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Vicario R, Fragkogianni S, Weber L, Lazarov T, Hu Y, Hayashi SY, Craddock BP, Socci ND, Alberdi A, Baako A, Ay O, Ogishi M, Lopez-Rodrigo E, Kappagantula R, Viale A, Iacobuzio-Donahue CA, Zhou T, Ransohoff RM, Chesworth R, Bank NB, Abdel-Wahab O, Boisson B, Elemento O, Casanova JL, Miller WT, Geissmann F. A microglia clonal inflammatory disorder in Alzheimer's Disease. bioRxiv 2024:2024.01.25.577216. [PMID: 38328106 PMCID: PMC10849735 DOI: 10.1101/2024.01.25.577216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Somatic genetic heterogeneity resulting from post-zygotic DNA mutations is widespread in human tissues and can cause diseases, however few studies have investigated its role in neurodegenerative processes such as Alzheimer's Disease (AD). Here we report the selective enrichment of microglia clones carrying pathogenic variants, that are not present in neuronal, glia/stromal cells, or blood, from patients with AD in comparison to age-matched controls. Notably, microglia-specific AD-associated variants preferentially target the MAPK pathway, including recurrent CBL ring-domain mutations. These variants activate ERK and drive a microglia transcriptional program characterized by a strong neuro-inflammatory response, both in vitro and in patients. Although the natural history of AD-associated microglial clones is difficult to establish in human, microglial expression of a MAPK pathway activating variant was previously shown to cause neurodegeneration in mice, suggesting that AD-associated neuroinflammatory microglial clones may contribute to the neurodegenerative process in patients.
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Affiliation(s)
- Rocio Vicario
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Stamatina Fragkogianni
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Leslie Weber
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Tomi Lazarov
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Yang Hu
- Department of Physiology and Biophysics, Institute for Compxutational Biomedicine,Weill Cornell New York, NY 10021, USA
| | - Samantha Y. Hayashi
- Department of Physiology and Biophysics, Stony Brook University School of Medicine, Stony Brook, NY, 11794-8661
| | - Barbara P. Craddock
- Department of Physiology and Biophysics, Stony Brook University School of Medicine, Stony Brook, NY, 11794-8661
| | - Nicholas D. Socci
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Araitz Alberdi
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Ann Baako
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Oyku Ay
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Masato Ogishi
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, 10065 NY, USA
| | - Estibaliz Lopez-Rodrigo
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Rajya Kappagantula
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Agnes Viale
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Christine A. Iacobuzio-Donahue
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Ting Zhou
- SKI Stem Cell Research Core, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | | | | | | | - Omar Abdel-Wahab
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Bertrand Boisson
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, 10065 NY, USA
| | - Olivier Elemento
- Department of Physiology and Biophysics, Institute for Compxutational Biomedicine,Weill Cornell New York, NY 10021, USA
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, 10065 NY, USA
| | - W. Todd Miller
- Department of Physiology and Biophysics, Stony Brook University School of Medicine, Stony Brook, NY, 11794-8661
| | - Frederic Geissmann
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
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Kim Y, Miller WT. Contrasting Effects of Cancer-Associated Mutations in EphA3 and EphB2 Kinases. Biochemistry 2024. [PMID: 38252844 DOI: 10.1021/acs.biochem.3c00674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Erythropoietin-producing hepatoma (Eph) receptors are a family of tyrosine kinases that can act as tumor promoters or tumor suppressors, depending on the receptor and cancer cell type. Cancer-associated somatic mutations have been identified in all Eph receptors, but in most cases, the functional effects of the mutations are unknown. In this study, we expressed and purified the kinase domains of wild-type (WT) EphA3 and EphB2 along with 16 cancer-associated mutants. We identified mutations that decrease EphA3 activity and both activating and inhibitory mutations in EphB2. To shed light on the mechanisms by which the mutations altered kinase activity, we measured the thermal stabilities of the enzymes and performed steady-state kinetic experiments. We also expressed the full-length receptors in HEK293T cells to determine the cellular effects. WT EphB2 promoted downstream ERK signaling, while a kinase-inactive mutant (S706F) was similar to the control cells. In contrast, WT EphA3 (but not loss-of-function mutants) inhibited ERK signaling. The reciprocal effects of EphB2 and EphA3 on ERK phosphorylation in HEK293T cells were also evident in Ras-GTP loading. Thus, consistent with the dual roles of Eph receptors as tumor promoters and tumor suppressors, somatic mutations have the potential to increase or decrease Eph function, resulting in changes in the downstream signaling transduction.
