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Fujioka Y, Satoh AO, Horiuchi K, Fujioka M, Tsutsumi K, Sasaki J, Nepal P, Kashiwagi S, Paudel S, Nishide S, Nanbo A, Sasaki T, Ohba Y. A Peptide Derived from Phosphoinositide 3-kinase Inhibits Endocytosis and Influenza Virus Infection. Cell Struct Funct 2019; 44:61-74. [PMID: 30905923 DOI: 10.1247/csf.19001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Endocytosis mediates the internalization and ingestion of a variety of endogenous or exogenous substances, including virus particles, under the control of intracellular signaling pathways. We have previously reported that the complex formed between the small GTPase Ras and phosphoinositide 3-kinase (PI3K) translocates from the plasma membrane to endosomes, signaling from which thereby regulates clathrin-independent endocytosis, endosome maturation, influenza virus internalization, and infection. However, the molecular mechanism by which the Ras-PI3K complex is recruited to endosomes remains unclear. Here, we have identified the amino acid sequence responsible for endosomal localization of the Ras-PI3K complex. PI3K lacking this sequence failed to translocate to endosomes, and expression of the peptide comprising this PI3K-derived sequence inhibited clathrin-independent endocytosis, influenza virus internalization, and infection. Moreover, treatment of cells with this peptide in an arginine-rich, cell-penetrating form successfully suppressed influenza virus infection in vitro and ex vivo, making this peptide a potential therapeutic agent against influenza virus infection.Key words: signal transduction, endocytosis, endosome, imaging, influenza virus.
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Affiliation(s)
- Yoichiro Fujioka
- Department of Cell Physiology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University
| | - Aya O Satoh
- Department of Cell Physiology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University
| | - Kosui Horiuchi
- Department of Cell Physiology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University
| | - Mari Fujioka
- Department of Cell Physiology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University
| | - Kaori Tsutsumi
- Department of Biological Sciences and Engineering, Faculty of Health Sciences, Hokkaido University
| | - Junko Sasaki
- Department of Biochemical Pathophysiology, Medical Research Institute, Tokyo Medical and Dental University
| | - Prabha Nepal
- Department of Cell Physiology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University
| | - Sayaka Kashiwagi
- Department of Cell Physiology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University
| | - Sarad Paudel
- Department of Cell Physiology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University
| | - Shinya Nishide
- Department of Cell Physiology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University
| | - Asuka Nanbo
- Department of Cell Physiology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University
| | - Takehiko Sasaki
- Department of Biochemical Pathophysiology, Medical Research Institute, Tokyo Medical and Dental University
| | - Yusuke Ohba
- Department of Cell Physiology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University.,Whitman Center, Marine Biological Laboratory
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102
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Al-Suhaimi E, Ravinayagam V, Jermy BR, Mohamad T, Elaissari A. Protein/ Hormone Based Nanoparticles as Carriers for Drugs Targeting Protein-Protein Interactions. Curr Top Med Chem 2019; 19:444-456. [PMID: 30836918 DOI: 10.2174/1568026619666190304152320] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 01/02/2019] [Accepted: 01/24/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND In this review, protein-protein interactions (PPIs) were defined, and their behaviors in normal in disease conditions are discussed. Their status at nuclear, molecular and cellular level was underscored, as for their interference in many diseases. Finally, the use of protein nanoscale structures as possible carriers for drugs targeting PPIs was highlighted. OBJECTIVE The objective of this review is to suggest a novel approach for targeting PPIs. By using protein nanospheres and nanocapsules, a promising field of study can be emerged. METHODS To solidify this argument, PPIs and their biological significance was discussed, same as their role in hormone signaling. RESULTS We shed the light on the drugs that targets PPI and we suggested the use of nanovectors to encapsulate these drugs to possibly achieve better results. CONCLUSION Protein based nanoparticles, due to their advantages, can be suitable carriers for drugs targeting PPIs. This can open a new opportunity in the emerging field of multifunctional therapeutics.
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Affiliation(s)
- Ebtesam Al-Suhaimi
- Biology Department, College of Science, Imam Abdulrahman Bin Faisal University, Dammam, 31441, Saudi Arabia
| | - Vijaya Ravinayagam
- Deanship of Scientific Research & Nanomedicine Research Department, Institute of Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, 31441, Saudi Arabia
| | - B. Rabindran Jermy
- Nanomedicine Research Department, Institute of Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, 31441, Saudi Arabia
| | - Tarhini Mohamad
- University Lyon, University Claude Bernard Lyon-1, CNRS, LAGEP-UMR 5007, F- 69622 Lyon, France
| | - Abdelhamid Elaissari
- University Lyon, University Claude Bernard Lyon-1, CNRS, LAGEP-UMR 5007, F- 69622 Lyon, France
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103
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Abstract
Proteins containing tyrosine kinase activity play critical roles in cancer signaling. Intracellular SRC-family kinases relay growth signals from numerous cell surface receptors and can be constitutively activated by oncogenic mutations, as can transmembrane growth factor receptors such as epidermal growth factor receptor (EGFR) and human epidermal growth factor receptor 2 (HER2) that signal via their tyrosine kinase activity. In this excerpt from his forthcoming book on the history of cancer research, Joe Lipsick looks back at the discovery of tyrosine kinases and the demonstration that the V-SRC protein encoded by Rous sarcoma virus was a tyrosine kinase.
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Affiliation(s)
- Joseph Lipsick
- Departments of Pathology, Genetics, and Biology, Stanford University, Stanford, California 94305-5324, USA
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104
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Liu H, Huang H, Voss C, Kaneko T, Qin WT, Sidhu S, Li SSC. Surface Loops in a Single SH2 Domain Are Capable of Encoding the Spectrum of Specificity of the SH2 Family. Mol Cell Proteomics 2019; 18:372-382. [PMID: 30482845 PMCID: PMC6356082 DOI: 10.1074/mcp.ra118.001123] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/05/2018] [Indexed: 12/15/2022] Open
Abstract
Src homology 2 (SH2) domains play an essential role in cellular signal transduction by binding to proteins phosphorylated on Tyr residue. Although Tyr phosphorylation (pY) is a prerequisite for binding for essentially all SH2 domains characterized to date, different SH2 domains prefer specific sequence motifs C-terminal to the pY residue. Because all SH2 domains adopt the same structural fold, it is not well understood how different SH2 domains have acquired the ability to recognize distinct sequence motifs. We have shown previously that the EF and BG loops that connect the secondary structure elements on an SH2 domain dictate its specificity. In this study, we investigated if these surface loops could be engineered to encode diverse specificities. By characterizing a group of SH2 variants selected by different pY peptides from phage-displayed libraries, we show that the EF and BG loops of the Fyn SH2 domain can encode a wide spectrum of specificities, including all three major specificity classes (p + 2, p + 3 and p + 4) of the SH2 domain family. Furthermore, we found that the specificity of a given variant correlates with the sequence feature of the bait peptide used for its isolation, suggesting that an SH2 domain may acquire specificity by co-evolving with its ligand. Intriguingly, we found that the SH2 variants can employ a variety of different mechanisms to confer the same specificity, suggesting the EF and BG loops are highly flexible and adaptable. Our work provides a plausible mechanism for the SH2 domain to acquire the wide spectrum of specificity observed in nature through loop variation with minimal disturbance to the SH2 fold. It is likely that similar mechanisms may have been employed by other modular interaction domains to generate diversity in specificity.
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Affiliation(s)
- Huadong Liu
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China;; Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1
| | - Haiming Huang
- Donnelly Centre for Cellular and Biomolecular Research, 160 College St., Toronto ON M5S 3E1, Canada
| | - Courtney Voss
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1
| | - Tomonori Kaneko
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1
| | - Wen Tao Qin
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1
| | - Sachdev Sidhu
- Donnelly Centre for Cellular and Biomolecular Research, 160 College St., Toronto ON M5S 3E1, Canada.
| | - Shawn S-C Li
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1;.
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105
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Clarke DT, Martin-Fernandez ML. A Brief History of Single-Particle Tracking of the Epidermal Growth Factor Receptor. Methods Protoc 2019; 2:mps2010012. [PMID: 31164594 PMCID: PMC6481046 DOI: 10.3390/mps2010012] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 01/21/2019] [Accepted: 01/21/2019] [Indexed: 12/15/2022] Open
Abstract
Single-particle tracking (SPT) has been used and developed over the last 25 years as a method to investigate molecular dynamics, structure, interactions, and function in the cellular context. SPT is able to show how fast and how far individual molecules move, identify different dynamic populations, measure the duration and strength of intermolecular interactions, and map out structures on the nanoscale in cells. In combination with other techniques such as macromolecular crystallography and molecular dynamics simulation, it allows us to build models of complex structures, and develop and test hypotheses of how these complexes perform their biological roles in health as well as in disease states. Here, we use the example of the epidermal growth factor receptor (EGFR), which has been studied extensively by SPT, demonstrating how the method has been used to increase our understanding of the receptor’s organization and function, including its interaction with the plasma membrane, its activation, clustering, and oligomerization, and the role of other receptors and endocytosis. The examples shown demonstrate how SPT might be employed in the investigation of other biomolecules and systems.
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Affiliation(s)
- David T Clarke
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0QX, UK.
| | - Marisa L Martin-Fernandez
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0QX, UK.
