1
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Yaron-Barir TM, Joughin BA, Huntsman EM, Kerelsky A, Cizin DM, Cohen BM, Regev A, Song J, Vasan N, Lin TY, Orozco JM, Schoenherr C, Sagum C, Bedford MT, Wynn RM, Tso SC, Chuang DT, Li L, Li SSC, Creixell P, Krismer K, Takegami M, Lee H, Zhang B, Lu J, Cossentino I, Landry SD, Uduman M, Blenis J, Elemento O, Frame MC, Hornbeck PV, Cantley LC, Turk BE, Yaffe MB, Johnson JL. The intrinsic substrate specificity of the human tyrosine kinome. Nature 2024; 629:1174-1181. [PMID: 38720073 PMCID: PMC11136658 DOI: 10.1038/s41586-024-07407-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 04/10/2024] [Indexed: 05/31/2024]
Abstract
Phosphorylation of proteins on tyrosine (Tyr) residues evolved in metazoan organisms as a mechanism of coordinating tissue growth1. Multicellular eukaryotes typically have more than 50 distinct protein Tyr kinases that catalyse the phosphorylation of thousands of Tyr residues throughout the proteome1-3. How a given Tyr kinase can phosphorylate a specific subset of proteins at unique Tyr sites is only partially understood4-7. Here we used combinatorial peptide arrays to profile the substrate sequence specificity of all human Tyr kinases. Globally, the Tyr kinases demonstrate considerable diversity in optimal patterns of residues surrounding the site of phosphorylation, revealing the functional organization of the human Tyr kinome by substrate motif preference. Using this information, Tyr kinases that are most compatible with phosphorylating any Tyr site can be identified. Analysis of mass spectrometry phosphoproteomic datasets using this compendium of kinase specificities accurately identifies specific Tyr kinases that are dysregulated in cells after stimulation with growth factors, treatment with anti-cancer drugs or expression of oncogenic variants. Furthermore, the topology of known Tyr signalling networks naturally emerged from a comparison of the sequence specificities of the Tyr kinases and the SH2 phosphotyrosine (pTyr)-binding domains. Finally we show that the intrinsic substrate specificity of Tyr kinases has remained fundamentally unchanged from worms to humans, suggesting that the fidelity between Tyr kinases and their protein substrate sequences has been maintained across hundreds of millions of years of evolution.
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Affiliation(s)
- Tomer M Yaron-Barir
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Brian A Joughin
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Emily M Huntsman
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Alexander Kerelsky
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Daniel M Cizin
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Benjamin M Cohen
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Amit Regev
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Junho Song
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Neil Vasan
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA
| | - Ting-Yu Lin
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Discovery Technologies, Calico Life Sciences, South San Francisco, CA, USA
| | - Jose M Orozco
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Christina Schoenherr
- Cancer Research United Kingdom Scotland Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Cari Sagum
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mark T Bedford
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - R Max Wynn
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Shih-Chia Tso
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - David T Chuang
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Lei Li
- School of Health and Life Sciences, University of Health and Rehabilitation Sciences, Qingdao, China
| | - Shawn S-C Li
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Canada
| | - Pau Creixell
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Cancer Research UK Cambridge Institute, University of Cambridge Li Ka Shing Centre, Cambridge, UK
| | - Konstantin Krismer
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mina Takegami
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Harin Lee
- Department Of Bioinformatics, Cell Signaling Technology, Danvers, MA, USA
| | - Bin Zhang
- Department Of Bioinformatics, Cell Signaling Technology, Danvers, MA, USA
| | - Jingyi Lu
- Department Of Bioinformatics, Cell Signaling Technology, Danvers, MA, USA
| | - Ian Cossentino
- Department Of Bioinformatics, Cell Signaling Technology, Danvers, MA, USA
| | - Sean D Landry
- Department Of Bioinformatics, Cell Signaling Technology, Danvers, MA, USA
| | - Mohamed Uduman
- Department Of Bioinformatics, Cell Signaling Technology, Danvers, MA, USA
| | - John Blenis
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, USA
| | - Olivier Elemento
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Margaret C Frame
- Cancer Research United Kingdom Scotland Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Peter V Hornbeck
- Department Of Bioinformatics, Cell Signaling Technology, Danvers, MA, USA
| | - Lewis C Cantley
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
| | - Benjamin E Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA.
| | - Michael B Yaffe
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Division of Acute Care Surgery, Trauma, and Surgical Critical Care, and Division of Surgical Oncology, Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
| | - Jared L Johnson
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
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2
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Castro-Cruz M, Lembo F, Borg JP, Travé G, Vincentelli R, Zimmermann P. The Human PDZome 2.0: Characterization of a New Resource to Test for PDZ Interactions by Yeast Two-Hybrid. MEMBRANES 2023; 13:737. [PMID: 37623798 PMCID: PMC10456741 DOI: 10.3390/membranes13080737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 07/28/2023] [Accepted: 08/10/2023] [Indexed: 08/26/2023]
Abstract
PSD95-disc large-zonula occludens (PDZ) domains are globular modules of 80-90 amino acids that co-evolved with multicellularity. They commonly bind to carboxy-terminal sequences of a plethora of membrane-associated proteins and influence their trafficking and signaling. We previously built a PDZ resource (PDZome) allowing us to unveil human PDZ interactions by Yeast two-hybrid. Yet, this resource is incomplete according to the current knowledge on the human PDZ proteome. Here we built the PDZome 2.0 library for Yeast two-hybrid, based on a PDZ library manually curated from online resources. The PDZome2.0 contains 305 individual clones (266 PDZ domains in isolation and 39 tandems), for which all boundaries were designed based on available PDZ structures. Using as bait the E6 oncoprotein from HPV16, a known promiscuous PDZ interactor, we show that PDZome 2.0 outperforms the previous resource.
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Affiliation(s)
- Monica Castro-Cruz
- Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium;
- Équipe Labellisée Ligue 2018, Centre de Recherche en Cancérologie de Marseille (CRCM), Aix-Marseille Université, 13009 Marseille, France;
| | - Frédérique Lembo
- Équipe Labellisée Ligue 2018, Centre de Recherche en Cancérologie de Marseille (CRCM), Aix-Marseille Université, 13009 Marseille, France;
| | - Jean-Paul Borg
- Marseille Proteomics Platform, CRCM, Institute Paoli-Calmettes, Aix-Marseille Université, Inserm, CNRS, 13009 Marseille, France;
| | - Gilles Travé
- Équipe Labellisée Ligue 2015, Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, 67404 Illkirch, France;
| | - Renaud Vincentelli
- Architecture et Fonction des Macromolécules Biologiques (AFMB), Unité Mixte de Recherche (UMR) 7257, Centre National de la Recherche Scientifique (CNRS), Aix-Marseille Université, 13009 Marseille, France;
| | - Pascale Zimmermann
- Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium;
- Équipe Labellisée Ligue 2018, Centre de Recherche en Cancérologie de Marseille (CRCM), Aix-Marseille Université, 13009 Marseille, France;
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3
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Backe SJ, Votra SD, Stokes MP, Sebestyén E, Castelli M, Torielli L, Colombo G, Woodford MR, Mollapour M, Bourboulia D. PhosY-secretome profiling combined with kinase-substrate interaction screening defines active c-Src-driven extracellular signaling. Cell Rep 2023; 42:112539. [PMID: 37243593 PMCID: PMC10569185 DOI: 10.1016/j.celrep.2023.112539] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 04/07/2023] [Accepted: 05/03/2023] [Indexed: 05/29/2023] Open
Abstract
c-Src tyrosine kinase is a renowned key intracellular signaling molecule and a potential target for cancer therapy. Secreted c-Src is a recent observation, but how it contributes to extracellular phosphorylation remains elusive. Using a series of domain deletion mutants, we show that the N-proximal region of c-Src is essential for its secretion. The tissue inhibitor of metalloproteinases 2 (TIMP2) is an extracellular substrate of c-Src. Limited proteolysis-coupled mass spectrometry and mutagenesis studies verify that the Src homology 3 (SH3) domain of c-Src and the P31VHP34 motif of TIMP2 are critical for their interaction. Comparative phosphoproteomic analyses identify an enrichment of PxxP motifs in phosY-containing secretomes from c-Src-expressing cells with cancer-promoting roles. Inhibition of extracellular c-Src using custom SH3-targeting antibodies disrupt kinase-substrate complexes and inhibit cancer cell proliferation. These findings point toward an intricate role for c-Src in generating phosphosecretomes, which will likely influence cell-cell communication, particularly in c-Src-overexpressing cancers.
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Affiliation(s)
- Sarah J Backe
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - SarahBeth D Votra
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | | | | | - Matteo Castelli
- Dipartimento di Chimica, Università di Pavia, 27100 Pavia, Italy
| | - Luca Torielli
- Dipartimento di Chimica, Università di Pavia, 27100 Pavia, Italy
| | - Giorgio Colombo
- Dipartimento di Chimica, Università di Pavia, 27100 Pavia, Italy
| | - Mark R Woodford
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Mehdi Mollapour
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Dimitra Bourboulia
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA.
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4
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Bajusz D, Pándy-Szekeres G, Takács Á, de Araujo ED, Keserű GM. SH2db, an information system for the SH2 domain. Nucleic Acids Res 2023:7173719. [PMID: 37207333 DOI: 10.1093/nar/gkad420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/04/2023] [Accepted: 05/07/2023] [Indexed: 05/21/2023] Open
Abstract
SH2 domains are key mediators of phosphotyrosine-based signalling, and therapeutic targets for diverse, mostly oncological, disease indications. They have a highly conserved structure with a central beta sheet that divides the binding surface of the protein into two main pockets, responsible for phosphotyrosine binding (pY pocket) and substrate specificity (pY + 3 pocket). In recent years, structural databases have proven to be invaluable resources for the drug discovery community, as they contain highly relevant and up-to-date information on important protein classes. Here, we present SH2db, a comprehensive structural database and webserver for SH2 domain structures. To organize these protein structures efficiently, we introduce (i) a generic residue numbering scheme to enhance the comparability of different SH2 domains, (ii) a structure-based multiple sequence alignment of all 120 human wild-type SH2 domain sequences and their PDB and AlphaFold structures. The aligned sequences and structures can be searched, browsed and downloaded from the online interface of SH2db (http://sh2db.ttk.hu), with functions to conveniently prepare multiple structures into a Pymol session, and to export simple charts on the contents of the database. Our hope is that SH2db can assist researchers in their day-to-day work by becoming a one-stop shop for SH2 domain related research.
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Affiliation(s)
- Dávid Bajusz
- Medicinal Chemistry Research Group and National Laboratory for Drug Researchand Development, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117 Budapest, Hungary
| | - Gáspár Pándy-Szekeres
- Medicinal Chemistry Research Group and National Laboratory for Drug Researchand Development, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117 Budapest, Hungary
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Ágnes Takács
- Medicinal Chemistry Research Group and National Laboratory for Drug Researchand Development, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117 Budapest, Hungary
| | - Elvin D de Araujo
- Centre for Medicinal Chemistry, University of Toronto at Mississauga, Mississauga, ON L5L 1C6, Canada
| | - György M Keserű
- Medicinal Chemistry Research Group and National Laboratory for Drug Researchand Development, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117 Budapest, Hungary
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3, 1111 Budapest, Hungary
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5
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Ayaz P, Lyczek A, Paung Y, Mingione VR, Iacob RE, de Waal PW, Engen JR, Seeliger MA, Shan Y, Shaw DE. Structural mechanism of a drug-binding process involving a large conformational change of the protein target. Nat Commun 2023; 14:1885. [PMID: 37019905 PMCID: PMC10076256 DOI: 10.1038/s41467-023-36956-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 02/24/2023] [Indexed: 04/07/2023] Open
Abstract
Proteins often undergo large conformational changes when binding small molecules, but atomic-level descriptions of such events have been elusive. Here, we report unguided molecular dynamics simulations of Abl kinase binding to the cancer drug imatinib. In the simulations, imatinib first selectively engages Abl kinase in its autoinhibitory conformation. Consistent with inferences drawn from previous experimental studies, imatinib then induces a large conformational change of the protein to reach a bound complex that closely resembles published crystal structures. Moreover, the simulations reveal a surprising local structural instability in the C-terminal lobe of Abl kinase during binding. The unstable region includes a number of residues that, when mutated, confer imatinib resistance by an unknown mechanism. Based on the simulations, NMR spectra, hydrogen-deuterium exchange measurements, and thermostability measurements and estimates, we suggest that these mutations confer imatinib resistance by exacerbating structural instability in the C-terminal lobe, rendering the imatinib-bound state energetically unfavorable.
