in cell signaling pathways is important for the development of therapeutic approaches. The AKT pathway is a frequently upregulated pathway in most cancer cells and the SH2-containing inositol 5-phosphatase SHIP1 is a negative regulator of the AKT pathway. In this study we investigated different mutations of the conserved FLVR motif of the SH2 domain and putative phosphorylation sites of SHIP1 which are located in close proximity to its FLVR motif. We demonstrate that patient-derived SHIP1-FLVR motif mutations e.g. F28L, and L29F possess reduced protein expression and increased phospho-AKT-S473 levels in comparison to SHIP1 wildtype. The estimated half-life of SHIP1-F28L protein was reduced from 23.2 h to 0.89 h in TF-1 cells and from 4.7 h to 0.6 h in Jurkat cells. These data indicate that the phenylalanine residue at position 28 of SHIP1 is important for its stability. Replacement of F28 with other aromatic residues like tyrosine and tryptophan preserves protein stability while replacement with non-aromatic amino acids like leucine, isoleucine, valine or alanine severely affects the stability of SHIP1. In consequence, a SHIP1-mutant with an aromatic amino acid at position 28 i.e. F28W can rescue the inhibitory function of wild type SHIP1, whereas SHIP1-mutants with non-aromatic amino acids i.e. F28V do not inhibit cell growth anymore. A detailed structural analysis revealed that F28 forms hydrophobic surface contacts in particular with W5, I83, L97 and P100 which can be maintained by tyrosine and tryptophan residues, but not by non-aromatic residues at position 28. In line with this model of mutation-induced instability of SHIP1-F28L, treatment of cells with proteasomal inhibitor MG132 was able to rescue expression of SHIP1-F28L. In addition, mutation of putative phosphorylation sites S27 and S33 adjacent to the FLVR motif of SHIP1 have an influence on its protein stability. These results further support a functional role of SHIP1 as tumor suppressor protein and indicate a regulation of protein expression of SH2 domain containing proteins via the FLVR motif.
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Affiliation(s)
- Patrick A H Ehm
- Institute of Biochemistry and Signal Transduction, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Fabiola Lange
- Institute of Biochemistry and Signal Transduction, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Carolin Hentschel
- Institute of Biochemistry and Signal Transduction, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Anneke Jepsen
- Institute of Biochemistry and Signal Transduction, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Madeleine Glück
- Institute of Biochemistry and Signal Transduction, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Nina Nelson
- Institute of Biochemistry and Signal Transduction, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Bettina Bettin
- Institute of Biochemistry and Signal Transduction, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Christina de Bruyn Kops
- Center for Bioinformatics (ZBH), Department of Informatics, Faculty of Mathematics, Informatics and Natural Sciences, University of Hamburg, 20146 Hamburg, Germany
| | - Johannes Kirchmair
- Center for Bioinformatics (ZBH), Department of Informatics, Faculty of Mathematics, Informatics and Natural Sciences, University of Hamburg, 20146 Hamburg, Germany; Department of Chemistry, University of Bergen, N-5020 Bergen, Norway; Computational Biology Unit (CBU), University of Bergen, N-5020 Bergen, Norway
| | - Marcus Nalaskowski
- Institute of Biochemistry and Signal Transduction, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Manfred Jücker
- Institute of Biochemistry and Signal Transduction, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany.
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Abstract
Although naturally occurring low-molecular-weight compounds have many known roles within the cell, these do not usually involve the direct inhibition of protein-protein interactions. Based on the results of high-throughput screening of a library of bioactive compounds and neurotransmitters, we report here that the four nucleoside triphosphates ATP, GTP, CTP and UTP inhibit the SH2 domain of the tumor-related transcription factor STAT5b. ATP and GTP are the most active nucleoside triphosphates and show specificity for STAT5b over STAT5a, STAT3, STAT6 and the p53-binding protein HDM2. As the inhibition constant of ATP against STAT5b is significantly lower than published values for the intracellular ATP concentration, our data suggest that ATP might inhibit the protein-protein interactions of STAT5b in living cells.