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106
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Erickson KE, Rukhlenko OS, Shahinuzzaman M, Slavkova KP, Lin YT, Suderman R, Stites EC, Anghel M, Posner RG, Barua D, Kholodenko BN, Hlavacek WS. Modeling cell line-specific recruitment of signaling proteins to the insulin-like growth factor 1 receptor. PLoS Comput Biol 2019; 15:e1006706. [PMID: 30653502 PMCID: PMC6353226 DOI: 10.1371/journal.pcbi.1006706] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 01/30/2019] [Accepted: 12/09/2018] [Indexed: 12/27/2022] Open
Abstract
Receptor tyrosine kinases (RTKs) typically contain multiple autophosphorylation sites in their cytoplasmic domains. Once activated, these autophosphorylation sites can recruit downstream signaling proteins containing Src homology 2 (SH2) and phosphotyrosine-binding (PTB) domains, which recognize phosphotyrosine-containing short linear motifs (SLiMs). These domains and SLiMs have polyspecific or promiscuous binding activities. Thus, multiple signaling proteins may compete for binding to a common SLiM and vice versa. To investigate the effects of competition on RTK signaling, we used a rule-based modeling approach to develop and analyze models for ligand-induced recruitment of SH2/PTB domain-containing proteins to autophosphorylation sites in the insulin-like growth factor 1 (IGF1) receptor (IGF1R). Models were parameterized using published datasets reporting protein copy numbers and site-specific binding affinities. Simulations were facilitated by a novel application of model restructuration, to reduce redundancy in rule-derived equations. We compare predictions obtained via numerical simulation of the model to those obtained through simple prediction methods, such as through an analytical approximation, or ranking by copy number and/or KD value, and find that the simple methods are unable to recapitulate the predictions of numerical simulations. We created 45 cell line-specific models that demonstrate how early events in IGF1R signaling depend on the protein abundance profile of a cell. Simulations, facilitated by model restructuration, identified pairs of IGF1R binding partners that are recruited in anti-correlated and correlated fashions, despite no inclusion of cooperativity in our models. This work shows that the outcome of competition depends on the physicochemical parameters that characterize pairwise interactions, as well as network properties, including network connectivity and the relative abundances of competitors. Cells rely on networks of interacting biomolecules to sense and respond to environmental perturbations and signals. However, it is unclear how information is processed to generate appropriate and specific responses to signals, especially given that these networks tend to share many components. For example, receptors that detect distinct ligands and regulate distinct cellular activities commonly interact with overlapping sets of downstream signaling proteins. Here, to investigate the downstream signaling of a well-studied receptor tyrosine kinase (RTK), the insulin-like growth factor 1 (IGF1) receptor (IGF1R), we formulated and analyzed 45 cell line-specific mathematical models, which account for recruitment of 18 different binding partners to six sites of receptor autophosphorylation in IGF1R. The models were parameterized using available protein copy number and site-specific affinity measurements, and restructured to allow for network generation. We find that recruitment is influenced by the protein abundance profile of a cell, with different patterns of recruitment in different cell lines. Furthermore, in a given cell line, we find that pairs of IGF1R binding partners may be recruited in a correlated or anti-correlated fashion. We demonstrate that the simulations of the model have greater predictive power than protein copy number and/or binding affinity data, and that even a simple analytical model cannot reproduce the predicted recruitment ranking obtained via simulations. These findings represent testable predictions and indicate that the outputs of IGF1R signaling depend on cell line-specific properties in addition to the properties that are intrinsic to the biomolecules involved.
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Affiliation(s)
- Keesha E. Erickson
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | | | - Md Shahinuzzaman
- Department of Chemical and Biochemical Engineering, University of Missouri Science and Technology, Rolla, Missouri, United States of America
| | - Kalina P. Slavkova
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Yen Ting Lin
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Ryan Suderman
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Edward C. Stites
- The Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - Marian Anghel
- Information Sciences Group, Computer, Computational and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Richard G. Posner
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Dipak Barua
- Department of Chemical and Biochemical Engineering, University of Missouri Science and Technology, Rolla, Missouri, United States of America
| | - Boris N. Kholodenko
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
- School of Medicine and Medical Science and Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland
| | - William S. Hlavacek
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- * E-mail:
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107
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Monitoring activities of receptor tyrosine kinases using a universal adapter in genetically encoded split TEV assays. Cell Mol Life Sci 2019; 76:1185-1199. [PMID: 30623207 PMCID: PMC6675780 DOI: 10.1007/s00018-018-03003-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 12/28/2018] [Indexed: 01/10/2023]
Abstract
Receptor tyrosine kinases (RTKs) play key roles in various aspects of
cell biology, including cell-to-cell communication, proliferation and
differentiation, survival, and tissue homeostasis, and have been implicated in
various diseases including cancer and neurodevelopmental disorders. Ligand-activated
RTKs recruit adapter proteins through a phosphotyrosine (p-Tyr) motif that is
present on the RTK and a p-Tyr-binding domain, like the Src homology 2 (SH2) domain
found in adapter proteins. Notably, numerous combinations of RTK/adapter
combinations exist, making it challenging to compare receptor activities in
standardised assays. In cell-based assays, a regulated adapter recruitment can be
investigated using genetically encoded protein–protein interaction detection
methods, such as the split TEV biosensor assay. Here, we applied the split TEV
technique to robustly monitor the dynamic recruitment of both naturally occurring
full-length adapters and artificial adapters, which are formed of clustered SH2
domains. The applicability of this approach was tested for RTKs from various
subfamilies including the epidermal growth factor (ERBB) family, the insulin
receptor (INSR) family, and the hepatocyte growth factor receptor (HGFR) family.
Best signal-to-noise ratios of ligand-activated RTK receptor activation was obtained
when clustered SH2 domains derived from GRB2 were used as adapters. The sensitivity
and robustness of the RTK recruitment assays were validated in dose-dependent
inhibition assays using the ERBB family-selective antagonists lapatinib and WZ4002.
The RTK split TEV recruitment assays also qualify for high-throughput screening
approaches, suggesting that the artificial adapter may be used as universal adapter
in cell-based profiling assays within pharmacological intervention studies.
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108
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Chen JQ, Yu LD, Zhang L, Liang RP, Cao SP, Qiu JD. Ultrasensitive detection of protein kinase activity based on the Au NPs mediated electrochemiluminescence amplification of S2O82−–O2 system. J Electroanal Chem (Lausanne) 2019. [DOI: 10.1016/j.jelechem.2018.12.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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109
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Yablonski D. Bridging the Gap: Modulatory Roles of the Grb2-Family Adaptor, Gads, in Cellular and Allergic Immune Responses. Front Immunol 2019; 10:1704. [PMID: 31402911 DOI: 10.3389/fimmu.2019.01704/full] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 07/08/2019] [Indexed: 05/22/2023] Open
Abstract
Antigen receptor signaling pathways are organized by adaptor proteins. Three adaptors, LAT, Gads, and SLP-76, form a heterotrimeric complex that mediates signaling by the T cell antigen receptor (TCR) and by the mast cell high affinity receptor for IgE (FcεRI). In both pathways, antigen recognition triggers tyrosine phosphorylation of LAT and SLP-76. The recruitment of SLP-76 to phospho-LAT is bridged by Gads, a Grb2 family adaptor composed of two SH3 domains flanking a central SH2 domain and an unstructured linker region. The LAT-Gads-SLP-76 complex is further incorporated into larger microclusters that mediate antigen receptor signaling. Gads is positively regulated by dimerization, which promotes its cooperative binding to LAT. Negative regulation occurs via phosphorylation or caspase-mediated cleavage of the linker region of Gads. FcεRI-mediated mast cell activation is profoundly impaired in LAT- Gads- or SLP-76-deficient mice. Unexpectedly, the thymic developmental phenotype of Gads-deficient mice is much milder than the phenotype of LAT- or SLP-76-deficient mice. This distinction suggests that Gads is not absolutely required for TCR signaling, but may modulate its sensitivity, or regulate a particular branch of the TCR signaling pathway; indeed, the phenotypic similarity of Gads- and Itk-deficient mice suggests a functional connection between Gads and Itk. Additional Gads binding partners include costimulatory proteins such as CD28 and CD6, adaptors such as Shc, ubiquitin regulatory proteins such as USP8 and AMSH, and kinases such as HPK1 and BCR-ABL, but the functional implications of these interactions are not yet fully understood. No interacting proteins or function have been ascribed to the evolutionarily conserved N-terminal SH3 of Gads. Here we explore the biochemical and functional properties of Gads, and its role in regulating allergy, T cell development and T-cell mediated immunity.
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Affiliation(s)
- Deborah Yablonski
- The Immune Cell Signaling Lab, Department of Immunology, Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
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110
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Cao M, Chen G, Yu J, Shi S. Computational prediction and analysis of species-specific fungi phosphorylation via feature optimization strategy. Brief Bioinform 2018; 21:595-608. [DOI: 10.1093/bib/bby122] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 11/16/2018] [Accepted: 11/22/2018] [Indexed: 11/12/2022] Open
Abstract
Abstract
Protein phosphorylation is a reversible and ubiquitous post-translational modification that primarily occurs at serine, threonine and tyrosine residues and regulates a variety of biological processes. In this paper, we first briefly summarized the current progresses in computational prediction of eukaryotic protein phosphorylation sites, which mainly focused on animals and plants, especially on human, with a less extent on fungi. Since the number of identified fungi phosphorylation sites has greatly increased in a wide variety of organisms and their roles in pathological physiology still remain largely unknown, more attention has been paid on the identification of fungi-specific phosphorylation. Here, experimental fungi phosphorylation sites data were collected and most of the sites were classified into different types to be encoded with various features and trained via a two-step feature optimization method. A novel method for prediction of species-specific fungi phosphorylation-PreSSFP was developed, which can identify fungi phosphorylation in seven species for specific serine, threonine and tyrosine residues (http://computbiol.ncu.edu.cn/PreSSFP). Meanwhile, we critically evaluated the performance of PreSSFP and compared it with other existing tools. The satisfying results showed that PreSSFP is a robust predictor. Feature analyses exhibited that there have some significant differences among seven species. The species-specific prediction via two-step feature optimization method to mine important features for training could considerably improve the prediction performance. We anticipate that our study provides a new lead for future computational analysis of fungi phosphorylation.
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Affiliation(s)
- Man Cao
- Department of Mathematics and Numerical Simulation and High-Performance Computing Laboratory, School of Sciences, Nanchang University, Nanchang, China
| | - Guodong Chen
- Department of Mathematics and Numerical Simulation and High-Performance Computing Laboratory, School of Sciences, Nanchang University, Nanchang, China
| | - Jialin Yu
- Department of Mathematics and Numerical Simulation and High-Performance Computing Laboratory, School of Sciences, Nanchang University, Nanchang, China
| | - Shaoping Shi
- Department of Mathematics and Numerical Simulation and High-Performance Computing Laboratory, School of Sciences, Nanchang University, Nanchang, China
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111
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Di Liberto V, Mudò G, Belluardo N. Crosstalk between receptor tyrosine kinases (RTKs) and G protein-coupled receptors (GPCR) in the brain: Focus on heteroreceptor complexes and related functional neurotrophic effects. Neuropharmacology 2018; 152:67-77. [PMID: 30445101 DOI: 10.1016/j.neuropharm.2018.11.018] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 11/01/2018] [Accepted: 11/12/2018] [Indexed: 01/11/2023]
Abstract
Neuronal events are regulated by the integration of several complex signaling networks in which G protein-coupled receptors (GPCRs) and receptor tyrosine kinases (RTKs) are considered key players of an intense bidirectional cross-communication in the cell, generating signaling mechanisms that, at the same time, connect and diversify the traditional signal transduction pathways activated by the single receptor. For this receptor-receptor crosstalk, the two classes of receptors form heteroreceptor complexes resulting in RTKs transactivation and in growth-promoting signals. In this review, we describe heteroreceptor complexes between GPCR and RTKs in the central nervous system (CNS) and their functional effects in controlling a variety of neuronal effects, ranging from development, proliferation, differentiation and migration, to survival, repair, synaptic transmission and plasticity. In this interaction, RTKs can also recruit components of the G protein signaling cascade, creating a bidirectional intricate interplay that provides complex control over multiple cellular events. These heteroreceptor complexes, by the integration of different signals, have recently attracted a growing interest as novel molecular target for depressive disorders. This article is part of the Special Issue entitled 'Receptor heteromers and their allosteric receptor-receptor interactions'.