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Affiliation(s)
- Yunyoung Kim
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York 11794, United States
| | - W Todd Miller
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York 11794, United States
- Department of Veterans Affairs Medical Center, Northport, New York 11768, United States
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Benedet PO, Safikhan NS, Pereira MJ, Lum BM, Botezelli JD, Kuo CH, Wu HL, Craddock BP, Miller WT, Eriksson JW, Yue JTY, Conway EM. CD248 promotes insulin resistance by binding to the insulin receptor and dampening its insulin-induced autophosphorylation. EBioMedicine 2024; 99:104906. [PMID: 38061240 PMCID: PMC10750038 DOI: 10.1016/j.ebiom.2023.104906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 11/24/2023] [Accepted: 11/25/2023] [Indexed: 12/29/2023] Open
Abstract
BACKGROUND In spite of new treatments, the incidence of type 2 diabetes (T2D) and its morbidities continue to rise. The key feature of T2D is resistance of adipose tissue and other organs to insulin. Approaches to overcome insulin resistance are limited due to a poor understanding of the mechanisms and inaccessibility of drugs to relevant intracellular targets. We previously showed in mice and humans that CD248, a pre/adipocyte cell surface glycoprotein, acts as an adipose tissue sensor that mediates the transition from healthy to unhealthy adipose, thus promoting insulin resistance. METHODS Molecular mechanisms by which CD248 regulates insulin signaling were explored using in vivo insulin clamp studies and biochemical analyses of cells/tissues from CD248 knockout (KO) and wild-type (WT) mice with diet-induced insulin resistance. Findings were validated with human adipose tissue specimens. FINDINGS Genetic deletion of CD248 in mice, overcame diet-induced insulin resistance with improvements in glucose uptake and lipolysis in white adipose tissue depots, effects paralleled by increased adipose/adipocyte GLUT4, phosphorylated AKT and GSK3β, and reduced ATGL. The insulin resistance of the WT mice could be attributed to direct interaction of the extracellular domains of CD248 and the insulin receptor (IR), with CD248 acting to block insulin binding to the IR. This resulted in dampened insulin-mediated autophosphorylation of the IR, with reduced downstream signaling/activation of intracellular events necessary for glucose and lipid homeostasis. INTERPRETATION Our discovery of a cell-surface CD248-IR complex that is accessible to pharmacologic intervention, opens research avenues toward development of new agents to prevent/reverse insulin resistance. FUNDING Funded by Canadian Institutes of Health Research (CIHR), Natural Sciences and Engineering Research Council of Canada (NSERC), Canada Foundations for Innovation (CFI), the Swedish Diabetes Foundation, Family Ernfors Foundation and Novo Nordisk Foundation.