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Affiliation(s)
- Angela Berg
- Institute of Organic Chemistry, University of Leipzig, Johannisallee 29, 04103, Leipzig, Germany
| | - Bianca Sperl
- Department of Molecular Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Thorsten Berg
- Institute of Organic Chemistry, University of Leipzig, Johannisallee 29, 04103, Leipzig, Germany
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38
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Funakoshi-Tago M, Tsuruya R, Ueda F, Ishihara A, Kasahara T, Tamura H, Tago K. Tyrosine-phosphorylated SOCS3 negatively regulates cellular transformation mediated by the myeloproliferative neoplasm-associated JAK2 V617F mutant. Cytokine 2019; 123:154753. [PMID: 31255914 DOI: 10.1016/j.cyto.2019.154753] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/31/2019] [Accepted: 06/07/2019] [Indexed: 01/30/2023]
Abstract
In the majority of myeloproliferative neoplasms (MPNs) patients, a point mutation, V617F has been found in Janus kinase 2 (JAK2) gene, and this JAK2 mutant provoked aberrant signaling pathway. In the current study, we found that suppressor of cytokine signaling proteins 3 (SOCS3) possessed the tumor suppressive activity against the JAK2 V617F mutant-provoked cellular transformation. The knockdown of SOCS3 increased the expression level of the JAK2 V617F mutant, which enhanced the activation of signaling mediators, including signal transducer and activator of transcription 3 and 5 (STAT3, STAT5) and extracellular signal-regulated kinase (ERK), and also increased of the proliferation rate and tumorigenesis activity of Ba/F3 cells expressing the JAK2 V617F mutant and erythropoietin receptor (EpoR). In contrast, the enforced expression of SOCS3 significantly inhibited the JAK2 V617F mutant-induced activation of downstream signaling molecules, cell proliferation, and tumorigenesis by down-regulating the expression level of the JAK2 V617F mutant. SOCS3 interacted with the JAK2V617F mutant through its SH2 domain and was phosphorylated at Tyr-204 and Tyr-221 in its SOCS box by the JAK2V617F mutant. SOCS3 mutants carrying a mutation in the SH2 domain (R71E) and a substitution at Tyr-221 (Y221F) failed to exert inhibitory effects on JAK2V617F mutant-induced cellular transformation and tumorigenesis. Collectively, these results imply that SOCS3 plays a negative role in the JAK2 V617F mutant-induced oncogenic signaling pathway through its SH2 domain and the phosphorylation of Tyr-221 in its SOCS box.
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Affiliation(s)
- Megumi Funakoshi-Tago
- Division of Hygienic Chemistry, Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan.
| | - Rina Tsuruya
- Division of Hygienic Chemistry, Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan
| | - Fumihito Ueda
- Division of Hygienic Chemistry, Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan
| | - Aki Ishihara
- Division of Hygienic Chemistry, Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan
| | - Tadashi Kasahara
- International University of Health and Welfare, Graduate School, 1-3-3 Minamiaoyama, Minato-ku, Tokyo 107-0062, Japan
| | - Hiroomi Tamura
- Division of Hygienic Chemistry, Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan
| | - Kenji Tago
- Division of Structural Biochemistry, Department of Biochemistry, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke-shi, Tochigi-ken 329-0498, Japan.
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39
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Abstract
Protein tyrosine O-sulfation is considered as one of the most common types of posttranslational modification of tyrosine in nature. The introduction of a negatively charged sulfate group plays crucial roles in extracellular biomolecular interactions that dictate various cellular processes, including cell adhesion, leukocyte trafficking, hormone activities, and immune responses. Despite substantial advances in our knowledge about protein tyrosine O-sulfation in recent years, our understanding of its biological significance is still in its infancy. This is largely hindered by a chronic lack of suitable biochemical tools. We seek to meet this challenge by engineering a small protein scaffold that can recognize sulfated tyrosine (sulfotyrosine) residues with high affinity. In this chapter, we describe the directed evolution of a Src Homology 2 (SH2) domain to recognize sulfotyrosine. In the first part, the design strategy for the phage display of SH2 variants is discussed. In the second part, the techniques required for phage propagation and selection are described. The evolved SH2 variants are characterized and validated in vitro through fluorescence polarization assays. Finally, the evolved SH2 domain mutants are applied to the visualization of sulfated proteins on the cell surface.
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Affiliation(s)
- Justin Lawrie
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Wei Niu
- Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE, United States.
| | - Jiantao Guo
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, United States.