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Affiliation(s)
- Valentina Di Liberto
- Department of Experimental Biomedicine and Clinical Neurosciences, University of Palermo, Palermo, Italy
| | - Giuseppa Mudò
- Department of Experimental Biomedicine and Clinical Neurosciences, University of Palermo, Palermo, Italy
| | - Natale Belluardo
- Department of Experimental Biomedicine and Clinical Neurosciences, University of Palermo, Palermo, Italy.
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112
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Cai H, Huang B, Lin R, Xu P, Liu Y, Zhao Y. A ‘‘turn-off’’ SERS assay for kinase detection based on arginine N-phosphorylation process. Talanta 2018; 189:353-358. [DOI: 10.1016/j.talanta.2018.07.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 06/20/2018] [Accepted: 07/01/2018] [Indexed: 02/01/2023]
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113
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Abstract
The MAPK pathway is a prominent intracellular signaling pathway regulating various intracellular functions. Components of this pathway are mutated in a related collection of congenital syndromes collectively referred to as neuro-cardio-facio-cutaneous syndromes (NCFC) or Rasopathies. Recently, it has been appreciated that these disorders are associated with autism spectrum disorders (ASD). In addition, idiopathic ASD has also implicated the MAPK signaling cascade as a common pathway that is affected by many of the genetic variants that have been found to be linked to ASDs. This chapter describes the components of the MAPK pathway and how it is regulated. Furthermore, this chapter will highlight the various functions of the MAPK pathway during both embryonic development of the central nervous system (CNS) and its roles in neuronal physiology and ultimately, behavior. Finally, we will summarize the perturbations to MAPK signaling in various models of autism spectrum disorders and Rasopathies to highlight how dysregulation of this pivotal pathway may contribute to the pathogenesis of autism.
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114
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Identification and characterization of a large family of superbinding bacterial SH2 domains. Nat Commun 2018; 9:4549. [PMID: 30382091 PMCID: PMC6208348 DOI: 10.1038/s41467-018-06943-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 10/02/2018] [Indexed: 11/27/2022] Open
Abstract
Src homology 2 (SH2) domains play a critical role in signal transduction in mammalian cells by binding to phosphorylated Tyr (pTyr). Apart from a few isolated cases in viruses, no functional SH2 domain has been identified to date in prokaryotes. Here we identify 93 SH2 domains from Legionella that are distinct in sequence and specificity from mammalian SH2 domains. The bacterial SH2 domains are not only capable of binding proteins or peptides in a Tyr phosphorylation-dependent manner, some bind pTyr itself with micromolar affinities, a property not observed for mammalian SH2 domains. The Legionella SH2 domains feature the SH2 fold and a pTyr-binding pocket, but lack a specificity pocket found in a typical mammalian SH2 domain for recognition of sequences flanking the pTyr residue. Our work expands the boundary of phosphotyrosine signalling to prokaryotes, suggesting that some bacterial effector proteins have acquired pTyr-superbinding characteristics to facilitate bacterium-host interactions. SH2 domains bind to tyrosine-phosphorylated proteins and play crucial roles in signal transduction in mammalian cells. Here, Kaneko et al. identify a large family of SH2 domains in the bacterial pathogen Legionella that bind to mammalian phosphorylated proteins, in some cases with very high affinity.
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Li Y, Li RH, Ran MX, Zhang Y, Liang K, Ren YN, He WC, Zhang M, Zhou GB, Qazi IH, Zeng CJ. High throughput small RNA and transcriptome sequencing reveal capacitation-related microRNAs and mRNA in boar sperm. BMC Genomics 2018; 19:736. [PMID: 30305024 PMCID: PMC6180635 DOI: 10.1186/s12864-018-5132-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 09/28/2018] [Indexed: 12/21/2022] Open
Abstract
Background Capacitation, a prerequisite for oocyte fertilization, is a complex process involving series of structural and functional changes in sperms such as membrane modifications, modulation of enzyme activities, and protein phosphorylation. In order to penetrate and fertilize an oocyte, mammalian sperms must undergo capacitation. Nevertheless, the process of sperm capacitation remains poorly understood and requires further elucidation. In the current study, via high throughput sequencing, we identified and explored the differentially expressed microRNAs (miRNAs) and mRNAs involved in boar sperm capacitation. Results We identified a total of 5342 mRNAs and 204 miRNAs that were differentially expressed in fresh and capacitated boar sperms. From these, 12 miRNAs (8 known and 4 newly identified miRNAs) and their differentially expressed target mRNAs were found to be involved in sperm capacitation-related PI3K-Akt, MAPK, cAMP-PKA and Ca2+signaling pathways. Conclusions Our study is first to provide the complete miRNA and transcriptome profiles of boar sperm. Our findings provide important insights for the understanding of the RNA profile in boar sperm and future elucidation of the underlying molecular mechanism relevant to mammalian sperm capacitation. Electronic supplementary material The online version of this article (10.1186/s12864-018-5132-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuan Li
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan Province, China
| | - Rong-Hong Li
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan Province, China
| | - Ming-Xia Ran
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan Province, China
| | - Yan Zhang
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan Province, China
| | - Kai Liang
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan Province, China
| | - Ying-Nan Ren
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan Province, China
| | - Wen-Cheng He
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan Province, China
| | - Ming Zhang
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan Province, China
| | - Guang-Bin Zhou
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan Province, China
| | - Izhar Hyder Qazi
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan Province, China.,Department of Veterinary Anatomy & Histology, Shaheed Benazir Bhutto University of Veterinary and Animal Sciences, Sakrand, Sindh, 67210, Pakistan
| | - Chang-Jun Zeng
- College of Animal Sciences and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China. .,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan Province, China.
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Wang H, Tian Z. Facile synthesis of titanium(IV) ion-immobilized poly-glycidyl methacrylate microparticles functionalized with polyethylenimine and adenosine triphosphate for highly specific enrichment of intact phosphoproteins. J Sep Sci 2018; 41:4194-4202. [PMID: 30239132 DOI: 10.1002/jssc.201800689] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 09/14/2018] [Accepted: 09/14/2018] [Indexed: 12/28/2022]
Abstract
In this study, a facile synthesis of the titanium(IV) ion-immobilized poly-glycidyl methacrylate microparticles functionalized with polyethylenimine and adenosine triphosphate was developed for efficient enrichment of intact phosphoproteins. The titanium(IV) ion-immobilized microparticles had higher saturated adsorption capacity for phosphoproteins (1217.6 mg/g for β-casein) than nonphosphoproteins (97.1 mg/g for bovine serum albumin) and the average particle diameter was about 1.4 μm with good dispersibility. In application, as demonstrated by SDS-PAGE, titanium(IV) ion-immobilized microparticles exhibited good performance in enriching intact phosphoproteins from standard protein mixtures of β-casein and bovine serum albumin with high specificity and selectivity. In addition, titanium(IV) ion-immobilized microparticles were also successfully applied in intact phosphoprotein enrichment from complex biological samples including nonfat milk, chicken egg white, and mouse heart tissue extract.
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Affiliation(s)
- Hao Wang
- School of Chemical Science and Engineering and Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai, P. R. China
| | - Zhixin Tian
- School of Chemical Science and Engineering and Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai, P. R. China
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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] [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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118
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Wang R, Leung PYM, Huang F, Tang Q, Kaneko T, Huang M, Li Z, Li SSC, Wang Y, Xia J. Reverse Binding Mode of Phosphotyrosine Peptides with SH2 Protein. Biochemistry 2018; 57:5257-5269. [PMID: 30091902 DOI: 10.1021/acs.biochem.8b00677] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Discerning the different interaction states during dynamic protein-ligand binding is difficult. Here we apply site-specific cysteine-α-chloroacetyl cross-linking to scrutinize the binding between the Src homology 2 (SH2) domain and phosphotyrosine (pY) peptides, a highly dynamic interaction that is a key to cellular signal transduction. From a model SH2 protein to a set of representative SH2 domains, we showed here that a proximity-induced cysteine-α-chloroacetyl reaction cross-linked two spatially adjacent chemical groups as a result of the binding interaction, and reciprocally, the information about the interaction states can be deduced from the cross-linked products. To our surprise, we found SH2 domains can adopt a reverse binding mode with "single-pronged", "two-pronged", and "half" pY peptides. This finding was further supported by a set of 500 ns molecular dynamics simulations. This serendipitous finding defies the canonical theory of SH2 binding, suggests a possible answer about the source of the versatility of SH2 signaling, and sets a model for other protein binding interactions.
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Affiliation(s)
- Rui Wang
- Department of Biochemistry and Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry , Western University , London , Ontario N6A 5C1 , Canada
| | | | | | | | - Tomonori Kaneko
- Department of Biochemistry and Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry , Western University , London , Ontario N6A 5C1 , Canada
| | - Mei Huang
- Department of Biochemistry and Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry , Western University , London , Ontario N6A 5C1 , Canada
| | - Zigang Li
- School of Chemical Biology and Biotechnology , Shenzhen Graduate School of Peking University , Shenzhen 518055 , China
| | - Shawn S C Li
- Department of Biochemistry and Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry , Western University , London , Ontario N6A 5C1 , Canada
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Kim E, Kim DH, Singaram I, Jeong H, Koh A, Lee J, Cho W, Ryu SH. Cellular phosphatase activity of C1-Ten/Tensin2 is controlled by Phosphatidylinositol-3,4,5-triphosphate binding through the C1-Ten/Tensin2 SH2 domain. Cell Signal 2018; 51:130-138. [PMID: 30092354 DOI: 10.1016/j.cellsig.2018.07.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 07/20/2018] [Accepted: 07/26/2018] [Indexed: 12/28/2022]
Abstract
Regulation of tyrosine phosphorylation on insulin receptor substrate-1 (IRS-1) is essential for insulin signaling. The protein tyrosine phosphatase (PTP) C1-Ten/Tensin2 has been implicated in the regulation of IRS-1, but the molecular basis of this dephosphorylation is not fully understood. Here, we demonstrate that the cellular phosphatase activity of C1-Ten/Tensin2 on IRS-1 is mediated by the binding of the C1-Ten/Tensin2 Src-homology 2 (SH2) domain to phosphatidylinositol-3,4,5-trisphosphate (PtdIns(3,4,5)P3). We show that the role of C1-Ten/Tensin2 is dependent on insulin-induced phosphoinositide 3-kinase activity. The C1-Ten/Tensin2 SH2 domain showed strong preference and high affinity for PtdIns(3,4,5)P3. Using site-directed mutagenesis, we identified three basic residues in the C1-Ten/Tensin2 SH2 domain that were critical for PtdIns(3,4,5)P3 binding but were not involved in phosphotyrosine binding and PTP activity. Using a PtdIns(3,4,5)P3 binding-deficient mutant, we showed that the specific binding of the C1-Ten/Tensin2 SH2 domain to PtdIns(3,4,5)P3 allowed C1-Ten/Tensin2 to function as a PTP in cells. Collectively, our findings suggest that the interaction between the C1-Ten/Tensin2 SH2 domain and PtdIns(3,4,5)P3 produces a negative feedback loop of insulin signaling through IRS-1.