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Affiliation(s)
- Pelin Ayaz
- D. E. Shaw Research, New York, NY, 10036, USA
| | - Agatha Lyczek
- Department of Pharmacological Sciences, Stony Brook University School of Medicine, Stony Brook, NY, 11794-8651, USA
| | - YiTing Paung
- Department of Pharmacological Sciences, Stony Brook University School of Medicine, Stony Brook, NY, 11794-8651, USA
| | - Victoria R Mingione
- Department of Pharmacological Sciences, Stony Brook University School of Medicine, Stony Brook, NY, 11794-8651, USA
| | - Roxana E Iacob
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115, USA
- Relay Therapeutics, 399 Binney St., Cambridge, MA, 02139, USA
| | | | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115, USA
| | - Markus A Seeliger
- Department of Pharmacological Sciences, Stony Brook University School of Medicine, Stony Brook, NY, 11794-8651, USA.
| | - Yibing Shan
- D. E. Shaw Research, New York, NY, 10036, USA.
| | - David E Shaw
- D. E. Shaw Research, New York, NY, 10036, USA.
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA.
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6
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Meirson T, Bomze D, Schueler-Furman O, Stemmer SM, Markel G. Systemic structural analysis of alterations reveals a common structural basis of driver mutations in cancer. NAR Cancer 2023; 5:zcac040. [PMID: 36683915 PMCID: PMC9846427 DOI: 10.1093/narcan/zcac040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/17/2022] [Accepted: 12/04/2022] [Indexed: 01/19/2023] Open
Abstract
A major effort in cancer research is to organize the complexities of the disease into fundamental traits. Despite conceptual progress in the last decades and the synthesis of hallmark features, no organizing principles governing cancer beyond cellular features exist. We analyzed experimentally determined structures harboring the most significant and prevalent driver missense mutations in human cancer, covering 73% (n = 168178) of the Catalog of Somatic Mutation in Cancer tumor samples (COSMIC). The results reveal that a single structural element-κ-helix (polyproline II helix)-lies at the core of driver point mutations, with significant enrichment in all major anatomical sites, suggesting that a small number of molecular traits are shared by most and perhaps all types of cancer. Thus, we uncovered the lowest possible level of organization at which carcinogenesis takes place at the protein level. This framework provides an initial scheme for a mechanistic understanding underlying the development of tumors and pinpoints key vulnerabilities.
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Affiliation(s)
- Tomer Meirson
- Davidoff Cancer Center, Rabin Medical Center-Beilinson Hospital, Petah Tikva, 49100, Israel
| | - David Bomze
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Ora Schueler-Furman
- Department of Microbiology and Molecular Genetics, Institute for Biomedical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 9112001, Israel
| | - Salomon M Stemmer
- Davidoff Cancer Center, Rabin Medical Center-Beilinson Hospital, Petah Tikva, 49100, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Gal Markel
- Davidoff Cancer Center, Rabin Medical Center-Beilinson Hospital, Petah Tikva, 49100, Israel
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel-Aviv, 6997801, Israel
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7
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Properties of FDA-approved small molecule protein kinase inhibitors: A 2023 update. Pharmacol Res 2023; 187:106552. [PMID: 36403719 DOI: 10.1016/j.phrs.2022.106552] [Citation(s) in RCA: 111] [Impact Index Per Article: 111.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 11/08/2022] [Indexed: 11/18/2022]
Abstract
Owing to the dysregulation of protein kinase activity in many diseases including cancer, this enzyme family has become one of the most important drug targets in the 21st century. There are 72 FDA-approved therapeutic agents that target about two dozen different protein kinases and three of these drugs were approved in 2022. Of the approved drugs, twelve target protein-serine/threonine protein kinases, four are directed against dual specificity protein kinases (MEK1/2), sixteen block nonreceptor protein-tyrosine kinases, and 40 target receptor protein-tyrosine kinases. The data indicate that 62 of these drugs are prescribed for the treatment of neoplasms (57 against solid tumors including breast, lung, and colon, ten against nonsolid tumors such as leukemia, and four against both solid and nonsolid tumors: acalabrutinib, ibrutinib, imatinib, and midostaurin). Four drugs (abrocitinib, baricitinib, tofacitinib, upadacitinib) are used for the treatment of inflammatory diseases (atopic dermatitis, psoriatic arthritis, rheumatoid arthritis, Crohn disease, and ulcerative colitis). Of the 72 approved drugs, eighteen are used in the treatment of multiple diseases. The following three drugs received FDA approval in 2022 for the treatment of these specified diseases: abrocitinib (atopic dermatitis), futibatinib (cholangiocarcinomas), pacritinib (myelofibrosis). All of the FDA-approved drugs are orally effective with the exception of netarsudil, temsirolimus, and trilaciclib. This review summarizes the physicochemical properties of all 72 FDA-approved small molecule protein kinase inhibitors including lipophilic efficiency and ligand efficiency.
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8
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Basant A, Way M. The relative binding position of Nck and Grb2 adaptors impacts actin-based motility of Vaccinia virus. eLife 2022; 11:74655. [PMID: 35796545 PMCID: PMC9333988 DOI: 10.7554/elife.74655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 07/06/2022] [Indexed: 11/19/2022] Open
Abstract
Phosphotyrosine (pTyr) motifs in unstructured polypeptides orchestrate important cellular processes by engaging SH2-containing adaptors to assemble complex signalling networks. The concept of phase separation has recently changed our appreciation of multivalent networks, however, the role of pTyr motif positioning in their function remains to be explored. We have now investigated this parameter in the operation of the signalling cascade driving actin-based motility and spread of Vaccinia virus. This network involves two pTyr motifs in the viral protein A36 that recruit the adaptors Nck and Grb2 upstream of N-WASP and Arp2/3 complex-mediated actin polymerisation. Manipulating the position of pTyr motifs in A36 and the unrelated p14 from Orthoreovirus, we find that only specific spatial arrangements of Nck and Grb2 binding sites result in robust N-WASP recruitment, Arp2/3 complex driven actin polymerisation and viral spread. This suggests that the relative position of pTyr adaptor binding sites is optimised for signal output. This finding may explain why the relative positions of pTyr motifs are frequently conserved in proteins from widely different species. It also has important implications for regulation of physiological networks, including those undergoing phase transitions.
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Affiliation(s)
- Angika Basant
- Cellular signalling and cytoskeletal function laboratory, The Francis Crick Institute, London, United Kingdom
| | - Michael Way
- Cellular signalling and cytoskeletal function laboratory, The Francis Crick Institute, London, United Kingdom
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9
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Bao Z, Liu J, Fu J. Comprehensive binary interaction mapping of τ phosphotyrosine sites with SH2 domains in the human genome: Implications for the rational design of self-inhibitory phosphopeptides to target τ hyperphosphorylation signaling in Alzheimer's Disease. Amino Acids 2022; 54:859-875. [PMID: 35622130 DOI: 10.1007/s00726-022-03171-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 05/08/2022] [Indexed: 11/01/2022]
Abstract
Human microtubule-associated protein Tau (τ) is abundant in the axons of neurons where it stabilizes microtubule bundles; abnormally hyperphosphorylated τ is a hallmark of Alzheimer's disease (AD) and related tauopathies. The hyperphosphorylation events can be recognized by phosphotyrosine-recognition domain SH2 (Src homology 2) to elicit downstream τ signaling in AD pathology. In this study, a comprehensive binary interaction map (CBIM) of all the 6 τ phosphotyrosine sites with 120 SH2 domains in the human genome was systematically created at structural level using computational analyses and binding assays, from which we were able to identify those of strong and moderate binding pairs of sites to domains. It is found that the SH2-recognition specificity of different τ phosphotyrosine sites has been evolutionally optimized to become roughly orthogonal to each other, and thus these site phosphorylations would regulate different but probably partially overlapped biological functions in τ signaling. Some SH2 groups such as SRC, RIN, PLCG, SOCS and SH2D were revealed to have effective binding potency as compared to others; they could be regarded as potential τ-associated proteins to transduce the downstream signaling. We further determined the systematic binding affinities of 6 τ-phosphopeptides to the 11 SH2 domains in SRC group, from which the FYN-τ18 and YES-τ29 pairs were identified as strong binders. Subsequently, rational molecular design was performed on τ18 and τ29 to derive a number of τ-phosphopeptide mutants with increased affinity; they are self-inhibitory candidates to competitively target τ hyperphosphorylation events in AD. In addition, it is revealed that the primary anchor pY0 and secondary anchor X+3 of τ-phosphopeptides play an important role in SRC-group SH2 recognition, which confer stability and specificity to the SH2-phosphopeptide binding, respectively.
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Affiliation(s)
- Zhonglei Bao
- Department of Neurology, the Second Affiliated Hospital, Harbin Medical University, Harbin, 150086, China
| | - Jianghua Liu
- Department of Neurology, Daqing Oilfield General Hospital, Daqing, 163001, China
| | - Jin Fu
- Department of Neurology, the Second Affiliated Hospital, Harbin Medical University, Harbin, 150086, China.
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10
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TIRAP-mediated activation of p38 MAPK in inflammatory signaling. Sci Rep 2022; 12:5601. [PMID: 35379857 PMCID: PMC8979995 DOI: 10.1038/s41598-022-09528-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 03/16/2022] [Indexed: 02/06/2023] Open
Abstract
AbstractThe role of TIRAP (toll/interleukin-1 receptor (TIR) domain-containing adapter protein) in macrophage inflammatory signalling has been significantly evolved since its discovery in 2001 due to its dynamic nature and subcellular localization to regulate multiple signaling through several protein–protein interactions (PPIs). Structural analysis of these interactions can reveal a better understanding of their conformational dynamics and the nature of their binding. Tyrosine phosphorylation in the TIR domain of TIRAP is very critical for its function. In toll-like receptor (TLR) 4/2 signalling, Bruton's tyrosine kinase (BTK) and Protein kinase C delta (PKCδ) are known to phosphorylate the Y86, Y106, Y159, and Y187 of TIRAP which is crucial for the downstream function of MAPKs (mitogen-activated protein kinases) activation. The objective of this study is to understand the interaction of TIRAP with p38 MAPK through molecular docking and identify the importance of TIRAP tyrosine phosphorylation in p38 MAPK interaction. In this structural study, we performed an in-silico molecular docking using HADDOCK 2.4, pyDockWEB, ClusPro 2.0, and ZDOCK 3.0.2 tools to unravel the interaction between TIRAP and p38 MAPK. Further, manual in-silico phosphorylations of TIRAP tyrosines; Y86, Y106, Y159, and Y187 was created in the Discovery Studio tool to study the conformational changes in protein docking and their binding affinities with p38 MAPK in comparison to non-phosphorylated state. Our molecular docking and 500 ns of molecular dynamic (MD) simulation study demonstrates that the Y86 phosphorylation (pY86) in TIRAP is crucial in promoting the higher binding affinity (∆Gbind) with p38 MAPK. The conformational changes due to the tyrosine phosphorylation mainly at the Y86 site pull the TIRAP closer to the active site in the kinase domain of p38 MAPK and plays a significant role at the interface site which is reversed in its dephosphorylated state. The heatmap of interactions between the TIRAP and p38 MAPK after the MD simulation shows that the TIRAP pY86 structure makes the highest number of stable hydrogen bonds with p38 MAPK residues. Our findings may further be validated in an in-vitro system and would be crucial for targeting the TIRAP and p38 MAPK interaction for therapeutic purposes against the chronic inflammatory response and associated diseases.