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40
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Varone A, Mariggiò S, Patheja M, Maione V, Varriale A, Vessichelli M, Spano D, Formiggini F, Lo Monte M, Brancati N, Frucci M, Del Vecchio P, D'Auria S, Flagiello A, Iannuzzi C, Luini A, Pucci P, Banci L, Valente C, Corda D. A signalling cascade involving receptor-activated phospholipase A 2, glycerophosphoinositol 4-phosphate, Shp1 and Src in the activation of cell motility. Cell Commun Signal 2019; 17:20. [PMID: 30823936 PMCID: PMC6396489 DOI: 10.1186/s12964-019-0329-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 02/13/2019] [Indexed: 12/28/2022] Open
Abstract
Background Shp1, a tyrosine-phosphatase-1 containing the Src-homology 2 (SH2) domain, is involved in inflammatory and immune reactions, where it regulates diverse signalling pathways, usually by limiting cell responses through dephosphorylation of target molecules. Moreover, Shp1 regulates actin dynamics. One Shp1 target is Src, which controls many cellular functions including actin dynamics. Src has been previously shown to be activated by a signalling cascade initiated by the cytosolic-phospholipase A2 (cPLA2) metabolite glycerophosphoinositol 4-phosphate (GroPIns4P), which enhances actin polymerisation and motility. While the signalling cascade downstream Src has been fully defined, the mechanism by which GroPIns4P activates Src remains unknown. Methods Affinity chromatography, mass spectrometry and co-immunoprecipitation studies were employed to identify the GroPIns4P-interactors; among these Shp1 was selected for further analysis. The specific Shp1 residues interacting with GroPIns4P were revealed by NMR and validated by site-directed mutagenesis and biophysical methods such as circular dichroism, isothermal calorimetry, fluorescence spectroscopy, surface plasmon resonance and computational modelling. Morphological and motility assays were performed in NIH3T3 fibroblasts. Results We find that Shp1 is the direct cellular target of GroPIns4P. GroPIns4P directly binds to the Shp1-SH2 domain region (with the crucial residues being Ser 118, Arg 138 and Ser 140) and thereby promotes the association between Shp1 and Src, and the dephosphorylation of the Src-inhibitory phosphotyrosine in position 530, resulting in Src activation. As a consequence, fibroblast cells exposed to GroPIns4P show significantly enhanced wound healing capability, indicating that GroPIns4P has a stimulatory role to activate fibroblast migration. GroPIns4P is produced by cPLA2 upon stimulation by diverse receptors, including the EGF receptor. Indeed, endogenously-produced GroPIns4P was shown to mediate the EGF-induced cell motility. Conclusions This study identifies a so-far undescribed mechanism of Shp1/Src modulation that promotes cell motility and that is dependent on the cPLA2 metabolite GroPIns4P. We show that GroPIns4P is required for EGF-induced fibroblast migration and that it is part of a cPLA2/GroPIns4P/Shp1/Src cascade that might have broad implications for studies of immune-inflammatory response and cancer. ![]()
Electronic supplementary material The online version of this article (10.1186/s12964-019-0329-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alessia Varone
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino 111, 80131, Naples, Italy.
| | - Stefania Mariggiò
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Manpreet Patheja
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Vincenzo Maione
- Magnetic Resonance Centre (CERM), University of Florence, 50019, Sesto Fiorentino, Italy
| | - Antonio Varriale
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino 111, 80131, Naples, Italy.,Institute of Food Science, National Research Council, Via Roma 64, 83100, Avellino, Italy
| | - Mariangela Vessichelli
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Daniela Spano
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Fabio Formiggini
- Italian Institute of Technology, Centre for Advanced Biomaterials for Health Care at CRIB, Largo Barsanti e Matteucci 53, 80125, Naples, Italy
| | - Matteo Lo Monte
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Nadia Brancati
- Institute of High Performance Computing and Networking, National Research Council, Via P. Castellino 111, 80131, Naples, Italy
| | - Maria Frucci
- Institute of High Performance Computing and Networking, National Research Council, Via P. Castellino 111, 80131, Naples, Italy
| | - Pompea Del Vecchio
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126, Naples, Italy
| | - Sabato D'Auria
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino 111, 80131, Naples, Italy.,Institute of Food Science, National Research Council, Via Roma 64, 83100, Avellino, Italy
| | - Angela Flagiello
- CEINGE Advanced Biotechnology, Via G. Salvatore 486, 80145, Naples, Italy
| | - Clara Iannuzzi
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino 111, 80131, Naples, Italy.,Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, Via L. de Crecchio 7, 80138, Naples, Italy
| | - Alberto Luini
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Piero Pucci
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126, Naples, Italy.,CEINGE Advanced Biotechnology, Via G. Salvatore 486, 80145, Naples, Italy
| | - Lucia Banci
- Magnetic Resonance Centre (CERM), University of Florence, 50019, Sesto Fiorentino, Italy
| | - Carmen Valente
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Daniela Corda
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino 111, 80131, Naples, Italy.