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Affiliation(s)
- Patricia O Benedet
- Centre for Blood Research, Life Sciences Institute, Faculty of Medicine, University of British Columbia, Vancouver, Canada; Departments of Medicine and Pathology and Laboratory Medicine, Life Sciences Institute, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Nooshin S Safikhan
- Centre for Blood Research, Life Sciences Institute, Faculty of Medicine, University of British Columbia, Vancouver, Canada; Departments of Medicine and Pathology and Laboratory Medicine, Life Sciences Institute, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Maria J Pereira
- Department of Medical Sciences, Clinical Diabetology & Metabolism, Uppsala University, Sweden
| | - Bryan M Lum
- Department of Physiology, Alberta Diabetes Institute and Group on Molecular and Cell Biology of Lipids, University of Alberta, Canada
| | - José Diego Botezelli
- Centre for Blood Research, Life Sciences Institute, Faculty of Medicine, University of British Columbia, Vancouver, Canada; Departments of Medicine and Pathology and Laboratory Medicine, Life Sciences Institute, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Cheng-Hsiang Kuo
- International Center for Wound Repair and Regeneration, National Cheng Kung University, Tainan, Taiwan
| | - Hua-Lin Wu
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Barbara P Craddock
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY, USA
| | - W Todd Miller
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY, USA; Veterans Affairs Medical Center, Northport, NY, USA
| | - Jan W Eriksson
- Department of Medical Sciences, Clinical Diabetology & Metabolism, Uppsala University, Sweden
| | - Jessica T Y Yue
- Department of Physiology, Alberta Diabetes Institute and Group on Molecular and Cell Biology of Lipids, University of Alberta, Canada
| | - Edward M Conway
- Centre for Blood Research, Life Sciences Institute, Faculty of Medicine, University of British Columbia, Vancouver, Canada; Departments of Medicine and Pathology and Laboratory Medicine, Life Sciences Institute, Faculty of Medicine, University of British Columbia, Vancouver, Canada.
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Krishnan H, Ahmed S, Hubbard SR, Miller WT. Biochemical characterization of the Drosophila insulin receptor kinase and longevity-associated mutants. FASEB J 2024; 38:e23355. [PMID: 38071609 DOI: 10.1096/fj.202301948r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/13/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023]
Abstract
Drosophila melanogaster (fruit fly) insulin receptor (D-IR) is highly homologous to the human counterpart. Like the human pathway, D-IR responds to numerous insulin-like peptides to activate cellular signals that regulate growth, development, and lipid metabolism in fruit flies. Allelic mutations in the D-IR kinase domain elevate life expectancy in fruit flies. We developed a robust heterologous expression system to express and purify wild-type and longevity-associated mutant D-IR kinase domains to investigate enzyme kinetics and substrate specificities. D-IR exhibits remarkable similarities to the human insulin receptor kinase domain but diverges in substrate preferences. We show that longevity-associated mutations reduce D-IR catalytic activity. Deletion of the unique kinase insert domain portion or mutations proximal to activating tyrosines do not influence kinase activity, suggesting their potential role in substrate recruitment and downstream signaling. Through biochemical investigations, this study enhances our comprehension of D-IR's role in Drosophila physiology, complementing genetic studies and expanding our knowledge on the catalytic functions of this conserved signaling pathway.
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Affiliation(s)
- Harini Krishnan
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Sultan Ahmed
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Stevan R Hubbard
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York, USA
| | - W Todd Miller
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, New York, USA
- Department of Veterans Affairs Medical Center, Northport, New York, USA
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Hayashi SY, Craddock BP, Miller WT. Phosphorylation of Ack1 by the Receptor Tyrosine Kinase Mer. Kinases Phosphatases 2023; 1:167-180. [PMID: 37662484 PMCID: PMC10473914 DOI: 10.3390/kinasesphosphatases1030011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Ack1 is a nonreceptor tyrosine kinase that is associated with cellular proliferation and survival. The receptor tyrosine kinase Mer, a member of the TAM family of receptors, has previously been reported to be an upstream activator of Ack1 kinase. The mechanism linking the two kinases, however, has not been investigated. We confirmed that Ack1 and Mer interact by co-immunoprecipitation experiments and found that Mer expression led to increased Ack1 activity. The effect on Ack1 was dependent on the kinase activity of Mer, whereas mutation of the Mer C-terminal tyrosines Y867 and Y924 did not significantly decrease the ability of Mer to activate Ack1. Ack1 possesses a Mig6 Homology Region (MHR) that contains adjacent regulatory tyrosines (Y859 and Y860). Using synthetic peptides, we showed that Mer preferentially binds and phosphorylates the MHR sequence containing phosphorylated pY860, as compared to the pY859 sequence. This suggested the possibility of sequential phosphorylation within the MHR of Ack1, as has been observed previously for other kinases. In cells co-expressing Mer and Ack1 MHR mutants, the Y859F mutant had higher activity than the Y860F mutant, consistent with this model. The interaction between Mer and Ack1 could play a role in immune cell signaling in normal physiology and could also contribute to the hyperactivation of Ack1 in prostate cancer and other tumors.