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Affiliation(s)
- Eui Kim
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang 37673, South Korea; Brain Korea 21 PLUS project of Bio-Molecular Function, Pohang University of Science and Technology, Pohang 37673, South Korea
| | - Do-Hyeon Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, South Korea
| | - Indira Singaram
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Heeyoon Jeong
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, South Korea; Brain Korea 21 PLUS project of Bio-Molecular Function, Pohang University of Science and Technology, Pohang 37673, South Korea
| | - Ara Koh
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, South Korea
| | - Jiyoun Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, South Korea; Brain Korea 21 PLUS project of Bio-Molecular Function, Pohang University of Science and Technology, Pohang 37673, South Korea
| | - Wonhwa Cho
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA.
| | - Sung Ho Ryu
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang 37673, South Korea; Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, South Korea; Brain Korea 21 PLUS project of Bio-Molecular Function, Pohang University of Science and Technology, Pohang 37673, South Korea.
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120
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Liu AD, Xu H, Gao YN, Luo DN, Li ZF, Voss C, Li SSC, Cao X. (Arg) 9-SH2 superbinder: a novel promising anticancer therapy to melanoma by blocking phosphotyrosine signaling. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2018; 37:138. [PMID: 29976230 PMCID: PMC6034221 DOI: 10.1186/s13046-018-0812-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 05/02/2018] [Indexed: 01/22/2023]
Abstract
Background Melanoma is a malignant tumor with high misdiagnosis rate and poor prognosis. The bio-targeted therapy is a prevailing method in the treatment of melanoma; however, the accompanying drug resistance is inevitable. SH2 superbinder, a triple-mutant of the Src Homology 2 (SH2) domain, shows potent antitumor ability by replacing natural SH2-containing proteins and blocking multiple pY-based signaling pathways. Polyarginine (Arg)9, a powerful vector for intracellular delivery of large molecules, could transport therapeutic agents across cell membrane. The purpose of this study is to construct (Arg)9-SH2 superbinder and investigate its effects on melanoma cells, expecting to provide potential new approaches for anti-cancer therapy and overcoming the unavoidable drug resistance of single-targeted antitumor agents. Methods (Arg)9 and SH2 superbinder were fused to form (Arg)9-SH2 superbinder via genetic engineering. Pull down assay was performed to identify that (Arg)9-SH2 superbinder could capture a wide variety of pY proteins. Immunofluorescence was used to detect the efficiency of (Arg)9-SH2 superbinder entering cells. The proliferation ability was assessed by MTT and colony formation assay. In addition, wound healing and transwell assay were performed to evaluate migration of B16F10, A375 and A375/DDP cells. Moreover, apoptosis caused by (Arg)9-SH2 superbinder was analyzed by flow cytometry-based Annexin V/PI. Furthermore, western blot revealed that (Arg)9-SH2 superbinder influenced some pY-related signaling pathways. Finally, B16F10 xenograft model was established to confirm whether (Arg)9-SH2 superbinder could restrain the growth of tumor. Results Our data showed that (Arg)9-SH2 superbinder had the ability to enter melanoma cells effectively and displayed strong affinities for various pY proteins. Furthermore, (Arg)9-SH2 superbinder could repress proliferation, migration and induce apoptosis of melanoma cells by regulating PI3K/AKT, MAPK/ERK and JAK/STAT signaling pathways. Importantly, (Arg)9-SH2 superbinder could significantly inhibit the growth of tumor in mice. Conclusions (Arg)9-SH2 superbinder exhibited high affinities for pY proteins, which showed effective anticancer ability by replacing SH2-containing proteins and blocking diverse pY-based pathways. The remarkable ability of (Arg)9-SH2 superbinder to inhibit cancer cell proliferation and tumor growth might open the door to explore the SH2 superbinder as a therapeutic agent for cancer treatment. Electronic supplementary material The online version of this article (10.1186/s13046-018-0812-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- An-Dong Liu
- Department of Medical Genetics, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Hui Xu
- Department of Medical Genetics, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.,Ultrastructural Pathology Laboratory, Department of Pathology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Ya-Nan Gao
- Department of Medical Genetics, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Dan-Ni Luo
- Department of Medical Genetics, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Zhao-Feng Li
- Department of Medical Genetics, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Courtney Voss
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Shawn S C Li
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Xuan Cao
- Department of Medical Genetics, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China. .,Institute for Brain Research, Huazhong University of Science and Technology, Wuhan, 430030, China. .,Key Laboratory of Neurological Disease of National Education Ministry, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China. .,Key Laboratory for Drug Target Researches and Pharmacodynamic Evaluation of Hubei Province, Wuhan, 430030, China.
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Copper nanoclusters/polydopamine nanospheres based fluorescence aptasensor for protein kinase activity determination. Anal Chim Acta 2018; 1035:184-191. [PMID: 30224138 DOI: 10.1016/j.aca.2018.06.043] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 06/13/2018] [Accepted: 06/15/2018] [Indexed: 11/22/2022]
Abstract
A fluorescence aptasensor was constructed for protein kinase (PKA) activity detection by utilizing copper nanoclusters (CuNCs) and polydopamine nanospheres (PDANS). Through the π-π stacking interactions between adenosine triphosphate (ATP) aptamer and PDANS, the ATP aptamer modified CuNCs (apt-CuNCs) were absorbed onto PDANS surface, thus the fluorescence of apt-CuNCs were quenched through fluorescence resonance energy transfer (FRET) from apt-CuNCs to PDANS. In the presence of ATP, ATP specifically bound to aptamer, causing the dissociation of apt-CuNCs from PDANS surface and restoring the fluorescence of apt-CuNCs. However, PKA translated ATP into adenosine diphosphate (ADP), and ADP had no competence to combine with ATP aptamer, thus, apt-CuNCs were released and absorbed onto the PDANS surface to cause the fluorescence quenching of apt-CuNCs again. Therefore, PKA activity was conveniently detected via the fluorescence signal change. Under the optimal conditions, PKA activity was detected in the range of 0.05-4.5 U mL-1 with a detection limit of 0.021 U mL-1. Furthermore, the feasibility of the aptasensor for kinase inhibitor screening was explored via assessment of kinase inhibitor H-89 as one model. This aptasensor was also performed for PKA activity determination in HepG2 cell lysates with satisfactory results.
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Ryabaya OO, Malysheva AA, Khochenkova YA, Solomko ES, Khochenkov DA. Inactivation of Receptor Tyrosine Kinases Overcomes Resistance to Targeted B-RAF Inhibitors in Melanoma Cell Lines. Mol Biol 2018. [DOI: 10.1134/s0026893318020115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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123
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Wang H, Tian Z. Facile synthesis of titanium (IV) ion immobilized adenosine triphosphate functionalized silica nanoparticles for highly specific enrichment and analysis of intact phosphoproteins. J Chromatogr A 2018; 1564:69-75. [PMID: 29907410 DOI: 10.1016/j.chroma.2018.06.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 05/29/2018] [Accepted: 06/05/2018] [Indexed: 02/08/2023]
Abstract
Analysis of phosphoproteins always faces the challenge of low stoichiometry, which demands highly selective and efficient enrichment in the initial sample preparation. Here we report our synthesis of the novel titanium (IV) ion immobilized adenosine triphosphate functionalized silica nanoparticles (Ti4+-ATP-NPs) for efficient enrichment of intact phosphoproteins. The average diameter of Ti4+-ATP-NPs was about 128 nm with good dispersibility and the saturated adsorption capacity for β-casein was 1046.5 mg/g. In addition, Ti4+-ATP-NPs exhibited high specificity and selectivity in enriching phosphoproteins from both standard protein mixtures and complex biological samples (non-fat milk, chicken egg white and mouse heart tissue extract) as demonstrated by SDS-PAGE.
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Affiliation(s)
- Hao Wang
- School of Chemical Science & Engineering and Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai 200092, China
| | - Zhixin Tian
- School of Chemical Science & Engineering and Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai 200092, China.
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Sidhanth C, Manasa P, Krishnapriya S, Sneha S, Bindhya S, Nagare R, Garg M, Ganesan T. A systematic understanding of signaling by ErbB2 in cancer using phosphoproteomics. Biochem Cell Biol 2018; 96:295-305. [DOI: 10.1139/bcb-2017-0020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
ErbB2 is an important receptor tyrosine kinase and a member of the ErbB family. Although it does not have a specific ligand, it transmits signals downstream by heterodimerization with other receptors in the family. It plays a major role in a variety of cellular responses like proliferation, differentiation, and adhesion. ErbB2 is amplified at the DNA level in breast cancer (20%–30%) and gastric cancer (10%–20%), and trastuzumab is effective as a therapeutic antibody. This review is a critical analysis of the currently published data on the signaling pathways of ErbB2 and the interacting proteins. It also focuses on the techniques that are currently available to evaluate the entire phosphoproteome following activation of ErbB2. Identification of new and relevant phosphoproteins can not only serve as new therapeutic targets but also as a surrogate marker in patients to assess the activity of compounds that inhibit ErbB2. Overall, such analysis will improve understanding of signaling by ErbB2.