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41
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Cheng H, Schwell V, Curtis BR, Fazlieva R, Roder H, Campbell KS. Conformational Changes in the Cytoplasmic Region of KIR3DL1 upon Interaction with SHP-2. Structure 2019; 27:639-650.e2. [PMID: 30773397 DOI: 10.1016/j.str.2019.01.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 11/07/2018] [Accepted: 01/18/2019] [Indexed: 12/29/2022]
Abstract
KIR3DL1 is an inhibitory killer cell immunoglobulin-like receptor (KIR) that negatively regulates natural killer cell cytotoxicity. The KIR3DL1 cytoplasmic region (3DL1-cyto) is disordered and can be dissected into three segments: (I) H340-V351; (II) M352-D371; and (III) P372-P423. NMR studies indicate that segment II can dynamically adopt a loop-like conformation, and segments I and III can form dynamic helices that may mediate binding to membranes, particularly in the region around the N-terminal (N) immunoreceptor tyrosine-based inhibitory motif (ITIM), consistent with its role in signaling. Furthermore, individual SH2 domains of SHP-2 strongly engage with the unphosphorylated N-ITIM of 3DL1-cyto, while binding of the tandem SHP-2 SH2 domains to the bis-phosphorylated ITIMs results in more extensive conformational changes in segments I and III. The findings enhance our understanding of KIR function and how ITIMs in a target receptor operate in concert to engage the tandem SH2 domains of SHP-2.
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Affiliation(s)
- Hong Cheng
- Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA.
| | - Vered Schwell
- Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
| | - Brett R Curtis
- Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
| | - Ruzaliya Fazlieva
- Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
| | - Heinrich Roder
- Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
| | - Kerry S Campbell
- Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
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42
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Veggiani G, Huang H, Yates BP, Tong J, Kaneko T, Joshi R, Li SSC, Moran MF, Gish G, Sidhu SS. Engineered SH2 domains with tailored specificities and enhanced affinities for phosphoproteome analysis. Protein Sci 2018; 28:403-413. [PMID: 30431205 DOI: 10.1002/pro.3551] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 11/09/2018] [Accepted: 11/12/2018] [Indexed: 02/05/2023]
Abstract
Protein phosphorylation is the most abundant post-translational modification in cells. Src homology 2 (SH2) domains specifically recognize phosphorylated tyrosine (pTyr) residues to mediate signaling cascades. A conserved pocket in the SH2 domain binds the pTyr side chain and the EF and BG loops determine binding specificity. By using large phage-displayed libraries, we engineered the EF and BG loops of the Fyn SH2 domain to alter specificity. Engineered SH2 variants exhibited distinct specificity profiles and were able to bind pTyr sites on the epidermal growth factor receptor, which were not recognized by the wild-type Fyn SH2 domain. Furthermore, mass spectrometry showed that SH2 variants with additional mutations in the pTyr-binding pocket that enhanced affinity were highly effective for enrichment of diverse pTyr peptides within the human proteome. These results showed that engineering of the EF and BG loops could be used to tailor SH2 domain specificity, and SH2 variants with diverse specificities and high affinities for pTyr residues enabled more comprehensive analysis of the human phosphoproteome. STATEMENT: Src Homology 2 (SH2) domains are modular domains that recognize phosphorylated tyrosine embedded in proteins, transducing these post-translational modifications into cellular responses. Here we used phage display to engineer hundreds of SH2 domain variants with altered binding specificities and enhanced affinities, which enabled efficient and differential enrichment of the human phosphoproteome for analysis by mass spectrometry. These engineered SH2 domain variants will be useful tools for elucidating the molecular determinants governing SH2 domains binding specificity and for enhancing analysis and understanding of the human phosphoproteome.