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Affiliation(s)
- Samantha Y. Hayashi
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Barbara P. Craddock
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY 11794, USA
| | - W. Todd Miller
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY 11794, USA
- Department of Veterans Affairs Medical Center, Northport, NY 11768, USA
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Kim Y, Ahmed S, Miller WT. Colorectal cancer-associated mutations impair EphB1 kinase function. J Biol Chem 2023; 299:105115. [PMID: 37527777 PMCID: PMC10463257 DOI: 10.1016/j.jbc.2023.105115] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/03/2023] Open
Abstract
Erythropoietin-producing hepatoma (Eph) receptor tyrosine kinases regulate the migration and adhesion of cells that are required for many developmental processes and adult tissue homeostasis. In the intestinal epithelium, Eph signaling controls the positioning of cell types along the crypt-villus axis. Eph activity can suppress the progression of colorectal cancer (CRC). The most frequently mutated Eph receptor in metastatic CRC is EphB1. However, the functional effects of EphB1 mutations are mostly unknown. We expressed and purified the kinase domains of WT and five cancer-associated mutant EphB1 and developed assays to assess the functional effects of the mutations. Using purified proteins, we determined that CRC-associated mutations reduce the activity and stability of the folded structure of EphB1. By mammalian cell expression, we determined that CRC-associated mutant EphB1 receptors inhibit signal transducer and activator of transcription 3 and extracellular signal-regulated kinases 1 and 2 signaling. In contrast to the WT, the mutant EphB1 receptors are unable to suppress the migration of human CRC cells. The CRC-associated mutations also impair cell compartmentalization in an assay in which EphB1-expressing cells are cocultured with ligand (ephrin B1)-expressing cells. These results suggest that somatic mutations impair the kinase-dependent tumor suppressor function of EphB1 in CRC.
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Affiliation(s)
- Yunyoung Kim
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York, USA
| | - Sultan Ahmed
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York, USA
| | - W Todd Miller
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York, USA; Department of Veterans Affairs Medical Center, Northport, New York, USA.
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Kan Y, Paung Y, Kim Y, Seeliger MA, Miller WT. Biochemical Studies of Systemic Lupus Erythematosus-Associated Mutations in Nonreceptor Tyrosine Kinases Ack1 and Brk. Biochemistry 2023; 62:1124-1137. [PMID: 36854171 PMCID: PMC10052838 DOI: 10.1021/acs.biochem.2c00685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Tyrosine kinases (TKs) play essential roles in signaling processes that regulate cell survival, migration, and proliferation. Dysregulation of tyrosine kinases underlies many disorders, including cancer, cardiovascular and developmental diseases, as well as pathologies of the immune system. Ack1 and Brk are nonreceptor tyrosine kinases (NRTKs) best known for their roles in cancer. Here, we have biochemically characterized novel Ack1 and Brk mutations identified in patients with systemic lupus erythematosus (SLE). These mutations are the first SLE-linked polymorphisms found among NRTKs. We show that two of the mutants are catalytically inactive, while the other three have reduced activity. To understand the structural changes associated with the loss-of-function phenotype, we solved the crystal structure of one of the Ack1 kinase mutants, K161Q. Furthermore, two of the mutated residues (Ack1 A156 and K161) critical for catalytic activity are highly conserved among other TKs, and their substitution in other members of the kinase family could have implications in cancer. In contrast to canonical gain-of-function mutations in TKs observed in many cancers, we report loss-of-function mutations in Ack1 and Brk, highlighting the complexity of TK involvement in human diseases.