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11
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Targeting BCR-Abl in the treatment of Philadelphia-chromosome positive chronic myelogenous leukemia. Pharmacol Res 2022; 178:106156. [DOI: 10.1016/j.phrs.2022.106156] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/02/2022] [Indexed: 02/07/2023]
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12
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Xue B, Jordan B, Rizvi S, Naegle KM. KinPred: A unified and sustainable approach for harnessing proteome-level human kinase-substrate predictions. PLoS Comput Biol 2021; 17:e1008681. [PMID: 33556051 PMCID: PMC7895412 DOI: 10.1371/journal.pcbi.1008681] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/19/2021] [Accepted: 01/07/2021] [Indexed: 12/22/2022] Open
Abstract
Tyrosine and serine/threonine kinases are essential regulators of cell processes and are important targets for human therapies. Unfortunately, very little is known about specific kinase-substrate relationships, making it difficult to infer meaning from dysregulated phosphoproteomic datasets or for researchers to identify possible kinases that regulate specific or novel phosphorylation sites. The last two decades have seen an explosion in algorithms to extrapolate from what little is known into the larger unknown-predicting kinase relationships with site-specific substrates using a variety of approaches that include the sequence-specificity of kinase catalytic domains and various other factors, such as evolutionary relationships, co-expression, and protein-protein interaction networks. Unfortunately, a number of limitations prevent researchers from easily harnessing these resources, such as loss of resource accessibility, limited information in publishing that results in a poor mapping to a human reference, and not being updated to match the growth of the human phosphoproteome. Here, we propose a methodological framework for publishing predictions in a unified way, which entails ensuring predictions have been run on a current reference proteome, mapping the same substrates and kinases across resources to a common reference, filtering for the human phosphoproteome, and providing methods for updating the resource easily in the future. We applied this framework on three currently available resources, published in the last decade, which provide kinase-specific predictions in the human proteome. Using the unified datasets, we then explore the role of study bias, the emergent network properties of these predictive algorithms, and comparisons within and between predictive algorithms. The combination of the code for unification and analysis, as well as the unified predictions are available under the resource we named KinPred. We believe this resource will be useful for a wide range of applications and establishes best practices for long-term usability and sustainability for new and existing predictive algorithms.
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Affiliation(s)
- Bingjie Xue
- Department of Biomedical Engineering and the Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Benjamin Jordan
- Department of Biomedical Engineering and the Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Saqib Rizvi
- Department of Biomedical Engineering and the Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Kristen M. Naegle
- Department of Biomedical Engineering and the Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
- * E-mail:
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13
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Hojjat-Farsangi M, Moshfegh A, Schultz J, Norin M, Olin T, Österborg A, Mellstedt H. Targeting the Receptor Tyrosine Kinase ROR1 by Small Molecules. Handb Exp Pharmacol 2021; 269:75-99. [PMID: 34490515 DOI: 10.1007/164_2021_535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Receptor tyrosine kinases (RTKs) are frequently dysregulated in malignancies and important for the malignant characteristics of tumor cells. RTKs are attractive structures for drug targeting of cancer. The RTK ROR1 is of significance during embryogenesis but downregulated in post-partum tissues. However, ROR1 is overexpressed in several hematological and solid tumors and important for tumor cell proliferation, survival, migration, and metastasis. WNT5a is a main ligand for ROR1. Several clinical trials are ongoing using anti-ROR1 antibody based drugs directed against the external domain (monoclonal antibodies, BiTE, CAR-T). We have produced small molecules (KAN834/1571c) fitting to the ATP pocket of the intracellular tyrosine kinase (TK) domain of ROR1 (TK inhibitor, TKI). These inhibitors of ROR1 prevented ROR1 phosphorylation and inactivated the WNT/β-catenin independent as well as WNT/β-catenin dependent pathways. ROR1-TKI induced apoptosis of ROR1 positive fresh patient derived tumor cells and appropriate cell lines and a dose and time dependent tumor reduction in animal models. In combination with other clinically relevant targeting drugs as venetoclax a synergistic apoptotic effect was seen. Two other small molecules (ARI-1 and strictinin) bound also to ROR1 and inhibited tumor growth. Development of small molecule ROR1 inhibitors is warranted to include this novel therapeutic approach for cancer therapy.
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Affiliation(s)
| | - Ali Moshfegh
- BioClinicum, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Johan Schultz
- Kancera AB, Karolinska Institutet Science Park, Stockholm, Sweden
| | - Martin Norin
- Kancera AB, Karolinska Institutet Science Park, Stockholm, Sweden
| | - Thomas Olin
- Kancera AB, Karolinska Institutet Science Park, Stockholm, Sweden
| | - Anders Österborg
- BioClinicum, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.,Department of Hematology, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Håkan Mellstedt
- BioClinicum, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.
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14
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Washington C, Chernet R, Gokhale RH, Martino-Cortez Y, Liu HY, Rosenberg AM, Shahar S, Pfleger CM. A conserved, N-terminal tyrosine signal directs Ras for inhibition by Rabex-5. PLoS Genet 2020; 16:e1008715. [PMID: 32559233 PMCID: PMC7329146 DOI: 10.1371/journal.pgen.1008715] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 07/01/2020] [Accepted: 03/13/2020] [Indexed: 01/08/2023] Open
Abstract
Dysregulation of the Ras oncogene in development causes developmental disorders, "Rasopathies," whereas mutational activation or amplification of Ras in differentiated tissues causes cancer. Rabex-5 (also called RabGEF1) inhibits Ras by promoting Ras mono- and di-ubiquitination. We report here that Rabex-5-mediated Ras ubiquitination requires Ras Tyrosine 4 (Y4), a site of known phosphorylation. Ras substitution mutants insensitive to Y4 phosphorylation did not undergo Rabex-5-mediated ubiquitination in cells and exhibited Ras gain-of-function phenotypes in vivo. Ras Y4 phosphomimic substitution increased Rabex-5-mediated ubiquitination in cells. Y4 phosphomimic substitution in oncogenic Ras blocked the morphological phenotypes associated with oncogenic Ras in vivo dependent on the presence of Rabex-5. We developed polyclonal antibodies raised against an N-terminal Ras peptide phosphorylated at Y4. These anti-phospho-Y4 antibodies showed dramatic recognition of recombinant wild-type Ras and RasG12V proteins when incubated with JAK2 or SRC kinases but not of RasY4F or RasY4F,G12V recombinant proteins suggesting that JAK2 and SRC could promote phosphorylation of Ras proteins at Y4 in vitro. Anti-phospho-Y4 antibodies also showed recognition of RasG12V protein, but not wild-type Ras, when incubated with EGFR. A role for JAK2, SRC, and EGFR (kinases with well-known roles to activate signaling through Ras), to promote Ras Y4 phosphorylation could represent a feedback mechanism to limit Ras activation and thus establish Ras homeostasis. Notably, rare variants of Ras at Y4 have been found in cerebellar glioblastomas. Therefore, our work identifies a physiologically relevant Ras ubiquitination signal and highlights a requirement for Y4 for Ras inhibition by Rabex-5 to maintain Ras pathway homeostasis and to prevent tissue transformation.
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Affiliation(s)
- Chalita Washington
- Department of Oncological Sciences, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Rachel Chernet
- Department of Oncological Sciences, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Rewatee H. Gokhale
- Department of Oncological Sciences, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Graduate School of Biomedical Sciences, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Tisch Cancer Institute, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Yesenia Martino-Cortez
- Department of Oncological Sciences, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Hsiu-Yu Liu
- Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Ashley M. Rosenberg
- Department of Oncological Sciences, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Columbia University, New York, New York, United States of America
| | - Sivan Shahar
- Department of Oncological Sciences, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- New York Medical College, Valhalla, New York, United States of America
| | - Cathie M. Pfleger
- Department of Oncological Sciences, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Graduate School of Biomedical Sciences, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Tisch Cancer Institute, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
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15
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de Araujo ED, Orlova A, Neubauer HA, Bajusz D, Seo HS, Dhe-Paganon S, Keserű GM, Moriggl R, Gunning PT. Structural Implications of STAT3 and STAT5 SH2 Domain Mutations. Cancers (Basel) 2019; 11:E1757. [PMID: 31717342 PMCID: PMC6895964 DOI: 10.3390/cancers11111757] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/02/2019] [Accepted: 11/05/2019] [Indexed: 01/13/2023] Open
Abstract
Src Homology 2 (SH2) domains arose within metazoan signaling pathways and are involved in protein regulation of multiple pleiotropic cascades. In signal transducer and activator of transcription (STAT) proteins, SH2 domain interactions are critical for molecular activation and nuclear accumulation of phosphorylated STAT dimers to drive transcription. Sequencing analysis of patient samples has revealed the SH2 domain as a hotspot in the mutational landscape of STAT proteins although the functional impact for the vast majority of these mutations remains poorly characterized. Despite several well resolved structures for SH2 domain-containing proteins, structural data regarding the distinctive STAT-type SH2 domain is limited. Here, we review the unique features of STAT-type SH2 domains in the context of all currently reported STAT3 and STAT5 SH2 domain clinical mutations. The genetic volatility of specific regions in the SH2 domain can result in either activating or deactivating mutations at the same site in the domain, underscoring the delicate evolutionary balance of wild type STAT structural motifs in maintaining precise levels of cellular activity. Understanding the molecular and biophysical impact of these disease-associated mutations can uncover convergent mechanisms of action for mutations localized within the STAT SH2 domain to facilitate the development of targeted therapeutic interventions.
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Affiliation(s)
- Elvin D. de Araujo
- Centre for Medicinal Chemistry, University of Toronto at Mississauga, Mississauga, ON L5L 1C6, Canada;
- Department of Chemical & Physical Sciences, University of Toronto at Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Anna Orlova
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, A-1210 Vienna, Austria; (A.O.); (H.A.N.); (R.M.)
| | - Heidi A. Neubauer
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, A-1210 Vienna, Austria; (A.O.); (H.A.N.); (R.M.)
| | - Dávid Bajusz
- Medicinal Chemistry Research Group, Research Center for Natural Sciences, 1117 Budapest, Hungary; (D.B.); (G.M.K.)
| | - Hyuk-Soo Seo
- Department of Cancer Biology, Dana-Farber Cancer Institute, Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; (H.-S.S.); (S.D.-P.)
- Department of Biological Chemistry, Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Sirano Dhe-Paganon
- Department of Cancer Biology, Dana-Farber Cancer Institute, Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; (H.-S.S.); (S.D.-P.)
- Department of Biological Chemistry, Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - György M. Keserű
- Medicinal Chemistry Research Group, Research Center for Natural Sciences, 1117 Budapest, Hungary; (D.B.); (G.M.K.)
| | - Richard Moriggl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, A-1210 Vienna, Austria; (A.O.); (H.A.N.); (R.M.)
| | - Patrick T. Gunning
- Centre for Medicinal Chemistry, University of Toronto at Mississauga, Mississauga, ON L5L 1C6, Canada;
- Department of Chemical & Physical Sciences, University of Toronto at Mississauga, Mississauga, ON L5L 1C6, Canada
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16
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Yu J, Adapala NS, Doherty L, Sanjay A. Cbl-PI3K interaction regulates Cathepsin K secretion in osteoclasts. Bone 2019; 127:376-385. [PMID: 31299383 PMCID: PMC6708784 DOI: 10.1016/j.bone.2019.07.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 07/06/2019] [Accepted: 07/08/2019] [Indexed: 10/26/2022]
Abstract
Effective bone resorption by osteoclasts is critical for balanced bone remodeling. We have previously reported that mice harboring a substitution mutation of tyrosine 737 to phenylalanine in the adapter protein Cbl (CblY737F, YF) have increased bone volume partly due to decreased osteoclast-mediated bone resorption. The CblY737F mutation abrogates interaction between Cbl and the p85 subunit of PI3K. Here, we studied the mechanism for defective resorptive function of YF mutant osteoclasts. The YF osteoclasts had intact actin cytoskeletons and sealing zones. Expression and localization of proteins needed for acidification of the resorptive lacunae were also comparable between the WT and YF osteoclasts. In contrast, secretion of Cathepsin K, a major protease needed to degrade collagen, was diminished in the conditioned media derived from YF osteoclasts. The targeting of Cathepsin K into LAMP2-positive vesicles was also compromised due to decreased number of LAMP2-positive vesicles in YF osteoclasts. Further, we found that in contrast to WT, conditioned media derived from YF osteoclasts promoted increased numbers of alkaline phosphatase positive colonies, and increased expression of osteogenic markers in WT calvarial cultures. Cumulatively, our results suggest that the Cbl-PI3K interaction regulates Cathepsin K secretion required for proper bone resorption, and secretion of factors which promote osteogenesis.
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Affiliation(s)
- Jungeun Yu
- Department of Orthopaedic Surgery, UConn Health, Farmington, CT 06030, United States of America
| | - Naga Suresh Adapala
- Department of Orthopaedic Surgery, UConn Health, Farmington, CT 06030, United States of America
| | - Laura Doherty
- Department of Orthopaedic Surgery, UConn Health, Farmington, CT 06030, United States of America
| | - Archana Sanjay
- Department of Orthopaedic Surgery, UConn Health, Farmington, CT 06030, United States of America.