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Affiliation(s)
- Gianluca Veggiani
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.,Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5S3E1, Canada
| | - Haiming Huang
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.,Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5S3E1, Canada
| | - Bradley P Yates
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.,Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5S3E1, Canada
| | - Jiefei Tong
- Program in Molecular Structure and Function, The Hospital for Sick Children, Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5G 0A4, Canada
| | - Tomonori Kaneko
- Department of Biochemistry, Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada
| | - Rakesh Joshi
- Department of Biochemistry, Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada
| | - Shawn S C Li
- Department of Biochemistry, Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada
| | - Michael F Moran
- Program in Molecular Structure and Function, The Hospital for Sick Children, Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 3E1, Canada.,The Hospital for Sick Children, SPARC Biocentre, Toronto, Ontario, M5G 0A4, Canada
| | - Gerald Gish
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada
| | - Sachdev S Sidhu
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.,Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5S3E1, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 3E1, Canada
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43
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Abstract
Tyrosine kinases were first discovered as the protein products of viral oncogenes. We now know that this large family of metazoan enzymes includes nearly one hundred structurally diverse members. Tyrosine kinases are broadly classified into two groups: the transmembrane receptor tyrosine kinases, which sense extracellular stimuli, and the cytoplasmic tyrosine kinases, which contain modular ligand-binding domains and propagate intracellular signals. Several families of cytoplasmic tyrosine kinases have in common a core architecture, the "Src module," composed of a Src-homology 3 (SH3) domain, a Src-homology 2 (SH2) domain, and a kinase domain. Each of these families is defined by additional elaborations on this core architecture. Structural, functional, and evolutionary studies have revealed a unifying set of principles underlying the activity and regulation of tyrosine kinases built on the Src module. The discovery of these conserved properties has shaped our knowledge of the workings of protein kinases in general, and it has had important implications for our understanding of kinase dysregulation in disease and the development of effective kinase-targeted therapies.
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Affiliation(s)
- Neel H. Shah
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Jeanine F. Amacher
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Laura M. Nocka
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - John Kuriyan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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44
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Wang Z, Nie Y, Zhang K, Xu H, Ramelot TA, Kennedy MA, Liu M, Zhu J, Yang Y. Solution structure of SHIP2 SH2 domain and its interaction with a phosphotyrosine peptide from c-MET. Arch Biochem Biophys 2018; 656:31-37. [PMID: 30165040 DOI: 10.1016/j.abb.2018.08.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/10/2018] [Accepted: 08/26/2018] [Indexed: 12/12/2022]
Abstract
SH2 domain-containing inositol 5-phosphatase 2 (SHIP2) binds with the Y1356-phosphorylated hepatocyte growth factor (HGF) receptor, c-MET, through its SH2 domain, which is essential for the role of SHIP2 in HGF-induced cell scattering and cell spreading. Previously, the experimental structure of the SH2 domain from SHIP2 (SHIP2-SH2) had not been reported, and its interaction with the Y1356-phosphorylated c-MET had not been investigated from a structural point of view. In this study, the solution structure of SHIP2-SH2 was determined by NMR spectroscopy, where it was found to adopt a typical SH2-domain fold that contains a positively-charged pocket for binding to phosphotyrosine (pY). The interaction between SHIP2-SH2 and a pY-containing peptide from c-MET (Y1356 phosphorylated) was investigated through NMR titrations. The results showed that the binding affinity of SHIP2-SH2 with the phosphopeptide is at low micromolar level, and the binding interface consists of the positively-charged pocket and its surrounding regions. Furthermore, R28, S49 and R70 were identified as key residues for the binding and may directly interact with the pY. Taken together, these findings provide structural insights into the binding of SHIP2-SH2 with the Y1356-phosphorylated c-MET, and lay a foundation for further studies of the interactions between SHIP2-SH2 and its various binding partners.