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Affiliation(s)
- C. Sidhanth
- Laboratory for Cancer Biology, Departments of Medical Oncology and Clinical Research, Cancer Institute (WIA), 38 Sardar Patel Road Guindy, Chennai-600036, India
- Laboratory for Cancer Biology, Departments of Medical Oncology and Clinical Research, Cancer Institute (WIA), 38 Sardar Patel Road Guindy, Chennai-600036, India
| | - P. Manasa
- Laboratory for Cancer Biology, Departments of Medical Oncology and Clinical Research, Cancer Institute (WIA), 38 Sardar Patel Road Guindy, Chennai-600036, India
- Laboratory for Cancer Biology, Departments of Medical Oncology and Clinical Research, Cancer Institute (WIA), 38 Sardar Patel Road Guindy, Chennai-600036, India
| | - S. Krishnapriya
- Laboratory for Cancer Biology, Departments of Medical Oncology and Clinical Research, Cancer Institute (WIA), 38 Sardar Patel Road Guindy, Chennai-600036, India
- Laboratory for Cancer Biology, Departments of Medical Oncology and Clinical Research, Cancer Institute (WIA), 38 Sardar Patel Road Guindy, Chennai-600036, India
| | - S. Sneha
- Laboratory for Cancer Biology, Departments of Medical Oncology and Clinical Research, Cancer Institute (WIA), 38 Sardar Patel Road Guindy, Chennai-600036, India
- Laboratory for Cancer Biology, Departments of Medical Oncology and Clinical Research, Cancer Institute (WIA), 38 Sardar Patel Road Guindy, Chennai-600036, India
| | - S. Bindhya
- Laboratory for Cancer Biology, Departments of Medical Oncology and Clinical Research, Cancer Institute (WIA), 38 Sardar Patel Road Guindy, Chennai-600036, India
- Laboratory for Cancer Biology, Departments of Medical Oncology and Clinical Research, Cancer Institute (WIA), 38 Sardar Patel Road Guindy, Chennai-600036, India
| | - R.P. Nagare
- Laboratory for Cancer Biology, Departments of Medical Oncology and Clinical Research, Cancer Institute (WIA), 38 Sardar Patel Road Guindy, Chennai-600036, India
- Laboratory for Cancer Biology, Departments of Medical Oncology and Clinical Research, Cancer Institute (WIA), 38 Sardar Patel Road Guindy, Chennai-600036, India
| | - M. Garg
- Laboratory for Cancer Biology, Departments of Medical Oncology and Clinical Research, Cancer Institute (WIA), 38 Sardar Patel Road Guindy, Chennai-600036, India
- Laboratory for Cancer Biology, Departments of Medical Oncology and Clinical Research, Cancer Institute (WIA), 38 Sardar Patel Road Guindy, Chennai-600036, India
| | - T.S. Ganesan
- Laboratory for Cancer Biology, Departments of Medical Oncology and Clinical Research, Cancer Institute (WIA), 38 Sardar Patel Road Guindy, Chennai-600036, India
- Laboratory for Cancer Biology, Departments of Medical Oncology and Clinical Research, Cancer Institute (WIA), 38 Sardar Patel Road Guindy, Chennai-600036, India
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Tsutsui Y, Hays FA. A Link Between Alzheimer's and Type II Diabetes Mellitus? Ca +2 -Mediated Signal Control and Protein Localization. Bioessays 2018; 40:e1700219. [PMID: 29694668 PMCID: PMC6166406 DOI: 10.1002/bies.201700219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 03/16/2018] [Indexed: 01/28/2023]
Abstract
We propose protein localization dependent signal activation (PLDSA) as a model to describe pre-existing protein partitioning between the cytosol, and membrane surface, as a means to modulate signal activation, specificity, and robustness. We apply PLDSA to explain possible molecular links between type II diabetes mellitus (T2DM) and Alzheimer's disease (AD) by describing Ca+2 -mediated interactions between the Src non-receptor tyrosine kinase and p52Shc adaptor protein. We suggest that these interactions may serve as a contributing factor to disease development and progression. In particular, we propose that signaling response is regulated, in part, by Ca+2 -mediated partitioning of lipid-bound and soluble forms of Src and p52shc. Thus, protein-protein interactions that drive signaling in response to extracellular ligand binding are also mediated by partitioning of signaling proteins between membrane-bound and soluble populations. We propose that PLDSA effects may explain, in part, the evolutionary basis of promiscuous protein interaction domains and their importance in cellular function.
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Affiliation(s)
- Yuko Tsutsui
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, United States
| | - Franklin A. Hays
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, United States
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, 73104, United States
- Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, 73104, United States
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126
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Núñez C, Chantada-Vázquez MDP, Bravo SB, Vázquez-Estévez S. Novel functionalized nanomaterials for the effective enrichment of proteins and peptides with post-translational modifications. J Proteomics 2018; 181:170-189. [DOI: 10.1016/j.jprot.2018.04.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 04/02/2018] [Accepted: 04/09/2018] [Indexed: 02/07/2023]
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127
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Cao M, Chen G, Wang L, Wen P, Shi S. Computational Prediction and Analysis for Tyrosine Post-Translational Modifications via Elastic Net. J Chem Inf Model 2018; 58:1272-1281. [DOI: 10.1021/acs.jcim.7b00688] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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128
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Mao YT, Zhu JX, Hanamura K, Iurilli G, Datta SR, Dalva MB. Filopodia Conduct Target Selection in Cortical Neurons Using Differences in Signal Kinetics of a Single Kinase. Neuron 2018; 98:767-782.e8. [PMID: 29731254 DOI: 10.1016/j.neuron.2018.04.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/26/2017] [Accepted: 04/09/2018] [Indexed: 02/07/2023]
Abstract
Dendritic filopodia select synaptic partner axons by interviewing the cell surface of potential targets, but how filopodia decipher the complex pattern of adhesive and repulsive molecular cues to find appropriate contacts is unknown. Here, we demonstrate in cortical neurons that a single cue is sufficient for dendritic filopodia to reject or select specific axonal contacts for elaboration as synaptic sites. Super-resolution and live-cell imaging reveals that EphB2 is located in the tips of filopodia and at nascent synaptic sites. Surprisingly, a genetically encoded indicator of EphB kinase activity, unbiased classification, and a photoactivatable EphB2 reveal that simple differences in the kinetics of EphB kinase signaling at the tips of filopodia mediate the choice between retraction and synaptogenesis. This may enable individual filopodia to choose targets based on differences in the activation rate of a single tyrosine kinase, greatly simplifying the process of partner selection and suggesting a general principle.
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Affiliation(s)
- Yu-Ting Mao
- Department of Neuroscience and Jefferson Synaptic Biology Center, The Vickie and Jack Farber Institute, Jefferson Hospital for Neuroscience, Thomas Jefferson University, Suite 461, 900 Walnut Street, Philadelphia, PA 19107, USA
| | - Julia X Zhu
- Department of Neuroscience and Jefferson Synaptic Biology Center, The Vickie and Jack Farber Institute, Jefferson Hospital for Neuroscience, Thomas Jefferson University, Suite 461, 900 Walnut Street, Philadelphia, PA 19107, USA
| | - Kenji Hanamura
- Department of Neuroscience and Jefferson Synaptic Biology Center, The Vickie and Jack Farber Institute, Jefferson Hospital for Neuroscience, Thomas Jefferson University, Suite 461, 900 Walnut Street, Philadelphia, PA 19107, USA; Department of Neurobiology and Behavior, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi City, Gunma 371-8511, Japan
| | - Giuliano Iurilli
- Department of Neurobiology, Harvard Medical School, Room 336 Warren Alpert Building, 220 Longwood Avenue, Boston, MA 02115, USA
| | - Sandeep Robert Datta
- Department of Neurobiology, Harvard Medical School, Room 336 Warren Alpert Building, 220 Longwood Avenue, Boston, MA 02115, USA
| | - Matthew B Dalva
- Department of Neuroscience and Jefferson Synaptic Biology Center, The Vickie and Jack Farber Institute, Jefferson Hospital for Neuroscience, Thomas Jefferson University, Suite 461, 900 Walnut Street, Philadelphia, PA 19107, USA.
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129
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Jiang D, Li X, Lv X, Jia Q. A magnetic hydrazine-functionalized dendrimer embedded with TiO 2 as a novel affinity probe for the selective enrichment of low-abundance phosphopeptides from biological samples. Talanta 2018; 185:461-468. [PMID: 29759228 DOI: 10.1016/j.talanta.2018.04.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 03/30/2018] [Accepted: 04/01/2018] [Indexed: 12/25/2022]
Abstract
Dendrimers exhibit tunable terminal functionality and bio-friendly nature, making them of being promising materials for applications in the field of separation and enrichment. In this work, we prepared magnetic hydrazide-functionalized poly-amidoamine (PAMAM) dendrimer embedded with TiO2 for the enrichment of phosphopeptides. The novel affinity probe possessed superparamagnetism, realizing its rapid separation from sample solution. Electrostatic attraction and hydrogen bonding existed between PAMAM and phosphopeptides while Lewis acid-base interaction was originated between TiO2 and the targets. The combined synergistic strength of multiple binding interactions contributed to the highly selective enrichment of phosphopeptides. The specificity for the capture of phosphopeptides was reflected in quantities as low as 1:1000 mass ratio of phosphopeptides to non-phosphopeptides. The detection limit of β-casein digests was low to 0.4 fmol, indicating the high sensitivity of the developed method. Fifteen and four phosphopeptides could be selectively captured from non-fat milk digests and human serum samples, which further confirmed the great potential of the affinity probe in the extraction of low-abundance phosphopeptides from real complex biological samples.
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Affiliation(s)
- Dandan Jiang
- College of Chemistry, Jilin University, Changchun 130012, China
| | - Xiqian Li
- China-Japan Hospital of Jilin University, Changchun 130033, China
| | - Xueju Lv
- College of Chemistry, Jilin University, Changchun 130012, China
| | - Qiong Jia
- College of Chemistry, Jilin University, Changchun 130012, China.
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130
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Development of Gd3+-immobilized glutathione-coated magnetic nanoparticles for highly selective enrichment of phosphopeptides. Talanta 2018; 180:368-375. [DOI: 10.1016/j.talanta.2017.12.048] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 12/01/2017] [Accepted: 12/14/2017] [Indexed: 01/19/2023]
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131
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Potel CM, Lin MH, Heck AJR, Lemeer S. Defeating Major Contaminants in Fe 3+- Immobilized Metal Ion Affinity Chromatography (IMAC) Phosphopeptide Enrichment. Mol Cell Proteomics 2018; 17:1028-1034. [PMID: 29449344 DOI: 10.1074/mcp.tir117.000518] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 02/15/2018] [Indexed: 11/06/2022] Open
Abstract
Here we demonstrate that biomolecular contaminants, such as nucleic acid molecules, can seriously interfere with immobilized metal ion affinity chromatography (IMAC)-based phosphopeptide enrichments. We address and largely solve this issue, developing a robust protocol implementing methanol/chloroform protein precipitation and enzymatic digestion using benzonase, which degrades all forms of DNA and RNA, before IMAC-column loading. This simple procedure resulted in a drastic increase of enrichment sensitivity, enabling the identification of around 17,000 unique phosphopeptides and 12,500 unambiguously localized phosphosites in human cell-lines from a single LC-MS/MS run, constituting a 50% increase when compared with the standard protocol. The improved protocol was also applied to bacterial samples, increasing the number of identified bacterial phosphopeptides even more strikingly, by a factor 10, when compared with the standard protocol. For E. coli we detected around 1300 unambiguously localized phosphosites per LC-MS/MS run. The preparation of these ultra-pure phosphopeptide samples only requires marginal extra costs and sample preparation time and should thus be adoptable by every laboratory active in the field of phosphoproteomics.