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17
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Corwin T, Woodsmith J, Apelt F, Fontaine JF, Meierhofer D, Helmuth J, Grossmann A, Andrade-Navarro MA, Ballif BA, Stelzl U. Defining Human Tyrosine Kinase Phosphorylation Networks Using Yeast as an In Vivo Model Substrate. Cell Syst 2019; 5:128-139.e4. [PMID: 28837810 DOI: 10.1016/j.cels.2017.08.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 05/02/2017] [Accepted: 08/03/2017] [Indexed: 12/13/2022]
Abstract
Systematic assessment of tyrosine kinase-substrate relationships is fundamental to a better understanding of cellular signaling and its profound alterations in human diseases such as cancer. In human cells, such assessments are confounded by complex signaling networks, feedback loops, conditional activity, and intra-kinase redundancy. Here we address this challenge by exploiting the yeast proteome as an in vivo model substrate. We individually expressed 16 human non-receptor tyrosine kinases (NRTKs) in Saccharomyces cerevisiae and identified 3,279 kinase-substrate relationships involving 1,351 yeast phosphotyrosine (pY) sites. Based on the yeast data without prior information, we generated a set of linear kinase motifs and assigned ∼1,300 known human pY sites to specific NRTKs. Furthermore, experimentally defined pY sites for each individual kinase were shown to cluster within the yeast interactome network irrespective of linear motif information. We therefore applied a network inference approach to predict kinase-substrate relationships for more than 3,500 human proteins, providing a resource to advance our understanding of kinase biology.
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Affiliation(s)
- Thomas Corwin
- Otto-Warburg Laboratory, Max-Planck Institute for Molecular Genetics (MPIMG), 14195 Berlin, Germany
| | - Jonathan Woodsmith
- Otto-Warburg Laboratory, Max-Planck Institute for Molecular Genetics (MPIMG), 14195 Berlin, Germany; Institute of Pharmaceutical Sciences, University of Graz and BioTechMed-Graz, 8010 Graz, Austria
| | - Federico Apelt
- Otto-Warburg Laboratory, Max-Planck Institute for Molecular Genetics (MPIMG), 14195 Berlin, Germany
| | - Jean-Fred Fontaine
- Genomics and Computational Biology, Kernel Press UG, 55128 Mainz, Germany; Faculty of Biology, Johannes Gutenberg University Mainz and Institute of Molecular Biology, 55128 Mainz, Germany
| | - David Meierhofer
- Otto-Warburg Laboratory, Max-Planck Institute for Molecular Genetics (MPIMG), 14195 Berlin, Germany
| | - Johannes Helmuth
- Otto-Warburg Laboratory, Max-Planck Institute for Molecular Genetics (MPIMG), 14195 Berlin, Germany
| | - Arndt Grossmann
- Otto-Warburg Laboratory, Max-Planck Institute for Molecular Genetics (MPIMG), 14195 Berlin, Germany
| | - Miguel A Andrade-Navarro
- Faculty of Biology, Johannes Gutenberg University Mainz and Institute of Molecular Biology, 55128 Mainz, Germany
| | - Bryan A Ballif
- Department of Biology, University of Vermont, Burlington, VT 05405, USA
| | - Ulrich Stelzl
- Otto-Warburg Laboratory, Max-Planck Institute for Molecular Genetics (MPIMG), 14195 Berlin, Germany; Institute of Pharmaceutical Sciences, University of Graz and BioTechMed-Graz, 8010 Graz, Austria.
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18
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Uhrig RG, Schläpfer P, Roschitzki B, Hirsch-Hoffmann M, Gruissem W. Diurnal changes in concerted plant protein phosphorylation and acetylation in Arabidopsis organs and seedlings. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:176-194. [PMID: 30920011 DOI: 10.1111/tpj.14315] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 02/24/2019] [Accepted: 02/26/2019] [Indexed: 05/22/2023]
Abstract
Protein phosphorylation and acetylation are the two most abundant post-translational modifications (PTMs) that regulate protein functions in eukaryotes. In plants, these PTMs have been investigated individually; however, their co-occurrence and dynamics on proteins is currently unknown. Using Arabidopsis thaliana, we quantified changes in protein phosphorylation, acetylation and protein abundance in leaf rosettes, roots, flowers, siliques and seedlings at the end of day (ED) and at the end of night (EN). This identified 2549 phosphorylated and 909 acetylated proteins, of which 1724 phosphorylated and 536 acetylated proteins were also quantified for changes in PTM abundance between ED and EN. Using a sequential dual-PTM workflow, we identified significant PTM changes and intersections in these organs and plant developmental stages. In particular, cellular process-, pathway- and protein-level analyses reveal that the phosphoproteome and acetylome predominantly intersect at the pathway- and cellular process-level at ED versus EN. We found 134 proteins involved in core plant cell processes, such as light harvesting and photosynthesis, translation, metabolism and cellular transport, that were both phosphorylated and acetylated. Our results establish connections between PTM motifs, PTM catalyzing enzymes and putative substrate networks. We also identified PTM motifs for further characterization of the regulatory mechanisms that control cellular processes during the diurnal cycle in different Arabidopsis organs and seedlings. The sequential dual-PTM analysis expands our understanding of diurnal plant cell regulation by PTMs and provides a useful resource for future analyses, while emphasizing the importance of analyzing multiple PTMs simultaneously to elucidate when, where and how they are involved in plant cell regulation.
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Affiliation(s)
- R Glen Uhrig
- Institute of Molecular Plant Biology, Department of Biology, ETH Zurich, 8092, Zurich, Switzerland
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Pascal Schläpfer
- Institute of Molecular Plant Biology, Department of Biology, ETH Zurich, 8092, Zurich, Switzerland
| | - Bernd Roschitzki
- Functional Genomics Center, ETH Zurich, 8092, Zurich, Switzerland
| | - Matthias Hirsch-Hoffmann
- Institute of Molecular Plant Biology, Department of Biology, ETH Zurich, 8092, Zurich, Switzerland
| | - Wilhelm Gruissem
- Institute of Molecular Plant Biology, Department of Biology, ETH Zurich, 8092, Zurich, Switzerland
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, 40227, Taiwan
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19
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Tossidou I, Teng B, Worthmann K, Müller-Deile J, Jobst-Schwan T, Kardinal C, Schroder P, Bolanos-Palmieri P, Haller H, Willerding J, Drost DM, de Jonge L, Reubold T, Eschenburg S, Johnson RI, Schiffer M. Tyrosine Phosphorylation of CD2AP Affects Stability of the Slit Diaphragm Complex. J Am Soc Nephrol 2019; 30:1220-1237. [PMID: 31235616 DOI: 10.1681/asn.2018080860] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 04/18/2019] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND CD2-associated protein (CD2AP), a slit diaphragm-associated scaffolding protein involved in survival and regulation of the cytoskeleton in podocytes, is considered a "stabilizer" of the slit diaphragm complex that connects the slit diaphragm protein nephrin to the cytoskeleton of the cell. Tyrosine phosphorylation of slit diaphragm molecules can influence their surface expression, but it is unknown whether tyrosine phosphorylation events of CD2AP are also physiologically relevant to slit diaphragm stability. METHODS We used isoelectric focusing, western blot analysis, and immunofluorescence to investigate phosphorylation of CD2AP, and phospho-CD2AP antibodies and site-directed mutagenesis to define the specific phosphorylated tyrosine residues. We used cross-species rescue experiments in Cd2apKD zebrafish and in Drosophila cindrRNAi mutants to define the physiologic relevance of CD2AP phosphorylation of the tyrosine residues. RESULTS We found that VEGF-A stimulation can induce a tyrosine phosphorylation response in CD2AP in podocytes, and that these phosphorylation events have an important effect on slit diaphragm protein localization and functionality in vivo. We demonstrated that tyrosine in position Y10 of the SH3-1 domain of CD2AP is indispensable for CD2AP function in vivo. We found that the binding affinity of nephrin to CD2AP is significantly enhanced in the absence of Y10; however, unexpectedly, this increased affinity leads not to stabilization but to functional impairment of the glomerular filtration barrier. CONCLUSIONS Our findings provide insight into CD2AP and its phosphorylation in the context of slit diaphragm functionality, and indicate a fine-tuned affinity balance of CD2AP and nephrin that is influenced by receptor tyrosine kinase stimulation.
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Affiliation(s)
- Irini Tossidou
- Division of Nephrology and Hypertension, Department of Medicine
| | - Beina Teng
- Department of Nephrology and Hypertension, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | | | - Janina Müller-Deile
- Division of Nephrology and Hypertension, Department of Medicine.,Department of Nephrology and Hypertension, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Tilman Jobst-Schwan
- Department of Nephrology and Hypertension, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | | | - Patricia Schroder
- Division of Nephrology and Hypertension, Department of Medicine.,Mount Desert Island Biological Laboratory, Salisbury Cove, Maine; and
| | - Patricia Bolanos-Palmieri
- Department of Nephrology and Hypertension, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Hermann Haller
- Division of Nephrology and Hypertension, Department of Medicine.,Mount Desert Island Biological Laboratory, Salisbury Cove, Maine; and
| | - Jonas Willerding
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
| | - Dana M Drost
- Department of Biology, Wesleyan University, Middletown, Connecticut
| | - Laura de Jonge
- Department of Biology, Wesleyan University, Middletown, Connecticut
| | - Thomas Reubold
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
| | - Susanne Eschenburg
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
| | - Ruth I Johnson
- Department of Biology, Wesleyan University, Middletown, Connecticut
| | - Mario Schiffer
- Division of Nephrology and Hypertension, Department of Medicine, .,Department of Nephrology and Hypertension, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.,Mount Desert Island Biological Laboratory, Salisbury Cove, Maine; and
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20
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Adapala NS, Root S, Lorenzo J, Aguila H, Sanjay A. PI3K activation increases SDF-1 production and number of osteoclast precursors, and enhances SDF-1-mediated osteoclast precursor migration. Bone Rep 2019; 10:100203. [PMID: 30989092 PMCID: PMC6449702 DOI: 10.1016/j.bonr.2019.100203] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 02/26/2019] [Accepted: 03/19/2019] [Indexed: 01/07/2023] Open
Abstract
Our previous studies showed that in a mouse model in which PI3K-AKT activation was increased (YF mice), osteoclast numbers and levels of SDF-1, a chemokine, were augmented. The purpose of this study was to delineate the role of PI3K activation in regulating SDF-1 production and examine whether SDF-1 can stimulate differentiation and/or migration of osteoclast precursors. Using flow cytometric analysis, we demonstrated that compared to wild type mice, bone marrow of YF mice had increased numbers of CXCL12 abundant reticular (CAR) cells, that are a major cell type responsible for producing SDF-1. At the molecular level, transcription factor specificity protein 1 (Sp1) induced an increased transcription of SDF-1 that was dependent on PI3K/AKT activation. YF mice also contained an increased number of osteoclast precursors, in which expression of CXCR4, a major receptor for SDF-1, was increased. SDF-1 did not induce differentiation of osteoclast precursors into mature osteoclasts; compared to cells derived from WT mice, cells obtained from YF mice were more responsive to SDF-1. In conclusion, we demonstrate that PI3K activation resulted in increased SDF-1, increased the number of osteoclast precursors, and enhanced osteoclast precursor migration in response to SDF-1. PI3K activation regulates the number of CAR cells in mouse bone marrow. PI3K activation regulates SDF-1/CXCL12 production by CAR cells in bone marrow. PI3K/AKT activation mediates transcription of SDF-1 by regulating transcription factor Sp1. SDF-1 enhances migration of osteoclast precursors via CXCR4.