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Affiliation(s)
- Zi Wang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yao Nie
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kunxiao Zhang
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Huaihai Institute of Technology, Lianyungang, 222005, China
| | - Henghao Xu
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Huaihai Institute of Technology, Lianyungang, 222005, China
| | - Theresa A Ramelot
- Department of Chemistry and Biochemistry, The Northeast Structural Genomics Consortium, Miami University, Oxford, OH, 45056, United States
| | - Michael A Kennedy
- Department of Chemistry and Biochemistry, The Northeast Structural Genomics Consortium, Miami University, Oxford, OH, 45056, United States
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Jiang Zhu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China.
| | - Yunhuang Yang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China.
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45
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Knight JM, Mandal P, Morlacchi P, Mak G, Li E, Madison M, Landers C, Saxton B, Felix E, Gilbert B, Sederstrom J, Varadhachary A, Singh MM, Chatterjee D, Corry DB, McMurray JS. Small molecule targeting of the STAT5/6 Src homology 2 (SH2) domains to inhibit allergic airway disease. J Biol Chem 2018; 293:10026-10040. [PMID: 29739850 PMCID: PMC6028980 DOI: 10.1074/jbc.ra117.000567] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Revised: 04/02/2018] [Indexed: 11/06/2022] Open
Abstract
Asthma is a chronic inflammatory disease of the lungs and airways and one of the most burdensome of all chronic maladies. Previous studies have established that expression of experimental and human asthma requires the IL-4/IL-13/IL-4 receptor α (IL-4Rα) signaling pathway, which activates the transcription factor STAT6. However, no small molecules targeting this important pathway are currently in clinical development. To this end, using a preclinical asthma model, we sought to develop and test a small-molecule inhibitor of the Src homology 2 domains in mouse and human STAT6. We previously developed multiple peptidomimetic compounds on the basis of blocking the docking site of STAT6 to IL-4Rα and phosphorylation of Tyr641 in STAT6. Here, we expanded the scope of our initial in vitro structure-activity relationship studies to include central and C-terminal analogs of these peptides to develop a lead compound, PM-43I. Conducting initial dose range, toxicity, and pharmacokinetic experiments with PM-43I, we found that it potently inhibits both STAT5- and STAT6-dependent allergic airway disease in mice. Moreover, PM-43I reversed preexisting allergic airway disease in mice with a minimum ED50 of 0.25 μg/kg. Of note, PM-43I was efficiently cleared through the kidneys with no long-term toxicity. We conclude that PM-43I represents the first of a class of small molecules that may be suitable for further clinical development against asthma.
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Affiliation(s)
- J Morgan Knight
- From the Departments of Medicine,
- Pathology and Immunology, and
| | - Pijus Mandal
- the Department of Experimental Therapeutics, MD Anderson Cancer Center, Houston, Texas
| | - Pietro Morlacchi
- the Department of Experimental Therapeutics, MD Anderson Cancer Center, Houston, Texas
| | | | - Evan Li
- From the Departments of Medicine
- the Biology of Inflammation Center, Baylor College of Medicine, Houston, Texas 77030
| | - Matthew Madison
- the Translational Biology and Molecular Medicine Program, and
| | - Cameron Landers
- the Translational Biology and Molecular Medicine Program, and
| | | | - Ed Felix
- the Department of Experimental Therapeutics, MD Anderson Cancer Center, Houston, Texas
| | | | - Joel Sederstrom
- the Flow Cytometry Core Facility, Baylor College of Medicine, Houston, Texas
| | - Atul Varadhachary
- Fannin Innovation Studio and Atrapos Therapeutics, LLC, Houston, Texas 77027
| | - Melissa M Singh
- Fannin Innovation Studio and Atrapos Therapeutics, LLC, Houston, Texas 77027
| | - Dev Chatterjee
- Fannin Innovation Studio and Atrapos Therapeutics, LLC, Houston, Texas 77027
| | - David B Corry
- From the Departments of Medicine,
- Pathology and Immunology, and
- the Biology of Inflammation Center, Baylor College of Medicine, Houston, Texas 77030
- the Translational Biology and Molecular Medicine Program, and
- the Michael E. Debakey Veterans Affairs Center for Translational Research in Inflammatory Diseases, Houston, Texas 77030, and
| | - John S McMurray
- the Department of Experimental Therapeutics, MD Anderson Cancer Center, Houston, Texas