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Affiliation(s)
- Yagmur Kan
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, New York 11794-8661, United States
| | - YiTing Paung
- Department of Pharmacology, School of Medicine, Stony Brook University, Stony Brook, New York 11794-8661, United States
| | - Yunyoung Kim
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, New York 11794-8661, United States
| | - Markus A Seeliger
- Department of Pharmacology, School of Medicine, Stony Brook University, Stony Brook, New York 11794-8661, United States
| | - W Todd Miller
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, New York 11794-8661, United States
- Department of Veterans Affairs Medical Center, Northport, New York 11768, United States
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Kan Y, Paung Y, Seeliger MA, Miller WT. Domain Architecture of the Nonreceptor Tyrosine Kinase Ack1. Cells 2023; 12:900. [PMID: 36980241 PMCID: PMC10047419 DOI: 10.3390/cells12060900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/09/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023] Open
Abstract
The nonreceptor tyrosine kinase (NRTK) Ack1 comprises a distinct arrangement of non-catalytic modules. Its SH3 domain has a C-terminal to the kinase domain (SH1), in contrast to the typical SH3-SH2-SH1 layout in NRTKs. The Ack1 is the only protein that shares a region of high homology to the tumor suppressor protein Mig6, a modulator of EGFR. The vertebrate Acks make up the only tyrosine kinase (TK) family known to carry a UBA domain. The GTPase binding and SAM domains are also uncommon in the NRTKs. In addition to being a downstream effector of receptor tyrosine kinases (RTKs) and integrins, Ack1 can act as an epigenetic regulator, modulate the degradation of the epidermal growth factor receptor (EGFR), confer drug resistance, and mediate the progression of hormone-sensitive tumors. In this review, we discuss the domain architecture of Ack1 in relation to other protein kinases that possess such defined regulatory domains.
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Affiliation(s)
- Yagmur Kan
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, NY 11794-8661, USA
| | - YiTing Paung
- Department of Pharmacology, School of Medicine, Stony Brook University, Stony Brook, NY 11794-8661, USA
| | - Markus A. Seeliger
- Department of Pharmacology, School of Medicine, Stony Brook University, Stony Brook, NY 11794-8661, USA
| | - W. Todd Miller
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, NY 11794-8661, USA
- Department of Veterans Affairs Medical Center, Northport, NY 11768-2200, USA
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9
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Collins SJ, Guo J, Rizzo RC, Miller WT. Inhibition of mutationally activated HER2. Chem Biol Drug Des 2023; 101:87-102. [PMID: 36029027 PMCID: PMC9879383 DOI: 10.1111/cbdd.14125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/24/2022] [Accepted: 07/30/2022] [Indexed: 01/28/2023]
Abstract
Human epidermal growth factor receptor 2 (HER2) is an oncogenic driver and key therapeutic target for human cancers. Current therapies targeting HER2 are primarily based on overexpression of the wild-type form of HER2. However, kinase domain mutations have been identified that can increase the activity of HER2 even when expressed at basal levels. Using purified enzymes, we confirmed the hyperactivity of two HER2 mutants (D769Y and P780insGSP). To identify small molecule inhibitors against these cancer-associated variants, we used a combined approach consisting of biochemical testing, similarity-based searching, and in silico modeling. These approaches resulted in the identification of a candidate molecule that inhibits mutant forms of HER2 in vitro and in cell-based assays. Our structural model predicts that the compound takes advantage of water-mediated interactions in the HER2 kinase binding pocket.