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Affiliation(s)
- Naga Suresh Adapala
- Department of Orthopaedic Surgery, Farmington, CT, USA.,U Conn Health, Farmington, CT, USA
| | - Sierra Root
- Department of Immunology, Farmington, CT, USA.,U Conn Health, Farmington, CT, USA
| | - Joseph Lorenzo
- Department of Endocrinology and Metabolism, Farmington, CT, USA.,U Conn Health, Farmington, CT, USA
| | - Hector Aguila
- Department of Immunology, Farmington, CT, USA.,U Conn Health, Farmington, CT, USA
| | - Archana Sanjay
- Department of Orthopaedic Surgery, Farmington, CT, USA.,U Conn Health, Farmington, CT, USA
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21
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Li B, He J, Lv H, Liu Y, Lv X, Zhang C, Zhu Y, Ai D. c-Abl regulates YAPY357 phosphorylation to activate endothelial atherogenic responses to disturbed flow. J Clin Invest 2019; 129:1167-1179. [PMID: 30629551 DOI: 10.1172/jci122440] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 01/03/2019] [Indexed: 12/26/2022] Open
Abstract
Local flow patterns determine the uneven distribution of atherosclerotic lesions. This research aims to elucidate the mechanism of regulation of nuclear translocation of Yes-associated protein (YAP) under oscillatory shear stress (OSS) in the atheroprone phenotype of endothelial cells (ECs). We report here that OSS led to tyrosine phosphorylation and strong, continuous nuclear translocation of YAP in ECs that is dependent on integrin α5β1 activation. YAP overexpression in ECs blunted the anti-atheroprone effect of an integrin α5β1-blocking peptide (ATN161) in Apoe-/- mice. Activation of integrin α5β1 induced tyrosine, but not serine, phosphorylation of YAP in ECs. Blockage of integrin α5β1 with ATN161 abolished the phosphorylation of YAP at Y357 induced by OSS. Mechanistic studies showed that c-Abl inhibitor attenuated the integrin α5β1-induced YAP tyrosine phosphorylation. Furthermore, the phosphorylation of c-Abl and YAPY357 was significantly increased in ECs in atherosclerotic vessels of mice and in human plaques versus normal vessels. Finally, bosutinib, a tyrosine kinase inhibitor, markedly reduced the level of YAPY357 and the development of atherosclerosis in Apoe-/- mice. The c-Abl/YAPY357 pathway serves as a mechanism for the activation of integrin α5β1 and the atherogenic phenotype of ECs in response to OSS, and provides a potential therapeutic strategy for atherogenesis.
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22
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Zhang J, Lei X, Wang D, Jiang Y, Zhan Y, Li M, Zhou Y, Qin Y, Liu J, Wang A, Yang Y, Wang N. Inhibition of Abl or Src tyrosine kinase decreased porcine circovirus type 2 production in PK15 cells. Res Vet Sci 2019; 124:1-9. [PMID: 30716585 DOI: 10.1016/j.rvsc.2019.01.024] [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] [Received: 09/07/2018] [Revised: 01/14/2019] [Accepted: 01/22/2019] [Indexed: 12/12/2022]
Abstract
Porcine circovirus type 2 (PCV2) causes huge economic losses in the global swine industry and has a complex and poorly understood virus-host interaction mechanism. We reported that the C-terminal of the capsid protein of all PCV2 isolates shared a strictly conserved PXXP motif that may interact with SH3 domain-containing tyrosine kinases; however, its roles in PCV2 cell entry and replication remain unknown. In this study, we determined that mRNA levels of two SH3 domain-containing tyrosine kinases family (Abl and Src) had distinct profiles (wild-type and PXXP-mutated) during PCV2 infections of PK15 cells. Therefore, we hypothesized that activities of tyrosine kinases (Abl and Fyn) in PK15 cells may be hijacked by PCV2 via its PXXP motif of the Cap, to favor virus replication. Specific inhibitors PP2 of Lck/Fyn and STI-571 of Abl family kinases decreased viral production through suppression of DNA and Cap synthesis at the replication stage. However, based on indirect immunofluorescence assay (IFA), entry of PCV2 virus-like particles (VLPs) into PK15 cells was not altered. Elucidating mechanisms of PCV2-host interactions should provide new insights for development of new compounds to prevent or reduce PCV2 infections.
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Affiliation(s)
- Jiaxin Zhang
- The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China
| | - Xinnuo Lei
- The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China
| | - Dongliang Wang
- The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China
| | - Yifan Jiang
- The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China
| | - Yang Zhan
- The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China
| | - Meng Li
- The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China
| | - Yawen Zhou
- The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China
| | - Yiwen Qin
- The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China
| | - Jue Liu
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, No. 9 Shuguang Garden Middle Road, Haidian District, Beijing 100097, China
| | - Aibing Wang
- The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China
| | - Yi Yang
- The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China
| | - Naidong Wang
- The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China.
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23
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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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24
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Shi S, Wang L, Cao M, Chen G, Yu J. Proteomic analysis and prediction of amino acid variations that influence protein posttranslational modifications. Brief Bioinform 2018; 20:1597-1606. [DOI: 10.1093/bib/bby036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 03/07/2018] [Indexed: 12/18/2022] Open
Abstract
Abstract
Accumulative studies have indicated that amino acid variations through changing the type of residues of the target sites or key flanking residues could directly or indirectly influence protein posttranslational modifications (PTMs) and bring about a detrimental effect on protein function. Computational mutation analysis can greatly narrow down the efforts on experimental work. To increase the utilization of current computational resources, we first provide an overview of computational prediction of amino acid variations that influence protein PTMs and their functional analysis. We also discuss the challenges that are faced while developing novel in silico approaches in the future. The development of better methods for mutation analysis-related protein PTMs will help to facilitate the development of personalized precision medicine.
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Affiliation(s)
- Shaoping Shi
- Department of Mathematics and Numerical Simulation and High-Performance Computing Laboratory, School of Sciences, Nanchang University, Nanchang, Jiangxi 330031, China
| | - Lina Wang
- Department of Science, Nanchang Institute of Technology, Nanchang, Jiangxi 330031, China
| | - Man Cao
- Department of Mathematics, School of Sciences, Nanchang University, Nanchang, Jiangxi 330031, China
| | - Guodong Chen
- Department of Mathematics, School of Sciences, Nanchang University, Nanchang, Jiangxi 330031, China
| | - Jialin Yu
- Department of Mathematics, School of Sciences, Nanchang University, Nanchang, Jiangxi 330031, China
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25
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A novel miR17/protein tyrosine phosphatase-oc/EphA4 regulatory axis of osteoclast activity. Arch Biochem Biophys 2018; 650:30-38. [PMID: 29763590 PMCID: PMC5985224 DOI: 10.1016/j.abb.2018.05.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 05/08/2018] [Accepted: 05/11/2018] [Indexed: 12/17/2022]
Abstract
Information about the molecular mechanisms leading to the activation of the osteoclast is relatively limited. While there is compelling evidence that the signaling mechanisms of Src and integrin β3 are essential for osteoclast activation, the regulation of these two signaling mechanisms is not fully understood. In this review, evidence supporting a novel regulatory axis of osteoclast activation that plays an upstream regulatory role in both the Src and integrin β3 signaling during osteoclast activation is discussed. This regulatory axis contains three unique components: a structurally unique transmembrane protein-tyrosine phosphatase, PTP-oc, EphA4, and miR17. In the first component, PTP-oc activates the Src signaling through dephosphorylation of the inhibitory tyr-527 of Src. This in turn activates the integrin β3 signaling, enhances the JNK2/NFκB signaling, promotes the ITAM/Syk signaling, and suppresses the ITIM/Shp1 signaling; the consequence of which is activation of the osteoclast. In the second component, EphA4 inhibits osteoclast activity by suppressing the integrin β3 signaling. PTP-oc relieves the suppressive actions of EphA4 by directly dephosphorylating EphA4. In the third component, PTP-oc expression is negatively regulated by miR17. Accordingly, suppression of miR17 during osteoclast activation upregulates the PTP-oc signaling and suppresses the EphA4 signaling, resulting in the activation of the osteoclast. This regulatory axis is unique, in that each of the three components acts to exert suppressive action on their respective immediate downstream inhibitory step. Because the final downstream event is the EphA4-mediated inhibition of osteoclast activation, the overall effect of this mechanism is the stimulation of osteoclast activity.
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26
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Jung W, Sierecki E, Bastiani M, O'Carroll A, Alexandrov K, Rae J, Johnston W, Hunter DJB, Ferguson C, Gambin Y, Ariotti N, Parton RG. Cell-free formation and interactome analysis of caveolae. J Cell Biol 2018; 217:2141-2165. [PMID: 29716956 PMCID: PMC5987714 DOI: 10.1083/jcb.201707004] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 01/24/2018] [Accepted: 03/29/2018] [Indexed: 02/07/2023] Open
Abstract
Caveolae are linked to signaling protein regulation through interactions with caveolins. We describe a cell-free system for the biogenesis of caveolae and show phosphorylated-caveolins preferentially bind signaling proteins. Our validation in vivo shows that phosphorylated CAV1 recruits TRAF2 to the endosome to form a signaling platform. Caveolae have been linked to the regulation of signaling pathways in eukaryotic cells through direct interactions with caveolins. Here, we describe a cell-free system based on Leishmania tarentolae (Lt) extracts for the biogenesis of caveolae and show its use for single-molecule interaction studies. Insertion of expressed caveolin-1 (CAV1) into Lt membranes was analogous to that of caveolin in native membranes. Electron tomography showed that caveolins generate domains of precise size and curvature. Cell-free caveolae were used in quantitative assays to test the interaction of membrane-inserted caveolin with signaling proteins and to determine the stoichiometry of interactions. Binding of membrane-inserted CAV1 to several proposed binding partners, including endothelial nitric-oxide synthase, was negligible, but a small number of proteins, including TRAF2, interacted with CAV1 in a phosphorylation-(CAV1Y14)–stimulated manner. In cells subjected to oxidative stress, phosphorylated CAV1 recruited TRAF2 to the early endosome forming a novel signaling platform. These findings lead to a novel model for cellular stress signaling by CAV1.
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Affiliation(s)
- WooRam Jung
- The University of Queensland, The Institute for Molecular Bioscience, Brisbane, Queensland, Australia
| | - Emma Sierecki
- The University of Queensland, The Institute for Molecular Bioscience, Brisbane, Queensland, Australia
| | - Michele Bastiani
- The University of Queensland, The Institute for Molecular Bioscience, Brisbane, Queensland, Australia
| | - Ailis O'Carroll
- The University of Queensland, The Institute for Molecular Bioscience, Brisbane, Queensland, Australia
| | - Kirill Alexandrov
- The University of Queensland, The Institute for Molecular Bioscience, Brisbane, Queensland, Australia
| | - James Rae
- The University of Queensland, The Institute for Molecular Bioscience, Brisbane, Queensland, Australia
| | - Wayne Johnston
- The University of Queensland, The Institute for Molecular Bioscience, Brisbane, Queensland, Australia
| | - Dominic J B Hunter
- The University of Queensland, The Institute for Molecular Bioscience, Brisbane, Queensland, Australia
| | - Charles Ferguson
- The University of Queensland, The Institute for Molecular Bioscience, Brisbane, Queensland, Australia
| | - Yann Gambin
- The University of Queensland, The Institute for Molecular Bioscience, Brisbane, Queensland, Australia
| | - Nicholas Ariotti
- The University of Queensland, The Institute for Molecular Bioscience, Brisbane, Queensland, Australia
| | - Robert G Parton
- The University of Queensland, The Institute for Molecular Bioscience, Brisbane, Queensland, Australia .,The University of Queensland, The Centre for Microscopy and Microanalysis, Brisbane, Queensland, Australia
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27
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Sánchez-Pozo J, Baker-Williams AJ, Woodford MR, Bullard R, Wei B, Mollapour M, Stetler-Stevenson WG, Bratslavsky G, Bourboulia D. Extracellular Phosphorylation of TIMP-2 by Secreted c-Src Tyrosine Kinase Controls MMP-2 Activity. iScience 2018; 1:87-96. [PMID: 30227959 PMCID: PMC6135941 DOI: 10.1016/j.isci.2018.02.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 01/29/2018] [Accepted: 02/08/2018] [Indexed: 12/31/2022] Open
Abstract
The tissue inhibitor of metalloproteinases 2 (TIMP-2) is a specific endogenous inhibitor of matrix metalloproteinase 2 (MMP-2), which is a key enzyme that degrades the extracellular matrix and promotes tumor cell invasion. Although the TIMP-2:MMP-2 complex controls proteolysis, the signaling mechanism by which the two proteins associate in the extracellular space remains unidentified. Here we report that TIMP-2 is phosphorylated outside the cell by secreted c-Src tyrosine kinase. As a consequence, phosphorylation at Y90 significantly enhances TIMP-2 potency as an MMP-2 inhibitor and weakens the catalytic action of the active enzyme. TIMP-2 phosphorylation also appears to be essential for its interaction with the latent enzyme proMMP-2 in vivo. Absence of the kinase or non-phosphorylatable Y90 abolishes TIMP-2 binding to the latent enzyme, ultimately hampering proMMP-2 activation. Together, TIMP-2 phosphorylation by secreted c-Src represents a critical extracellular regulatory mechanism that controls the proteolytic function of MMP-2. c-Src tyrosine kinase phosphorylates TIMP-2 Secreted c-Src phosphorylates TIMP-2 extracellularly TIMP-2 Y90 phosphorylation promotes extracellular interaction with proMMP-2 Tyrosine phosphorylation of TIMP-2 regulates proMMP-2 processing and MMP-2 activity
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Affiliation(s)
- Javier Sánchez-Pozo
- Department of Urology, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA; Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA
| | - Alexander J Baker-Williams
- Department of Urology, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA; Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA
| | - Mark R Woodford
- Department of Urology, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA; Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA
| | - Renee Bullard
- Department of Urology, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA; Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA
| | - Beiyang Wei
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Mehdi Mollapour
- Department of Urology, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA; Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA
| | - William G Stetler-Stevenson
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Gennady Bratslavsky
- Department of Urology, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA
| | - Dimitra Bourboulia
- Department of Urology, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA; Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA.