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46
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Hayashi T, Senda M, Suzuki N, Nishikawa H, Ben C, Tang C, Nagase L, Inoue K, Senda T, Hatakeyama M. Differential Mechanisms for SHP2 Binding and Activation Are Exploited by Geographically Distinct Helicobacter pylori CagA Oncoproteins. Cell Rep 2018; 20:2876-2890. [PMID: 28930683 DOI: 10.1016/j.celrep.2017.08.080] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 06/26/2017] [Accepted: 08/23/2017] [Indexed: 12/28/2022] Open
Abstract
Helicobacter pylori East Asian CagA is more closely associated with gastric cancer than Western CagA. Here we show that, upon tyrosine phosphorylation, the East Asian CagA-specific EPIYA-D segment binds to the N-SH2 domain of pro-oncogenic SHP2 phosphatase two orders of magnitude greater than Western CagA-specific EPIYA-C. This high-affinity binding is achieved via cryptic interaction between Phe at the +5 position from phosphotyrosine in EPIYA-D and a hollow on the N-SH2 phosphopeptide-binding floor. Also, duplication of EPIYA-C in Western CagA, which increases gastric cancer risk, enables divalent high-affinity binding with SHP2 via N-SH2 and C-SH2. These strong CagA bindings enforce enzymatic activation of SHP2, which endows cells with neoplastic traits. Mechanistically, N-SH2 in SHP2 is in an equilibrium between stimulatory "relaxed" and inhibitory "squeezed" states, which is fixed upon high-affinity CagA binding to the "relaxed" state that stimulates SHP2. Accordingly, East Asian CagA and Western CagA exploit distinct mechanisms for SHP2 deregulation.
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Affiliation(s)
- Takeru Hayashi
- Department of Microbiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Miki Senda
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801, Japan
| | - Nobuhiro Suzuki
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801, Japan
| | - Hiroko Nishikawa
- Department of Microbiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan; Max Planck-The University of Tokyo Center for Integrative Inflammology, Tokyo 113-0033, Japan
| | - Chi Ben
- Department of Microbiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Chao Tang
- Department of Microbiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Lisa Nagase
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801, Japan
| | - Kaori Inoue
- Department of Microbiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Toshiya Senda
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba 305-0801, Japan; Department of Materials Structure Science, School of High Energy Accelerator Science, The Graduate University of Advanced Studies, Tsukuba 305-0801, Japan.
| | - Masanori Hatakeyama
- Department of Microbiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan; Max Planck-The University of Tokyo Center for Integrative Inflammology, Tokyo 113-0033, Japan.
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47
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Abstract
Recombinant proteins expressed in bacteria are sometimes insoluble, aggregated, and incorrectly folded. For those Src homology 2 (SH2) domains that are insoluble in bacteria, baculovirus-insect cell expression systems can be an alternative to produce soluble and functionally active proteins. We describe a protocol for cloning and purification of GST-tagged SH2 domains using the Bac-to-Bac baculovirus expression system.
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48
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Buhs S, Gerull H, Nollau P. Identification of Tyrosine Phosphorylated Proteins by SH2 Domain Affinity Purification and Mass Spectrometry. Methods Mol Biol 2017; 1555:407-18. [PMID: 28092046 DOI: 10.1007/978-1-4939-6762-9_23] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Phosphotyrosine signaling plays a major role in the control of many important biological functions such as cell proliferation and apoptosis. Deciphering of phosphotyrosine-dependent signaling is therefore of great interest paving the way for the understanding of physiological and pathological processes of signal transduction. On the basis of the specific binding of SH2 domains to phosphotyrosine residues, we here present an experimental workflow for affinity purification and subsequent identification of tyrosine phosphorylated proteins by mass spectrometry. In combination with SH2 profiling, a broadly applicable platform for the characterization of phosphotyrosine profiles in cell extracts, our pull down strategy enables researchers by now to identify proteins in signaling cascades which are differentially phosphorylated and selectively recognized by distinct SH2 domains.