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Affiliation(s)
- Clement M Potel
- From the ‡Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Miao-Hsia Lin
- From the ‡Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Albert J R Heck
- From the ‡Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Simone Lemeer
- From the ‡Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
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132
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Evolution, dynamics and dysregulation of kinase signalling. Curr Opin Struct Biol 2018; 48:133-140. [DOI: 10.1016/j.sbi.2017.12.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Revised: 12/19/2017] [Accepted: 12/21/2017] [Indexed: 12/31/2022]
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133
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Bell DR, Kang SG, Huynh T, Zhou R. Concentration-dependent binding of CdSe quantum dots on the SH3 domain. NANOSCALE 2017; 10:351-358. [PMID: 29215114 DOI: 10.1039/c7nr06148j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Quantum dots (QDs) are being used increasingly in applications for solar panels, consumer electronics, and biomedical imaging. For biomedical applications, QDs are typically coated with a biocompatible molecule for the system of interest. Experiments have indicated a QD dose-dependent and surface coating-dependent toxicity, with a portion of the toxicity being ascribed to interference with biomolecules. In this work, the interaction of trioctylphosphine oxide (TOPO) coated (CdSe)13 QDs with the SRC homology 3 domain (SH3) protein domain are explored using molecular dynamics simulations. The results of this research agree well with experiments that show that at the lowest concentration, the QDs have little affinity for the native proline-rich motif (PRM) binding site of SH3. At higher concentrations, the QDs aggregate and increasingly prefer the PRM binding site, indicating that the normal SH3 function is impeded. This binding dependence is attributed to changes in the local density of the surface coated TOPO molecules upon aggregation. These results present possible interesting QD toxicity patterns and reveal the interdependence between dose and surface coating effects in QD toxicity.
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Affiliation(s)
- David R Bell
- Computational Biology Center, IBM Thomas J Watson Research Center, Yorktown Heights, NY 10598, USA.
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134
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Liu X, Xu Y, Zhou Q, Chen M, Zhang Y, Liang H, Zhao J, Zhong W, Wang M. PI3K in cancer: its structure, activation modes and role in shaping tumor microenvironment. Future Oncol 2017; 14:665-674. [PMID: 29219001 DOI: 10.2217/fon-2017-0588] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The role of PI3K in cancer has been well established, and mutations of PIK3CA, the gene coding for catalytic subunit p110α of PI3K, are found in approximately 30% human cancers. The hyperactivated PI3K pathway plays a central role in the tumor cell activities such as proliferation, differentiation, chemotaxis, survival, trafficking and metabolism. Besides, PI3K pathway is involved in the regulation of angiogenesis and the host immune response against cancer. Therefore, the inhibition of PI3K pathway can yield multifaceted tumor cell-extrinsic effects that may synergize with chemotherapy, and more importantly, with the newly revived immunotherapy. Here, we review the structures and activation modes of PI3Ks and its implications in angiogenesis, extracellular matrix remodeling and tumor immunity.
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Affiliation(s)
- Xiaoyan Liu
- Department of Pulmonary Medicine, Lung Cancer Center, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, PR China
| | - Yan Xu
- Department of Pulmonary Medicine, Lung Cancer Center, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, PR China
| | - Qing Zhou
- Department of Pulmonary Medicine, Lung Cancer Center, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, PR China
| | - Minjiang Chen
- Department of Pulmonary Medicine, Lung Cancer Center, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, PR China
| | - Yu Zhang
- Department of Pulmonary Medicine, Lung Cancer Center, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, PR China
| | - Hongge Liang
- Department of Pulmonary Medicine, Lung Cancer Center, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, PR China
| | - Jing Zhao
- Department of Pulmonary Medicine, Lung Cancer Center, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, PR China
| | - Wei Zhong
- Department of Pulmonary Medicine, Lung Cancer Center, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, PR China
| | - Mengzhao Wang
- Department of Pulmonary Medicine, Lung Cancer Center, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, PR China
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135
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Jadwin JA, Curran TG, Lafontaine AT, White FM, Mayer BJ. Src homology 2 domains enhance tyrosine phosphorylation in vivo by protecting binding sites in their target proteins from dephosphorylation. J Biol Chem 2017; 293:623-637. [PMID: 29162725 DOI: 10.1074/jbc.m117.794412] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 11/17/2017] [Indexed: 02/03/2023] Open
Abstract
Phosphotyrosine (pTyr)-dependent signaling is critical for many cellular processes. It is highly dynamic, as signal output depends not only on phosphorylation and dephosphorylation rates but also on the rates of binding and dissociation of effectors containing phosphotyrosine-dependent binding modules such as Src homology 2 (SH2) and phosphotyrosine-binding (PTB) domains. Previous in vitro studies suggested that binding of SH2 and PTB domains can enhance protein phosphorylation by protecting the sites bound by these domains from phosphatase-mediated dephosphorylation. To test whether this occurs in vivo, we used the binding of growth factor receptor bound 2 (GRB2) to phosphorylated epidermal growth factor receptor (EGFR) as a model system. We analyzed the effects of SH2 domain overexpression on protein tyrosine phosphorylation by quantitative Western and far-Western blotting, mass spectrometry, and computational modeling. We found that SH2 overexpression results in a significant, dose-dependent increase in EGFR tyrosine phosphorylation, particularly of sites corresponding to the binding specificity of the overexpressed SH2 domain. Computational models using experimentally determined EGFR phosphorylation and dephosphorylation rates, and pTyr-EGFR and GRB2 concentrations, recapitulated the experimental findings. Surprisingly, both modeling and biochemical analyses suggested that SH2 domain overexpression does not result in a major decrease in the number of unbound phosphorylated SH2 domain-binding sites. Our results suggest that signaling via SH2 domain binding is buffered over a relatively wide range of effector concentrations and that SH2 domain proteins with overlapping binding specificities are unlikely to compete with one another for phosphosites in vivo.
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Affiliation(s)
- Joshua A Jadwin
- From the Raymond and Beverly Sackler Laboratory of Molecular Medicine, Department of Genetics and Genome Sciences, and the Richard D. Berlin Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, Connecticut 06030 and
| | - Timothy G Curran
- the Department of Biological Engineering and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Adam T Lafontaine
- From the Raymond and Beverly Sackler Laboratory of Molecular Medicine, Department of Genetics and Genome Sciences, and the Richard D. Berlin Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, Connecticut 06030 and
| | - Forest M White
- the Department of Biological Engineering and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Bruce J Mayer
- From the Raymond and Beverly Sackler Laboratory of Molecular Medicine, Department of Genetics and Genome Sciences, and the Richard D. Berlin Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, Connecticut 06030 and
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136
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Abstract
Over the past two decades, hundreds of new somatic mutations have been identified in tumours, and a few dozen novel cancer therapeutics that selectively target these mutated oncoproteins have entered clinical practice. This development has resulted in clinical breakthroughs for a few tumour types, but more commonly patients' overall survival has not improved because of the development of drug resistance. Furthermore, only a very limited number of oncoproteins, largely protein kinases, are successfully targeted, whereas most non-kinase oncoproteins inside cancer cells remain untargeted. Engineered small protein inhibitors offer great promise in targeting a larger variety of oncoproteins with better efficacy and higher selectivity. In this article, I focus on a promising class of synthetic binding proteins, termed monobodies, that we have shown to inhibit previously untargetable protein-protein interactions in different oncoproteins. I will discuss the great promise alongside the technical challenges inherent in converting monobodies from potent pre-clinical target validation tools to next-generation protein-based therapeutics.
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Affiliation(s)
- Oliver Hantschel
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École polytechnique fédérale de Lausanne (EPFL), Lausanne, Switzerland
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137
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Gógl G, Biri-Kovács B, Póti ÁL, Vadászi H, Szeder B, Bodor A, Schlosser G, Ács A, Turiák L, Buday L, Alexa A, Nyitray L, Reményi A. Dynamic control of RSK complexes by phosphoswitch-based regulation. FEBS J 2017; 285:46-71. [PMID: 29083550 DOI: 10.1111/febs.14311] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 10/18/2017] [Accepted: 10/25/2017] [Indexed: 12/19/2022]
Abstract
Assembly and disassembly of protein-protein complexes needs to be dynamically controlled and phosphoswitches based on linear motifs are crucial in this process. Extracellular signal-regulated kinase 2 (ERK2) recognizes a linear-binding motif at the C-terminal tail (CTT) of ribosomal S6 kinase 1 (RSK1), leading to phosphorylation and subsequent activation of RSK1. The CTT also contains a classical PDZ domain-binding motif which binds RSK substrates (e.g. MAGI-1). We show that autophosphorylation of the disordered CTT promotes the formation of an intramolecular charge clamp, which efficiently masks critical residues and indirectly hinders ERK binding. Thus, RSK1 CTT operates as an autoregulated phosphoswitch: its phosphorylation at specific sites affects its protein-binding capacity and its conformational dynamics. These biochemical feedbacks, which form the structural basis for the rapid dissociation of ERK2-RSK1 and RSK1-PDZ substrate complexes under sustained epidermal growth factor (EGF) stimulation, were structurally characterized and validated in living cells. Overall, conformational changes induced by phosphorylation in disordered regions of protein kinases, coupled to allosteric events occurring in the kinase domain cores, may provide mechanisms that contribute to the emergence of complex signaling activities. In addition, we show that phosphoswitches based on linear motifs can be functionally classified as ON and OFF protein-protein interaction switches or dimmers, depending on the specific positioning of phosphorylation target sites in relation to functional linear-binding motifs. Moreover, interaction of phosphorylated residues with positively charged residues in disordered regions is likely to be a common mechanism of phosphoregulation. DATABASE Structural data are available in the PDB database under the accession numbers 5N7D, 5N7F and 5N7G. NMR spectral assignation data are available in the BMRB database under the accession numbers 27213 and 27214.