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28
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Roskoski R. The role of small molecule platelet-derived growth factor receptor (PDGFR) inhibitors in the treatment of neoplastic disorders. Pharmacol Res 2018; 129:65-83. [DOI: 10.1016/j.phrs.2018.01.021] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 01/29/2018] [Indexed: 12/15/2022]
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29
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Zhang X, Hu H. Investigating and characterizing the binding activity of the immobilized calmodulin to calmodulin-dependent protein kinase I binding domain with atomic force microscopy. Chem Cent J 2017; 11:128. [PMID: 29214517 PMCID: PMC5718999 DOI: 10.1186/s13065-017-0360-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 11/30/2017] [Indexed: 12/03/2022] Open
Abstract
Protein–protein interactions are responsible for many biological processes, and the study of how proteins undergo a conformational change induced by other proteins in the immobilized state can help us to understand a protein’s function and behavior, empower the current knowledge on molecular etiology of disease, as well as the discovery of putative protein targets of therapeutic interest. In this study, a bottom-up approach was utilized to fabricate micro/nanometer-scale protein patterns. One cysteine mutated calmodulin (CaM), as a model protein, was immobilized on thiol-terminated pattern surfaces. Atomic Force Microscopy (AFM) was then employed as a tool to investigate the interactions between CaM and CaM kinase I binding domain, and show that the immobilized CaM retains its activity to interact with its target protein. Our work demonstrate the potential of employing AFM to the research and assay works evolving surface-based protein–protein interactions biosensors, bioelectronics or drug screening.
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Affiliation(s)
- Xiaoning Zhang
- College of Biotechnology, Southwest University, Chongqing, 400715, China.
| | - Hongmei Hu
- Key Laboratory of Mariculture and Enhancement of Zhejiang Province, Marine Fishery Institute of Zhejiang Province, Zhoushan, 316021, China
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30
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Moraga I, Spangler JB, Mendoza JL, Gakovic M, Wehrman TS, Krutzik P, Garcia KC. Synthekines are surrogate cytokine and growth factor agonists that compel signaling through non-natural receptor dimers. eLife 2017; 6. [PMID: 28498099 PMCID: PMC5429090 DOI: 10.7554/elife.22882] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 03/14/2017] [Indexed: 12/22/2022] Open
Abstract
Cytokine and growth-factor ligands typically signal through homo- or hetero-dimeric cell surface receptors via Janus Kinase (JAK/TYK), or Receptor Tyrosine Kinase (RTK)-mediated trans-phosphorylation. However, the number of receptor dimer pairings occurring in nature is limited to those driven by natural ligands encoded within our genome. We have engineered synthethic cytokines (synthekines) that drive formation of cytokine receptor dimer pairings that are not formed by endogenous cytokines and that are not found in nature, and which activate distinct signaling programs. We show that a wide range of non-natural cytokine receptor hetero-dimers are competent to elicit a signaling output. We engineered synthekine ligands that assembled IL-2Rβ/IL-4Rα or IL-4Rα/IFNAR2 receptor heterodimers, that do not occur naturally, triggering signaling and functional responses distinct from those activated by the endogenous cytokines IL-2, IL-4, and IFN. Furthermore, hybrid synthekine ligands that dimerized a JAK/STAT cytokine receptor with a receptor tyrosine kinase (RTK) also elicited a signaling response. Synthekines represent a new family of synthetic ligands with pre-defined receptors, but 'orphan' functions, that enable the full combinatorial scope of dimeric signaling receptors encoded within the human genome to be exploited for basic research and drug discovery.
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Affiliation(s)
- Ignacio Moraga
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, United States.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States.,Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Jamie B Spangler
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, United States.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States.,Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Juan L Mendoza
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, United States.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States.,Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Milica Gakovic
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, United States.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States.,Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | | | | | - K Christopher Garcia
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, United States.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States.,Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
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31
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Abstract
The Src Homology 2 (SH2) domain is the prototypical protein interaction module that lies at the heart of phosphotyrosine signaling. Since its serendipitous discovery, there has been a tremendous advancement in technologies and an array of techniques available for studying SH2 domains and phosphotyrosine signaling. In this chapter, we provide a glimpse of the history of SH2 domains and describe many of the tools and techniques that have been developed along the way and discuss future directions for SH2 domain studies. We highlight the gist of each chapter in this volume in the context of: the structural biology and phosphotyrosine binding; characterizing SH2 specificity and generating prediction models; systems biology and proteomics; SH2 domains in signal transduction; and SH2 domains in disease, diagnostics, and therapeutics. Many of the individual chapters provide an in-depth approach that will allow scientists to interrogate the function and role of SH2 domains.
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Affiliation(s)
- Bernard A Liu
- Broad Institute of Harvard and MIT, 415 Main St., 5175 JJ, Cambridge, MA, 02142, USA.
| | - Kazuya Machida
- Raymond and Beverly Sackler Laboratory of Genetics and Molecular Medicine, Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, 400 Farmington Ave., Farmington, CT, 06030, USA.
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32
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Xu M, Liu C, Zhou M, Li Q, Wang R, Kang J. Screening of Small-Molecule Inhibitors of Protein–Protein Interaction with Capillary Electrophoresis Frontal Analysis. Anal Chem 2016; 88:8050-7. [DOI: 10.1021/acs.analchem.6b01430] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Mei Xu
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai
Institute of Organic Chemistry, Chinese Academy of Sciences, Lingling Road 345, Shanghai 200032, China
| | - Chao Liu
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai
Institute of Organic Chemistry, Chinese Academy of Sciences, Lingling Road 345, Shanghai 200032, China
| | - Mi Zhou
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai
Institute of Organic Chemistry, Chinese Academy of Sciences, Lingling Road 345, Shanghai 200032, China
| | - Qing Li
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai
Institute of Organic Chemistry, Chinese Academy of Sciences, Lingling Road 345, Shanghai 200032, China
| | - Renxiao Wang
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai
Institute of Organic Chemistry, Chinese Academy of Sciences, Lingling Road 345, Shanghai 200032, China
| | - Jingwu Kang
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai
Institute of Organic Chemistry, Chinese Academy of Sciences, Lingling Road 345, Shanghai 200032, China
- ShanghaiTech University, Yueyang Road
319, Shanghai 200031, China
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JNK Signaling: Regulation and Functions Based on Complex Protein-Protein Partnerships. Microbiol Mol Biol Rev 2016; 80:793-835. [PMID: 27466283 DOI: 10.1128/mmbr.00043-14] [Citation(s) in RCA: 321] [Impact Index Per Article: 40.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The c-Jun N-terminal kinases (JNKs), as members of the mitogen-activated protein kinase (MAPK) family, mediate eukaryotic cell responses to a wide range of abiotic and biotic stress insults. JNKs also regulate important physiological processes, including neuronal functions, immunological actions, and embryonic development, via their impact on gene expression, cytoskeletal protein dynamics, and cell death/survival pathways. Although the JNK pathway has been under study for >20 years, its complexity is still perplexing, with multiple protein partners of JNKs underlying the diversity of actions. Here we review the current knowledge of JNK structure and isoforms as well as the partnerships of JNKs with a range of intracellular proteins. Many of these proteins are direct substrates of the JNKs. We analyzed almost 100 of these target proteins in detail within a framework of their classification based on their regulation by JNKs. Examples of these JNK substrates include a diverse assortment of nuclear transcription factors (Jun, ATF2, Myc, Elk1), cytoplasmic proteins involved in cytoskeleton regulation (DCX, Tau, WDR62) or vesicular transport (JIP1, JIP3), cell membrane receptors (BMPR2), and mitochondrial proteins (Mcl1, Bim). In addition, because upstream signaling components impact JNK activity, we critically assessed the involvement of signaling scaffolds and the roles of feedback mechanisms in the JNK pathway. Despite a clarification of many regulatory events in JNK-dependent signaling during the past decade, many other structural and mechanistic insights are just beginning to be revealed. These advances open new opportunities to understand the role of JNK signaling in diverse physiological and pathophysiological states.
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Lai S, Winkler DFH, Zhang H, Pelech S. Determination of the Substrate Specificity of Protein Kinases with Peptide Micro- and Macroarrays. Methods Mol Biol 2016; 1360:183-202. [PMID: 26501911 DOI: 10.1007/978-1-4939-3073-9_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Elucidation of the key determinants for the phosphorylation site specificities of protein kinases facilitates identification of their physiological substrates, and serves to better define their critical roles in the signaling networks that underlie a multitude of cellular activities. Albeit with some apparent limitations, such as the lack of contextual information for secondary substrate-binding sites, the synthetic peptide-based approach has been adopted widely for the kinase specificity profiling studies, especially when they are used in an array format, which permits the screening of large numbers of potential peptide substrates in parallel. In this chapter, we present detailed protocols for determining protein kinase substrate specificity using an approach that involves both peptide microarrays and macroarrays. In particular, SPOT synthesis on macroarrays can be used to follow up on in silico predictions of protein kinase substrate specificity with predictive algorithms.
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Affiliation(s)
- Shenshen Lai
- Kinexus Bioinformatics Corporation, Suite 1, 8755 Ash Street, Vancouver, British Columbia, Canada, V6P 6T3
| | - Dirk F H Winkler
- Kinexus Bioinformatics Corporation, Suite 1, 8755 Ash Street, Vancouver, British Columbia, Canada, V6P 6T3
| | - Hong Zhang
- Kinexus Bioinformatics Corporation, Suite 1, 8755 Ash Street, Vancouver, British Columbia, Canada, V6P 6T3
| | - Steven Pelech
- Kinexus Bioinformatics Corporation, Suite 1, 8755 Ash Street, Vancouver, British Columbia, Canada, V6P 6T3.
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
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35
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Tsui T, Miller WT. Cancer-Associated Mutations in Breast Tumor Kinase/PTK6 Differentially Affect Enzyme Activity and Substrate Recognition. Biochemistry 2015; 54:3173-82. [PMID: 25940761 DOI: 10.1021/acs.biochem.5b00303] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Brk (breast tumor kinase, also known as PTK6) is a nonreceptor tyrosine kinase that is aberrantly expressed in several cancers and promotes cell proliferation and transformation. Genome sequencing studies have revealed a number of cancer-associated somatic mutations in the Brk gene; however, their effect on Brk activity has not been examined. We analyzed a panel of cancer-associated mutations and determined that several of the mutations activate Brk, while two eliminated enzymatic activity. Three of the mutations (L16F, R131L, and P450L) are located in important regulatory domains of Brk (the SH3, SH2 domains, and C-terminal tail, respectively). Biochemical data suggest that they activate Brk by disrupting intramolecular interactions that normally maintain Brk in an autoinhibited conformation. We also observed differential effects on recognition and phosphorylation of substrates, suggesting that the mutations can influence downstream Brk signaling by multiple mechanisms.