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49
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Chi PB, Kim D, Lai JK, Bykova N, Weber CC, Kubelka J, Liberles DA. A new parameter-rich structure-aware mechanistic model for amino acid substitution during evolution. Proteins 2017; 86:218-228. [PMID: 29178386 DOI: 10.1002/prot.25429] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 11/14/2017] [Accepted: 11/22/2017] [Indexed: 02/06/2023]
Abstract
Improvements in the description of amino acid substitution are required to develop better pseudo-energy-based protein structure-aware models for use in phylogenetic studies. These models are used to characterize the probabilities of amino acid substitution and enable better simulation of protein sequences over a phylogeny. A better characterization of amino acid substitution probabilities in turn enables numerous downstream applications, like detecting positive selection, ancestral sequence reconstruction, and evolutionarily-motivated protein engineering. Many existing Markov models for amino acid substitution in molecular evolution disregard molecular structure and describe the amino acid substitution process over longer evolutionary periods poorly. Here, we present a new model upgraded with a site-specific parameterization of pseudo-energy terms in a coarse-grained force field, which describes local heterogeneity in physical constraints on amino acid substitution better than a previous pseudo-energy-based model with minimum cost in runtime. The importance of each weight term parameterization in characterizing underlying features of the site, including contact number, solvent accessibility, and secondary structural elements was evaluated, returning both expected and biologically reasonable relationships between model parameters. This results in the acceptance of proposed amino acid substitutions that more closely resemble those observed site-specific frequencies in gene family alignments. The modular site-specific pseudo-energy function is made available for download through the following website: https://liberles.cst.temple.edu/Software/CASS/index.html.
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Affiliation(s)
- Peter B Chi
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, Pennsylvania, 19122.,Department of Mathematics and Computer Science, Ursinus College, Collegeville, Pennsylvania, 19426
| | - Dohyup Kim
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming, 82071
| | - Jason K Lai
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming, 82071
| | - Nadia Bykova
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming, 82071.,Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow, 119234, Russia
| | - Claudia C Weber
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, Pennsylvania, 19122
| | - Jan Kubelka
- Department of Chemistry, University of Wyoming, Laramie, Wyoming, 82071
| | - David A Liberles
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, Pennsylvania, 19122.,Department of Molecular Biology, University of Wyoming, Laramie, Wyoming, 82071
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50
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McKercher MA, Guan X, Tan Z, Wuttke DS. Diversity in peptide recognition by the SH2 domain of SH2B1. Proteins 2017; 86:164-176. [PMID: 29127727 DOI: 10.1002/prot.25420] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 10/30/2017] [Accepted: 11/09/2017] [Indexed: 11/07/2022]
Abstract
SH2B1 is a multidomain protein that serves as a key adaptor to regulate numerous cellular events, such as insulin, leptin, and growth hormone signaling pathways. Many of these protein-protein interactions are mediated by the SH2 domain of SH2B1, which recognizes ligands containing a phosphorylated tyrosine (pY), including peptides derived from janus kinase 2, insulin receptor, and insulin receptor substrate-1 and -2. Specificity for the SH2 domain of SH2B1 is conferred in these ligands either by a hydrophobic or an acidic side chain at the +3 position C-terminal to the pY. This specificity for chemically disparate species suggests that SH2B1 relies on distinct thermodynamic or structural mechanisms to bind to peptides. Using binding and structural strategies, we have identified unique thermodynamic signatures for each peptide binding mode, and several SH2B1 residues, including K575 and R578, that play distinct roles in peptide binding. The high-resolution structure of the SH2 domain of SH2B1 further reveals conformationally plastic protein loops that may contribute to the ability of the protein to recognize dissimilar ligands. Together, numerous hydrophobic and electrostatic interactions, in addition to backbone conformational flexibility, permit the recognition of diverse peptides by SH2B1. An understanding of this expanded peptide recognition will allow for the identification of novel physiologically relevant SH2B1/peptide interactions, which can contribute to the design of obesity and diabetes pharmaceuticals to target the ligand-binding interface of SH2B1 with high specificity.
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Affiliation(s)
- Marissa A McKercher
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado
| | - Xiaoyang Guan
- Department of Chemistry and Biochemistry, BioFrontiers Institute, University of Colorado, Boulder, Colorado
| | - Zhongping Tan
- Department of Chemistry and Biochemistry, BioFrontiers Institute, University of Colorado, Boulder, Colorado
| | - Deborah S Wuttke
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado
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