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Affiliation(s)
- Gergő Gógl
- Department of Biochemistry, ELTE Eötvös Loránd University, Budapest, Hungary.,Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Beáta Biri-Kovács
- Department of Biochemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Ádám L Póti
- Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Henrietta Vadászi
- Department of Biochemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Bálint Szeder
- Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Andrea Bodor
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Gitta Schlosser
- MTA-ELTE Research Group of Peptide Chemistry, Hungarian Academy of Sciences, ELTE Eötvös Loránd University, Budapest, Hungary
| | - András Ács
- MS Proteomics Research Group, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Lilla Turiák
- MS Proteomics Research Group, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - László Buday
- Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Anita Alexa
- Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - László Nyitray
- Department of Biochemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Attila Reményi
- Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
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138
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Dehghani A, Gödderz M, Winter D. Tip-Based Fractionation of Batch-Enriched Phosphopeptides Facilitates Easy and Robust Phosphoproteome Analysis. J Proteome Res 2017; 17:46-54. [DOI: 10.1021/acs.jproteome.7b00256] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Alireza Dehghani
- Institute for Biochemistry
and Molecular Biology, University of Bonn, Bonn D-53115, Germany
| | - Markus Gödderz
- Institute for Biochemistry
and Molecular Biology, University of Bonn, Bonn D-53115, Germany
| | - Dominic Winter
- Institute for Biochemistry
and Molecular Biology, University of Bonn, Bonn D-53115, Germany
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139
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Watson GM, Kulkarni K, Sang J, Ma X, Gunzburg MJ, Perlmutter P, Wilce MC, Wilce JA. Discovery, Development, and Cellular Delivery of Potent and Selective Bicyclic Peptide Inhibitors of Grb7 Cancer Target. J Med Chem 2017; 60:9349-9359. [DOI: 10.1021/acs.jmedchem.7b01320] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Gabrielle M. Watson
- Biomedicine Discovery
Institute, Department of Biochemistry and Molecular Biology, Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - Ketav Kulkarni
- Biomedicine Discovery
Institute, Department of Biochemistry and Molecular Biology, Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - Jianrong Sang
- Biomedicine Discovery
Institute, Department of Biochemistry and Molecular Biology, Monash University, Wellington Road, Clayton, VIC 3800, Australia
- Department of Physiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, P.R. China
| | - Xiuquan Ma
- Biomedicine Discovery
Institute, Department of Biochemistry and Molecular Biology, Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - Menachem J. Gunzburg
- Biomedicine Discovery
Institute, Department of Biochemistry and Molecular Biology, Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - Patrick Perlmutter
- School of Chemistry, Monash University, Wellington
Road, Clayton, VIC 3800, Australia
| | - Matthew C.J. Wilce
- Biomedicine Discovery
Institute, Department of Biochemistry and Molecular Biology, Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - Jacqueline A. Wilce
- Biomedicine Discovery
Institute, Department of Biochemistry and Molecular Biology, Monash University, Wellington Road, Clayton, VIC 3800, Australia
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140
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Chen S, Maini R, Bai X, Nangreave RC, Dedkova LM, Hecht SM. Incorporation of Phosphorylated Tyrosine into Proteins: In Vitro Translation and Study of Phosphorylated IκB-α and Its Interaction with NF-κB. J Am Chem Soc 2017; 139:14098-14108. [PMID: 28898075 PMCID: PMC5901656 DOI: 10.1021/jacs.7b05168] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Phosphorylated proteins play important roles in the regulation of many different cell networks. However, unlike the preparation of proteins containing unmodified proteinogenic amino acids, which can be altered readily by site-directed mutagenesis and expressed in vitro and in vivo, the preparation of proteins phosphorylated at predetermined sites cannot be done easily and in acceptable yields. To enable the synthesis of phosphorylated proteins for in vitro studies, we have explored the use of phosphorylated amino acids in which the phosphate moiety bears a chemical protecting group, thus eliminating the negative charges that have been shown to have a negative effect on protein translation. Bis-o-nitrobenzyl protection of tyrosine phosphate enabled its incorporation into DHFR and IκB-α using wild-type ribosomes, and the elaborated proteins could subsequently be deprotected by photolysis. Also investigated in parallel was the re-engineering of the 23S rRNA of Escherichia coli, guided by the use of a phosphorylated puromycin, to identify modified ribosomes capable of incorporating unprotected phosphotyrosine into proteins from a phosphotyrosyl-tRNACUA by UAG codon suppression during in vitro translation. Selection of a library of modified ribosomal clones with phosphorylated puromycin identified six modified ribosome variants having mutations in nucleotides 2600-2605 of 23S rRNA; these had enhanced sensitivity to the phosphorylated puromycin. The six clones demonstrated some sequence homology in the region 2600-2605 and incorporated unprotected phosphotyrosine into IκB-α using a modified gene having a TAG codon in the position corresponding to amino acid 42 of the protein. The purified phosphorylated protein bound to a phosphotyrosine specific antibody and permitted NF-κB binding to a DNA duplex sequence corresponding to its binding site in the IL-2 gene promoter. Unexpectedly, phosphorylated IκB-α also mediated the exchange of exogenous DNA into an NF-κB-cellular DNA complex isolated from the nucleus of activated Jurkat cells.
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Affiliation(s)
- Shengxi Chen
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Rumit Maini
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Xiaoguang Bai
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Ryan C. Nangreave
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Larisa M. Dedkova
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Sidney M. Hecht
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
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141
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Li C, Park S, Zhang X, Eisenberg LM, Zhao H, Darzynkiewicz Z, Xu D. Nuclear Gene 33/Mig6 regulates the DNA damage response through an ATM serine/threonine kinase-dependent mechanism. J Biol Chem 2017; 292:16746-16759. [PMID: 28842482 PMCID: PMC5633135 DOI: 10.1074/jbc.m117.803338] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Revised: 08/22/2017] [Indexed: 12/17/2022] Open
Abstract
Gene 33 (Mig6, ERRFI1) is an adaptor protein with multiple cellular functions. We recently linked Gene 33 to the DNA damage response (DDR) induced by hexavalent chromium (Cr(VI)), but the molecular mechanism remains unknown. Here we show that ectopic expression of Gene 33 triggers DDR in an ATM serine/threonine kinase (ATM)-dependent fashion and through pathways dependent or not dependent on ABL proto-oncogene 1 non-receptor tyrosine kinase (c-Abl). We observed the clear presence of Gene 33 in the nucleus and chromatin fractions of the cell. We also found that the nuclear localization of Gene 33 is regulated by its 14-3-3-binding domain and that the chromatin localization of Gene 33 is partially dependent on its ErbB-binding domain. Our data further indicated that Gene 33 may regulate the targeting of c-Abl to chromatin. Moreover, we observed a clear association of Gene 33 with histone H2AX and that ectopic expression of Gene 33 promotes the interaction between ATM and histone H2AX without triggering DNA damage. In summary, our results reveal nuclear functions of Gene 33 that regulate DDR. The nuclear localization of Gene 33 also provides a spatial explanation of the previously reported regulation of apoptosis by Gene 33 via the c-Abl/p73 pathway. On the basis of these findings and our previous studies, we propose that Gene 33 is a proximal regulator of DDR that promotes DNA repair.
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Affiliation(s)
- Cen Li
- From the Department of Pathology
| | | | | | | | - Hong Zhao
- From the Department of Pathology
- the Brander Cancer Research Institute, School of Medicine, New York Medical College, Valhalla, New York 10595
| | - Zbigniew Darzynkiewicz
- From the Department of Pathology
- the Brander Cancer Research Institute, School of Medicine, New York Medical College, Valhalla, New York 10595
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142
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Watson GM, Lucas WAH, Gunzburg MJ, Wilce JA. Insight into the Selectivity of the G7-18NATE Inhibitor Peptide for the Grb7-SH2 Domain Target. Front Mol Biosci 2017; 4:64. [PMID: 29018805 PMCID: PMC5623053 DOI: 10.3389/fmolb.2017.00064] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 09/13/2017] [Indexed: 12/28/2022] Open
Abstract
Growth factor receptor bound protein 7 (Grb7) is an adaptor protein with established roles in the progression of both breast and pancreatic cancers. Through its C-terminal SH2 domain, Grb7 binds to phosphorylated tyrosine kinases to promote proliferative and migratory signaling. Here, we investigated the molecular basis for the specificity of a Grb7 SH2-domain targeted peptide inhibitor. We identified that arginine 462 in the BC loop is unique to Grb7 compared to Grb2, another SH2 domain bearing protein that shares the same consensus binding motif as Grb7. Using surface plasmon resonance we demonstrated that Grb7-SH2 binding to G7-18NATE is reduced 3.3-fold when the arginine is mutated to the corresponding Grb2 amino acid. The reverse mutation in Grb2-SH2 (serine to arginine), however, was insufficient to restore binding of G7-18NATE to Grb2-SH2. Further, using a microarray, we confirmed that G7-18NATE is specific for Grb7 over a panel of 79 SH2 domains, and identified that leucine at the βD6 position may also be a requirement for Grb7-SH2 binding. This study provides insight into the specificity defining features of Grb7 for the inhibitor molecule G7-18NATE, that will assist in the development of improved Grb7 targeted inhibitors.
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Affiliation(s)
| | | | | | - Jacqueline A. Wilce
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
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143
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Damayanti NP, Buno K, Cui Y, Voytik-Harbin SL, Pili R, Freeman J, Irudayaraj JMK. Real-Time Multiplex Kinase Phosphorylation Sensors in Living Cells. ACS Sens 2017; 2:1225-1230. [PMID: 28838242 DOI: 10.1021/acssensors.7b00359] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Phosphorylation is an important post-translational modification implicated in cellular signaling and regulation. However, current methods to study protein phosphorylation by various kinases lack spatiotemporal resolution or the ability to simultaneously observe in real time the activity of multiple kinases in live cells. We present a peptide biosensor strategy with time correlated single photon counting-fluorescence lifetime imaging (TCSPC-FLIM) to interrogate the spatial and temporal dynamics of VEGFR-2 and AKT phosphorylation activity in real time in live 2D and 3D cell culture models at single cell resolution. By recording the increase in fluorescence lifetime due to a change in the solvatochromic environment of the sensor upon phosphorylation, we demonstrate that spatiotemporal maps of protein kinase activity can be obtained. Our results suggest that fluorescence lifetime imaging of peptide biosensors can be effectively and specifically used to monitor and quantify phosphorylation of multiple kinases in live cells.