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Affiliation(s)
- Tiffany Tsui
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, New York 11794, United States
| | - W Todd Miller
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, New York 11794, United States
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36
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Abstract
Cellular responses to environmental cues involve the mobilization of GTPases, protein kinases and phosphoprotein phosphatases. The spatial organization of these signalling enzymes by scaffold proteins helps to guide the flow of molecular information. Allosteric modulation of scaffolded enzymes can alter their catalytic activity or sensitivity to second messengers in a manner that augments, insulates or terminates local cellular events. This Review examines the features of scaffold proteins and highlights examples of locally organized groups of signalling enzymes that drive essential physiological processes, including hormone action, heart rate, cell division, organelle movement and synaptic transmission.
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37
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An SH2 domain model of STAT5 in complex with phospho-peptides define "STAT5 Binding Signatures". J Comput Aided Mol Des 2015; 29:451-70. [PMID: 25752764 DOI: 10.1007/s10822-015-9835-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 02/04/2015] [Indexed: 10/23/2022]
Abstract
The signal transducer and activator of transcription 5 (STAT5) is a member of the STAT family of proteins, implicated in cell growth and differentiation. STAT activation is regulated by phosphorylation of protein monomers at conserved tyrosine residues, followed by binding to phospho-peptide pockets and subsequent dimerization. STAT5 is implicated in the development of severe pathological conditions, including many cancer forms. However, nowadays a few STAT5 inhibitors are known, and only one crystal structure of the inactive STAT5 dimer is publicly available. With a view to enabling structure-based drug design, we have: (1) analyzed phospho-peptide binding pockets on SH2 domains of STAT5, STAT1 and STAT3; (2) generated a model of STAT5 bound to phospho-peptides; (3) assessed our model by docking against a class of known STAT5 inhibitors (Müller et al. in ChemBioChem 9:723-727, 2008); (4) used molecular dynamics simulations to optimize the molecular determinants responsible for binding and (5) proposed unique "Binding Signatures" of STAT5. Our results put in place the foundations to address STAT5 as a target for rational drug design, from sequence, structural and functional perspectives.
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Witucki LA, Borowicz LS, Pedley AM, Curtis-Fisk J, Kuszpit EG. Identification of FAK substrate peptides via colorimetric screening of a one-bead one-peptide combinatorial library. J Pept Sci 2015; 21:302-11. [PMID: 25728406 DOI: 10.1002/psc.2751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 12/19/2014] [Accepted: 12/30/2014] [Indexed: 11/09/2022]
Abstract
Focal adhesion kinase (FAK) is a protein tyrosine kinase that is associated with regulating cellular functions such as cell adhesion and migration and has emerged as an important target for cancer research. Short peptide substrates that are selectively and efficiently phosphorylated by FAK have not been previously identified and tested. Here we report the synthesis and screening of a one-bead one-peptide combinatorial library to identify novel substrates for FAK. Using a solid-phase colorimetric antibody tagging detection platform, the peptide beads phosphorylated by FAK were sequenced via Edman degradation and then validated through radioisotope kinetic studies with [γ-(32)P] ATP to derive Michaelis-Menton constants. The combination of results gathered from both colorimetric and radioisotope kinase assays led to the rational design of a second generation of FAK peptide substrates. Out of all the potential peptide substrates evaluated, the most active was GDYVEFKKK with a K(M) = 92 μM and a Vmax = 1920 nmol/min/mg. Peptide substrates discovered within this study may be useful diagnostic tools for future kinase investigations and may lead to novel therapeutic agents.
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Affiliation(s)
- Laurie A Witucki
- Department of Chemistry, Grand Valley State University, Allendale, MI, 49401, USA
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39
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Roskoski R. Src protein-tyrosine kinase structure, mechanism, and small molecule inhibitors. Pharmacol Res 2015; 94:9-25. [PMID: 25662515 DOI: 10.1016/j.phrs.2015.01.003] [Citation(s) in RCA: 369] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 01/26/2015] [Indexed: 12/13/2022]
Abstract
The physiological Src proto-oncogene is a protein-tyrosine kinase that plays key roles in cell growth, division, migration, and survival signaling pathways. From the N- to C-terminus, Src contains a unique domain, an SH3 domain, an SH2 domain, a protein-tyrosine kinase domain, and a regulatory tail. The chief phosphorylation sites of human Src include an activating pTyr419 that results from phosphorylation in the kinase domain by an adjacent Src molecule and an inhibitory pTyr530 in the regulatory tail that results from phosphorylation by C-terminal Src kinase (Csk) or Chk (Csk homologous kinase). The oncogenic Rous sarcoma viral protein lacks the equivalent of Tyr530 and is constitutively activated. Inactive Src is stabilized by SH2 and SH3 domains on the rear of the kinase domain where they form an immobilizing and inhibitory clamp. Protein kinases including Src contain hydrophobic regulatory and catalytic spines and collateral shell residues that are required to assemble the active enzyme. In the inactive enzyme, the regulatory spine contains a kink or a discontinuity with a structure that is incompatible with catalysis. The conversion of inactive to active Src is accompanied by electrostatic exchanges involving the breaking and making of distinct sets of kinase domain salt bridges and hydrogen bonds. Src-catalyzed protein phosphorylation requires the participation of two Mg(2+) ions. Although nearly all protein kinases possess a common K/E/D/D signature, each enzyme exhibits its unique variations of the protein-kinase reaction template. Bosutinib, dasatinib, and ponatinib are Src/multikinase inhibitors that are approved by the FDA for the treatment of chronic myelogenous leukemia and vandetanib is approved for the treatment of medullary thyroid cancer. The Src and BCR-Abl inhibitors saracatinib and AZD0424, along with the previous four drugs, are in clinical trials for a variety of solid tumors including breast and lung cancers. Both ATP and targeted therapeutic Src protein kinase inhibitors such as dasatinib and ponatinib make hydrophobic contacts with catalytic spine residues and form hydrogen bonds with hinge residues connecting the small and large kinase lobes.
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Affiliation(s)
- Robert Roskoski
- Blue Ridge Institute for Medical Research, 3754 Brevard Road, Suite 116, Box 19, Horse Shoe, NC 28742-8814, United States.
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40
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Debebe Z, Rathmell WK. Ror2 as a therapeutic target in cancer. Pharmacol Ther 2015; 150:143-8. [PMID: 25614331 DOI: 10.1016/j.pharmthera.2015.01.010] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 01/15/2015] [Indexed: 11/30/2022]
Abstract
Ror2 is a signaling receptor for Wnt ligands that is known to play important roles in limb development, but having no essential roles known in adult tissues. Recent evidence has implicated Ror2 in mediating both canonical and non-canonical signaling pathways. Ror2 was initially found to be highly expressed in osteosarcoma and renal cell carcinomas, and has recently been found in an increasingly long list of cancers currently including melanoma, colon cancer, melanoma, squamous cell carcinoma of the head and neck, and breast cancer. In the majority of these cancer types, Ror2 expression is associated with more aggressive disease states, consistent with a role mediating Wnt signaling regardless of the canonical or noncanonical signal. Because of the pattern of tissue distribution, the association with high-risk diseases, and the cell surface localization of this receptor, Ror2 has been identified as a potential high value target for therapeutic development. However, the recent discovery that Ror2 may function through non-kinase activities challenges this strategy and opens up opportunities to target this important molecule through alternative means.
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Affiliation(s)
- Zufan Debebe
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - W Kimryn Rathmell
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States; Department of Medicine, Division of Hematology and Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States; Department of Urology, Division of Hematology and Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States; Department of Genetics, Division of Hematology and Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States.
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41
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Adapala NS, Barbe MF, Tsygankov AY, Lorenzo JA, Sanjay A. Loss of Cbl-PI3K interaction enhances osteoclast survival due to p21-Ras mediated PI3K activation independent of Cbl-b. J Cell Biochem 2015; 115:1277-89. [PMID: 24470255 DOI: 10.1002/jcb.24779] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 01/24/2014] [Indexed: 01/14/2023]
Abstract
Cbl family proteins, Cbl and Cbl-b, are E3 ubiquitin ligases and adaptor proteins, which play important roles in bone-resorbing osteoclasts. Loss of Cbl in mice decreases osteoclast migration, resulting in delayed bone development where as absence of Cbl-b decreases bone volume due to hyper-resorptive osteoclasts. A major structural difference between Cbl and Cbl-b is tyrosine 737 (in YEAM motif) only on Cbl, which upon phosphorylation interacts with the p85 subunit of phosphatidylinositol-3 Kinase (PI3K). In contrast to Cbl(-/-) and Cbl-b(-/-) , mice lacking Cbl-PI3K interaction due to a Y737F (tyrosine to phenylalanine, YF) mutation showed enhanced osteoclast survival, but defective bone resorption. To investigate whether Cbl-PI3K interaction contributes to distinct roles of Cbl and Cbl-b in osteoclasts, mice bearing CblY737F mutation in the Cbl-b(-/-) background (YF/YF;Cbl-b(-/-) ) were generated. The differentiation and survival were augmented similarly in YF/YF and YF/YF;Cbl-b(-/-) osteoclasts, associated with enhanced PI3K signaling suggesting an exclusive role of Cbl-PI3K interaction, independent of Cbl-b. In addition to PI3K, the small GTPase Ras also regulates osteoclast survival. In the absence of Cbl-PI3K interaction, increased Ras GTPase activity and Ras-PI3K binding were observed and inhibition of Ras activation attenuated PI3K mediated osteoclast survival. In contrast to differentiation and survival, increased osteoclast activity observed in Cbl-b(-/-) mice persisted even after introduction of the resorption-defective YF mutation in YF/YF;Cbl-b(-/-) mice. Hence, Cbl and Cbl-b play mutually exclusive roles in osteoclasts. Whereas Cbl-PI3K interaction regulates differentiation and survival, bone resorption is predominantly regulated by Cbl-b in osteoclasts.
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Affiliation(s)
- Naga Suresh Adapala
- Department of Orthopedic Surgery, University of Connecticut Health Center, Farmington, Connecticut, 06032
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42
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Systematic analysis of the in situ crosstalk of tyrosine modifications reveals no additional natural selection on multiply modified residues. Sci Rep 2014; 4:7331. [PMID: 25476580 PMCID: PMC4256647 DOI: 10.1038/srep07331] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 11/11/2014] [Indexed: 12/16/2022] Open
Abstract
Recent studies have indicated that different post-translational modifications (PTMs) synergistically orchestrate specific biological processes by crosstalks. However, the preference of the crosstalk among different PTMs and the evolutionary constraint on the PTM crosstalk need further dissections. In this study, the in situ crosstalk at the same positions among three tyrosine PTMs including sulfation, nitration and phosphorylation were systematically analyzed. The experimentally identified sulfation, nitration and phosphorylation sites were collected and integrated with reliable predictions to perform large-scale analyses of in situ crosstalks. From the results, we observed that the in situ crosstalk between sulfation and nitration is significantly under-represented, whereas both sulfation and nitration prefer to co-occupy with phosphorylation at same tyrosines. Further analyses suggested that sulfation and nitration preferentially co-occur with phosphorylation at specific positions in proteins, and participate in distinct biological processes and functions. More interestingly, the long-term evolutionary analysis indicated that multi-PTM targeting tyrosines didn't show any higher conservation than singly modified ones. Also, the analysis of human genetic variations demonstrated that there is no additional functional constraint on inherited disease, cancer or rare mutations of multiply modified tyrosines. Taken together, our systematic analyses provided a better understanding of the in situ crosstalk among PTMs.
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43
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Engineered kinase activation reveals unique morphodynamic phenotypes and associated trafficking for Src family isoforms. Proc Natl Acad Sci U S A 2014; 111:12420-5. [PMID: 25118278 DOI: 10.1073/pnas.1404487111] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The Src kinase family comprises nine homologous members whose distinct expression patterns and cellular distributions indicate that they have unique roles. These roles have not been determined because genetic manipulation has not produced clearly distinct phenotypes, and the kinases' homology complicates generation of specific inhibitors. Through insertion of a modified FK506 binding protein (insertable FKBP12, iFKBP) into the protein kinase isoforms Fyn, Src, Lyn, and Yes, we engineered kinase analogs that can be activated within minutes in living cells (RapR analogs). Combining our RapR analogs with computational tools for quantifying and characterizing cellular dynamics, we demonstrate that Src family isoforms produce very different phenotypes, encompassing cell spreading, polarized motility, and production of long, thin cell extensions. Activation of Src and Fyn led to patterns of kinase translocation that correlated with morphological changes in temporally distinct stages. Phenotypes were dependent on N-terminal acylation, not on Src homology 3 (SH3) and Src homology 2 (SH2) domains, and correlated with movement between a perinuclear compartment, adhesions, and the plasma membrane.