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Affiliation(s)
- Nur P. Damayanti
- Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | | | | | | | - Roberto Pili
- Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Jennifer Freeman
- School of Health Sciences, West Lafayette, Indiana 47907, United States
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144
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Dong M, Bian Y, Wang Y, Dong J, Yao Y, Deng Z, Qin H, Zou H, Ye M. Sensitive, Robust, and Cost-Effective Approach for Tyrosine Phosphoproteome Analysis. Anal Chem 2017; 89:9307-9314. [DOI: 10.1021/acs.analchem.7b02078] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Mingming Dong
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yangyang Bian
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
- Medical Research Center, The First Affiliated
Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Yan Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Dong
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Yating Yao
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhenzhen Deng
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongqiang Qin
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Hanfa Zou
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
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145
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Jiang D, Song N, Li X, Ma J, Jia Q. Highly selective enrichment of phosphopeptides by on-chip indium oxide functionalized magnetic nanoparticles coupled with MALDI-TOF MS. Proteomics 2017; 17. [PMID: 28722797 DOI: 10.1002/pmic.201700213] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/01/2017] [Accepted: 07/14/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Dandan Jiang
- College of Chemistry; Jilin University; Changchun P. R. China
| | - Naizhong Song
- College of Chemistry; Jilin University; Changchun P. R. China
| | - Xiqian Li
- China-Japan Hospital of Jilin University; Changchun P. R. China
| | - Jiutong Ma
- College of Chemistry; Jilin University; Changchun P. R. China
| | - Qiong Jia
- College of Chemistry; Jilin University; Changchun P. R. China
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146
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Hanamura K, Washburn HR, Sheffler-Collins SI, Xia NL, Henderson N, Tillu DV, Hassler S, Spellman DS, Zhang G, Neubert TA, Price TJ, Dalva MB. Extracellular phosphorylation of a receptor tyrosine kinase controls synaptic localization of NMDA receptors and regulates pathological pain. PLoS Biol 2017; 15:e2002457. [PMID: 28719605 PMCID: PMC5515392 DOI: 10.1371/journal.pbio.2002457] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 06/12/2017] [Indexed: 11/18/2022] Open
Abstract
Extracellular phosphorylation of proteins was suggested in the late 1800s when it was demonstrated that casein contains phosphate. More recently, extracellular kinases that phosphorylate extracellular serine, threonine, and tyrosine residues of numerous proteins have been identified. However, the functional significance of extracellular phosphorylation of specific residues in the nervous system is poorly understood. Here we show that synaptic accumulation of GluN2B-containing N-methyl-D-aspartate receptors (NMDARs) and pathological pain are controlled by ephrin-B-induced extracellular phosphorylation of a single tyrosine (p*Y504) in a highly conserved region of the fibronectin type III (FN3) domain of the receptor tyrosine kinase EphB2. Ligand-dependent Y504 phosphorylation modulates the EphB-NMDAR interaction in cortical and spinal cord neurons. Furthermore, Y504 phosphorylation enhances NMDAR localization and injury-induced pain behavior. By mediating inducible extracellular interactions that are capable of modulating animal behavior, extracellular tyrosine phosphorylation of EphBs may represent a previously unknown class of mechanism mediating protein interaction and function. The activity of proteins can be finely and reversibly tuned by post-translational modifications. The attachment of phosphate groups to tyrosine residues is one of such modifications. While the existence of extracellular phosphoproteins has been known, the functional significance of extracellular phosphorylation is poorly understood. Here we describe a single extracellular tyrosine whose inducible phosphorylation may represent an archetype for a new class of mechanism mediating protein—protein interaction and regulating protein function. We show that the interaction between EphB2—which occurs upon receptor activation by its ligand ephrin-B—and the N-methyl-D-aspartate receptor (NMDAR) depends on extracellular phosphorylation of EphB2. This interaction regulates the localization of the NMDA receptor to synaptic sites in neurons. In vivo, EphB2 is phosphorylated in response to injury, and the subsequent up-regulation of the interaction between EphB2 and NMDA receptors enhances injury-induced pain behavior and mechanical hypersensitivity in mice. Importantly, our study defines a specific extracellular phosphorylation event as a mechanism driving protein interaction and suggests that extracellular phosphorylation of proteins is an underappreciated mechanism contributing to the development and function of the nervous system and synapse.
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Affiliation(s)
- Kenji Hanamura
- Department of Neuroscience and Farber Institute for Neurosciences, Thomas Jefferson University, Jefferson Hospital for Neuroscience, Philadelphia, Pennsylvania, United States of America
- Department of Neurobiology and Behavior, Gunma University Graduate School of Medicine, Maebashi City, Gunma, Japan
| | - Halley R. Washburn
- Department of Neuroscience and Farber Institute for Neurosciences, Thomas Jefferson University, Jefferson Hospital for Neuroscience, Philadelphia, Pennsylvania, United States of America
| | - Sean I. Sheffler-Collins
- Department of Neuroscience and Farber Institute for Neurosciences, Thomas Jefferson University, Jefferson Hospital for Neuroscience, Philadelphia, Pennsylvania, United States of America
- Neuroscience Graduate Group, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Nan L. Xia
- Department of Neuroscience and Farber Institute for Neurosciences, Thomas Jefferson University, Jefferson Hospital for Neuroscience, Philadelphia, Pennsylvania, United States of America
| | - Nathan Henderson
- Department of Neuroscience and Farber Institute for Neurosciences, Thomas Jefferson University, Jefferson Hospital for Neuroscience, Philadelphia, Pennsylvania, United States of America
| | - Dipti V. Tillu
- Department of Pharmacology, University of Arizona College of Medicine, Tucson, Arizona, United States of America
- School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, Texas, United States of America
| | - Shayne Hassler
- School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, Texas, United States of America
| | - Daniel S. Spellman
- Department of Cell Biology and Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, New York, United States of America
| | - Guoan Zhang
- Department of Cell Biology and Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, New York, United States of America
| | - Thomas A. Neubert
- Department of Cell Biology and Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, New York, United States of America
| | - Theodore J. Price
- Department of Pharmacology, University of Arizona College of Medicine, Tucson, Arizona, United States of America
- School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, Texas, United States of America
| | - Matthew B. Dalva
- Department of Neuroscience and Farber Institute for Neurosciences, Thomas Jefferson University, Jefferson Hospital for Neuroscience, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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147
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Dey N, De P, Leyland-Jones B. PI3K-AKT-mTOR inhibitors in breast cancers: From tumor cell signaling to clinical trials. Pharmacol Ther 2017; 175:91-106. [DOI: 10.1016/j.pharmthera.2017.02.037] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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148
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Design and synthesis of an immobilized metal affinity chromatography and metal oxide affinity chromatography hybrid material for improved phosphopeptide enrichment. J Chromatogr A 2017; 1505:56-62. [DOI: 10.1016/j.chroma.2017.05.025] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 05/05/2017] [Accepted: 05/08/2017] [Indexed: 01/12/2023]
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149
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Luo X, Fu G, Wang RE, Zhu X, Zambaldo C, Liu R, Liu T, Lyu X, Du J, Xuan W, Yao A, Reed SA, Kang M, Zhang Y, Guo H, Huang C, Yang PY, Wilson IA, Schultz PG, Wang F. Genetically encoding phosphotyrosine and its nonhydrolyzable analog in bacteria. Nat Chem Biol 2017; 13:845-849. [PMID: 28604693 PMCID: PMC5577365 DOI: 10.1038/nchembio.2405] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 03/14/2017] [Indexed: 01/14/2023]
Abstract
Tyrosine phosphorylation is a common protein posttranslational modification, which plays a critical role in signal transduction and the regulation of many cellular processes. Using a pro-peptide strategy to increase cellular uptake of O-phosphotyrosine (pTyr) and its nonhydrolyzable analog 4-phosphomethyl-L-phenylalanine (Pmp), we identified an orthogonal aminoacyl-tRNA synthetase/tRNA pair that allows the site-specific incorporation of both pTyr and Pmp into recombinant proteins in response to the amber stop codon in Escherichia coli in good yields. The X-ray crystal structure of the synthetase reveals a reconfigured substrate binding site formed by non-conservative mutations and substantial local structural perturbations. We demonstrate the utility of this method by introducing Pmp into a putative phosphorylation site whose corresponding kinase is unknown and determined the affinities of the individual variants for the substrate 3BP2. In summary, this work provides a useful recombinant tool to dissect the biological functions of tyrosine phosphorylation at specific sites in the proteome.
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Affiliation(s)
- Xiaozhou Luo
- Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA.,Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Guangsen Fu
- California Institute for Biomedical Research (Calibr), La Jolla, California, USA
| | - Rongsheng E Wang
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Claudio Zambaldo
- Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA.,Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Renhe Liu
- California Institute for Biomedical Research (Calibr), La Jolla, California, USA
| | - Tao Liu
- Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA.,Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Xiaoxuan Lyu
- California Institute for Biomedical Research (Calibr), La Jolla, California, USA
| | - Jintang Du
- California Institute for Biomedical Research (Calibr), La Jolla, California, USA
| | - Weimin Xuan
- Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA.,Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Anzhi Yao
- Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA.,Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Sean A Reed
- Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA.,Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Mingchao Kang
- Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA.,Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Yuhan Zhang
- California Institute for Biomedical Research (Calibr), La Jolla, California, USA
| | - Hui Guo
- California Institute for Biomedical Research (Calibr), La Jolla, California, USA
| | - Chunhui Huang
- Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA.,Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Peng-Yu Yang
- Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA.,Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Ian A Wilson
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Peter G Schultz
- Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA.,Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA.,California Institute for Biomedical Research (Calibr), La Jolla, California, USA
| | - Feng Wang
- California Institute for Biomedical Research (Calibr), La Jolla, California, USA
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150
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Sanchez-Quiles V, Akimov V, Osinalde N, Francavilla C, Puglia M, Barrio-Hernandez I, Kratchmarova I, Olsen JV, Blagoev B. Cylindromatosis Tumor Suppressor Protein (CYLD) Deubiquitinase is Necessary for Proper Ubiquitination and Degradation of the Epidermal Growth Factor Receptor. Mol Cell Proteomics 2017; 16:1433-1446. [PMID: 28572092 DOI: 10.1074/mcp.m116.066423] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 05/08/2017] [Indexed: 11/06/2022] Open
Abstract
Cylindromatosis tumor suppressor protein (CYLD) is a deubiquitinase, best known as an essential negative regulator of the NFkB pathway. Previous studies have suggested an involvement of CYLD in epidermal growth factor (EGF)-dependent signal transduction as well, as it was found enriched within the tyrosine-phosphorylated complexes in cells stimulated with the growth factor. EGF receptor (EGFR) signaling participates in central cellular processes and its tight regulation, partly through ubiquitination cascades, is decisive for a balanced cellular homeostasis. Here, using a combination of mass spectrometry-based quantitative proteomic approaches with biochemical and immunofluorescence strategies, we demonstrate the involvement of CYLD in the regulation of the ubiquitination events triggered by EGF. Our data show that CYLD regulates the magnitude of ubiquitination of several major effectors of the EGFR pathway by assisting the recruitment of the ubiquitin ligase Cbl-b to the activated EGFR complex. Notably, CYLD facilitates the interaction of EGFR with Cbl-b through its Tyr15 phosphorylation in response to EGF, which leads to fine-tuning of the receptor's ubiquitination and subsequent degradation. This represents a previously uncharacterized strategy exerted by this deubiquitinase and tumors suppressor for the negative regulation of a tumorigenic signaling pathway.
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Affiliation(s)
- Virginia Sanchez-Quiles
- From the ‡Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Vyacheslav Akimov
- From the ‡Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Nerea Osinalde
- From the ‡Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Chiara Francavilla
- §Proteomics Program, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Michele Puglia
- From the ‡Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Inigo Barrio-Hernandez
- From the ‡Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Irina Kratchmarova
- From the ‡Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Jesper V Olsen
- §Proteomics Program, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Blagoy Blagoev
- From the ‡Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark;
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