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44
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Hojjat-Farsangi M, Moshfegh A, Daneshmanesh AH, Khan AS, Mikaelsson E, Osterborg A, Mellstedt H. The receptor tyrosine kinase ROR1--an oncofetal antigen for targeted cancer therapy. Semin Cancer Biol 2014; 29:21-31. [PMID: 25068995 DOI: 10.1016/j.semcancer.2014.07.005] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 07/17/2014] [Indexed: 11/26/2022]
Abstract
Targeted cancer therapies have emerged as new treatment options for various cancer types. Among targets, receptor tyrosine kinases (RTKs) are among the most promising. ROR1 is a transmembrane RTK of importance during the normal embryogenesis for the central nervous system, heart, lung and skeletal systems, but is not expressed in normal adult tissues. However, ROR1 is overexpressed in several human malignancies and may act as a survival factor for tumor cells. Its unique expression by malignant cells may provide a target for novel therapeutics including monoclonal antibodies (mAbs) and small molecule inhibitors of tyrosine kinases (TKI) for the treatment of cancer. Promising preclinical results have been reported in e.g. chronic lymphocytic leukemia, pancreatic carcinoma, lung and breast cancer. ROR1 might also be an interesting oncofetal antigen for active immunotherapy. In this review, we provide an overview of the ROR1 structure and functions in cancer and highlight emerging therapeutic options of interest for targeting ROR1 in tumor therapy.
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Affiliation(s)
- Mohammad Hojjat-Farsangi
- Department of Oncology-Pathology, Immune and Gene Therapy Lab, Cancer Center Karolinska (CCK), Karolinska University Hospital Solna and Karolinska Institutet, Stockholm, Sweden
| | - Ali Moshfegh
- Department of Oncology-Pathology, Immune and Gene Therapy Lab, Cancer Center Karolinska (CCK), Karolinska University Hospital Solna and Karolinska Institutet, Stockholm, Sweden
| | - Amir Hossein Daneshmanesh
- Department of Oncology-Pathology, Immune and Gene Therapy Lab, Cancer Center Karolinska (CCK), Karolinska University Hospital Solna and Karolinska Institutet, Stockholm, Sweden
| | - Abdul Salam Khan
- Department of Oncology-Pathology, Immune and Gene Therapy Lab, Cancer Center Karolinska (CCK), Karolinska University Hospital Solna and Karolinska Institutet, Stockholm, Sweden
| | - Eva Mikaelsson
- Department of Oncology-Pathology, Immune and Gene Therapy Lab, Cancer Center Karolinska (CCK), Karolinska University Hospital Solna and Karolinska Institutet, Stockholm, Sweden
| | - Anders Osterborg
- Department of Oncology-Pathology, Immune and Gene Therapy Lab, Cancer Center Karolinska (CCK), Karolinska University Hospital Solna and Karolinska Institutet, Stockholm, Sweden; Department of Hematology, Karolinska University Hospital Solna, Stockholm, Sweden; Department of Oncology, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Håkan Mellstedt
- Department of Oncology-Pathology, Immune and Gene Therapy Lab, Cancer Center Karolinska (CCK), Karolinska University Hospital Solna and Karolinska Institutet, Stockholm, Sweden.
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45
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Leung KK, Hause RJ, Barkinge JL, Ciaccio MF, Chuu CP, Jones RB. Enhanced prediction of Src homology 2 (SH2) domain binding potentials using a fluorescence polarization-derived c-Met, c-Kit, ErbB, and androgen receptor interactome. Mol Cell Proteomics 2014; 13:1705-23. [PMID: 24728074 PMCID: PMC4083110 DOI: 10.1074/mcp.m113.034876] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Many human diseases are associated with aberrant regulation of phosphoprotein signaling networks. Src homology 2 (SH2) domains represent the major class of protein domains in metazoans that interact with proteins phosphorylated on the amino acid residue tyrosine. Although current SH2 domain prediction algorithms perform well at predicting the sequences of phosphorylated peptides that are likely to result in the highest possible interaction affinity in the context of random peptide library screens, these algorithms do poorly at predicting the interaction potential of SH2 domains with physiologically derived protein sequences. We employed a high throughput interaction assay system to empirically determine the affinity between 93 human SH2 domains and phosphopeptides abstracted from several receptor tyrosine kinases and signaling proteins. The resulting interaction experiments revealed over 1000 novel peptide-protein interactions and provided a glimpse into the common and specific interaction potentials of c-Met, c-Kit, GAB1, and the human androgen receptor. We used these data to build a permutation-based logistic regression classifier that performed considerably better than existing algorithms for predicting the interaction potential of several SH2 domains.
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Affiliation(s)
| | - Ronald J Hause
- ¶Committee on Genetics, Genomics, and Systems Biology, and
| | - John L Barkinge
- From the ‡Committee on Cancer Biology, ¶Committee on Genetics, Genomics, and Systems Biology, and ‡‡Committee on Cellular and Molecular Physiology, The Ben May Department for Cancer Research and the Institute for Genomics and Systems Biology, The Gwen and Jules Knapp Center for Biomedical Discovery, University of Chicago, Chicago, Illinois 60637
| | - Mark F Ciaccio
- ‡‡Committee on Cellular and Molecular Physiology, The Ben May Department for Cancer Research and the Institute for Genomics and Systems Biology, The Gwen and Jules Knapp Center for Biomedical Discovery, University of Chicago, Chicago, Illinois 60637
| | - Chih-Pin Chuu
- From the ‡Committee on Cancer Biology, ¶Committee on Genetics, Genomics, and Systems Biology, and ‡‡Committee on Cellular and Molecular Physiology, The Ben May Department for Cancer Research and the Institute for Genomics and Systems Biology, The Gwen and Jules Knapp Center for Biomedical Discovery, University of Chicago, Chicago, Illinois 60637
| | - Richard B Jones
- From the ‡Committee on Cancer Biology, ¶Committee on Genetics, Genomics, and Systems Biology, and
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46
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Engelke M, Oellerich T, Dittmann K, Hsiao HH, Urlaub H, Serve H, Griesinger C, Wienands J. Cutting Edge: Feed-Forward Activation of Phospholipase Cγ2 via C2 Domain–Mediated Binding to SLP65. THE JOURNAL OF IMMUNOLOGY 2013; 191:5354-8. [DOI: 10.4049/jimmunol.1301326] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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47
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Jones RB. Do low-affinity ErbB receptor protein interactions represent the base of a cell signaling iceberg? Expert Rev Proteomics 2013; 10:115-8. [PMID: 23573776 DOI: 10.1586/epr.12.78] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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48
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Wnt signaling through the Ror receptor in the nervous system. Mol Neurobiol 2013; 49:303-15. [PMID: 23990374 DOI: 10.1007/s12035-013-8520-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 07/18/2013] [Indexed: 01/04/2023]
Abstract
The receptor tyrosine kinase-like orphan receptor (Ror) proteins are conserved tyrosine kinase receptors that play roles in a variety of cellular processes that pattern tissues and organs during vertebrate and invertebrate development. Ror signaling is required for skeleton and neuronal development and modulates cell migration, cell polarity, and convergent extension. Ror has also been implicated in two human skeletal disorders, brachydactyly type B and Robinow syndrome. Rors are widely expressed during metazoan development including domains in the nervous system. Here, we review recent progress in understanding the roles of the Ror receptors in neuronal migration, axonal pruning, axon guidance, and synaptic plasticity. The processes by which Ror signaling execute these diverse roles are still largely unknown, but they likely converge on cytoskeletal remodeling. In multiple species, Rors have been shown to act as Wnt receptors signaling via novel non-canonical Wnt pathways mediated in some tissues by the adapter protein disheveled and the non-receptor tyrosine kinase Src. Rors can either activate or repress Wnt target expression depending on the cellular context and can also modulate signal transduction by sequestering Wnt ligands away from their signaling receptors. Future challenges include the identification of signaling components of the Ror pathways and bettering our understanding of the roles of these pleiotropic receptors in patterning the nervous system.
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49
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Whyte GF, Vilar R, Woscholski R. Molecular recognition with boronic acids-applications in chemical biology. J Chem Biol 2013; 6:161-74. [PMID: 24432132 PMCID: PMC3787204 DOI: 10.1007/s12154-013-0099-0] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 05/19/2013] [Indexed: 01/14/2023] Open
Abstract
Small molecules have long been used for the selective recognition of a wide range of analytes. The ability of these chemical receptors to recognise and bind to specific targets mimics certain biological processes (such as protein-substrate interactions) and has therefore attracted recent interest. Due to the abundance of biological molecules possessing polyhydroxy motifs, boronic acids-which form five-membered boronate esters with diols-have become increasingly popular in the synthesis of small chemical receptors. Their targets include biological materials and natural products including phosphatidylinositol bisphosphate, saccharides and polysaccharides, nucleic acids, metal ions and the neurotransmitter dopamine. This review will focus on the many ways in which small chemical receptors based on boronic acids have been used as biochemical tools for various purposes, including sensing and detection of analytes, interference in signalling pathways, enzyme inhibition and cell delivery systems. The most recent developments in each area will be highlighted.
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Affiliation(s)
- Gillian F. Whyte
- Institute of Chemical Biology and Department of Chemistry, Imperial College London, London, UK
| | - Ramon Vilar
- Institute of Chemical Biology and Department of Chemistry, Imperial College London, London, UK
| | - Rudiger Woscholski
- Institute of Chemical Biology and Department of Chemistry, Imperial College London, London, UK
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Kundu K, Costa F, Huber M, Reth M, Backofen R. Semi-supervised prediction of SH2-peptide interactions from imbalanced high-throughput data. PLoS One 2013; 8:e62732. [PMID: 23690949 PMCID: PMC3656881 DOI: 10.1371/journal.pone.0062732] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 03/22/2013] [Indexed: 01/08/2023] Open
Abstract
Src homology 2 (SH2) domains are the largest family of the peptide-recognition modules (PRMs) that bind to phosphotyrosine containing peptides. Knowledge about binding partners of SH2-domains is key for a deeper understanding of different cellular processes. Given the high binding specificity of SH2, in-silico ligand peptide prediction is of great interest. Currently however, only a few approaches have been published for the prediction of SH2-peptide interactions. Their main shortcomings range from limited coverage, to restrictive modeling assumptions (they are mainly based on position specific scoring matrices and do not take into consideration complex amino acids inter-dependencies) and high computational complexity. We propose a simple yet effective machine learning approach for a large set of known human SH2 domains. We used comprehensive data from micro-array and peptide-array experiments on 51 human SH2 domains. In order to deal with the high data imbalance problem and the high signal-to-noise ration, we casted the problem in a semi-supervised setting. We report competitive predictive performance w.r.t. state-of-the-art. Specifically we obtain 0.83 AUC ROC and 0.93 AUC PR in comparison to 0.71 AUC ROC and 0.87 AUC PR previously achieved by the position specific scoring matrices (PSSMs) based SMALI approach. Our work provides three main contributions. First, we showed that better models can be obtained when the information on the non-interacting peptides (negative examples) is also used. Second, we improve performance when considering high order correlations between the ligand positions employing regularization techniques to effectively avoid overfitting issues. Third, we developed an approach to tackle the data imbalance problem using a semi-supervised strategy. Finally, we performed a genome-wide prediction of human SH2-peptide binding, uncovering several findings of biological relevance. We make our models and genome-wide predictions, for all the 51 SH2-domains, freely available to the scientific community under the following URLs: http://www.bioinf.uni-freiburg.de/Software/SH2PepInt/SH2PepInt.tar.gz and http://www.bioinf.uni-freiburg.de/Software/SH2PepInt/Genome-wide-predictions.tar.gz, respectively.
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Affiliation(s)
- Kousik Kundu
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
- Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Freiburg, Germany
| | - Fabrizio Costa
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
| | - Michael Huber
- Institute of Biochemistry and Molecular Immunology, University Clinic, RWTH Aachen University, Aachen, Germany
| | - Michael Reth
- Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Freiburg, Germany
- Department of Molecular Immunology, Max Planck Institute of Immunology, Freiburg, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
- Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Freiburg, Germany
- Centre for Biological Systems Analysis (ZBSA), University of Freiburg, Freiburg, Germany
- Center for non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark
- * E-mail:
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