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Affiliation(s)
- Stephen J. Collins
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York, USA
| | - Jiaye Guo
- Department of Applied Mathematics & Statistics, Stony Brook University, Stony Brook, New York, USA
| | - Robert C. Rizzo
- Department of Applied Mathematics & Statistics, Stony Brook University, Stony Brook, New York, USA,Laufer Center for Physical & Quantitative Biology, Stony Brook University, Stony Brook, New York, USA,Institute of Chemical Biology & Drug Discovery, Stony Brook University, Stony Brook, New York, USA
| | - W. Todd Miller
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York, USA,Institute of Chemical Biology & Drug Discovery, Stony Brook University, Stony Brook, New York, USA,Department of Veterans Affairs Medical Center, Northport, New York, USA
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10
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Sridaran D, Chouhan S, Mahajan K, Renganathan A, Weimholt C, Bhagwat S, Reimers M, Kim EH, Thakur MK, Saeed MA, Pachynski RK, Seeliger MA, Miller WT, Feng FY, Mahajan NP. Inhibiting ACK1-mediated phosphorylation of C-terminal Src kinase counteracts prostate cancer immune checkpoint blockade resistance. Nat Commun 2022; 13:6929. [PMID: 36376335 PMCID: PMC9663509 DOI: 10.1038/s41467-022-34724-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/04/2022] [Indexed: 11/16/2022] Open
Abstract
Solid tumours are highly refractory to immune checkpoint blockade (ICB) therapies due to the functional impairment of effector T cells and their inefficient trafficking to tumours. T-cell activation is negatively regulated by C-terminal Src kinase (CSK); however, the exact mechanism remains unknown. Here we show that the conserved oncogenic tyrosine kinase Activated CDC42 kinase 1 (ACK1) is able to phosphorylate CSK at Tyrosine 18 (pY18), which enhances CSK function, constraining T-cell activation. Mice deficient in the Tnk2 gene encoding Ack1, are characterized by diminished CSK Y18-phosphorylation and spontaneous activation of CD8+ and CD4+ T cells, resulting in inhibited growth of transplanted ICB-resistant tumours. Furthermore, ICB treatment of castration-resistant prostate cancer (CRPC) patients results in re-activation of ACK1/pY18-CSK signalling, confirming the involvement of this pathway in ICB insensitivity. An ACK1 small-molecule inhibitor, (R)-9b, recapitulates inhibition of ICB-resistant tumours, which provides evidence for ACK1 enzymatic activity playing a pivotal role in generating ICB resistance. Overall, our study identifies an important mechanism of ICB resistance and holds potential for expanding the scope of ICB therapy to tumours that are currently unresponsive.
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Affiliation(s)
- Dhivya Sridaran
- Department of Surgery, Washington University at St Louis, St Louis, MO, 63110, USA
- Division of Urologic Surgery, Washington University at St Louis, St Louis, MO, 63110, USA
| | - Surbhi Chouhan
- Department of Surgery, Washington University at St Louis, St Louis, MO, 63110, USA
- Division of Urologic Surgery, Washington University at St Louis, St Louis, MO, 63110, USA
| | - Kiran Mahajan
- Department of Surgery, Washington University at St Louis, St Louis, MO, 63110, USA
- Division of Urologic Surgery, Washington University at St Louis, St Louis, MO, 63110, USA
- Siteman Cancer Center, Washington University at St Louis, St Louis, MO, 63110, USA
| | - Arun Renganathan
- Department of Surgery, Washington University at St Louis, St Louis, MO, 63110, USA
- Division of Urologic Surgery, Washington University at St Louis, St Louis, MO, 63110, USA
| | - Cody Weimholt
- Department of Surgery, Washington University at St Louis, St Louis, MO, 63110, USA
- Division of Oncology, Department of Medicine, Washington University at St Louis, St Louis, MO, 63110, USA
- Anatomic and Clinical Pathology, Washington University at St Louis, St Louis, MO, 63110, USA
| | - Shambhavi Bhagwat
- Department of Surgery, Washington University at St Louis, St Louis, MO, 63110, USA
- Division of Urologic Surgery, Washington University at St Louis, St Louis, MO, 63110, USA
| | - Melissa Reimers
- Siteman Cancer Center, Washington University at St Louis, St Louis, MO, 63110, USA
- Division of Oncology, Department of Medicine, Washington University at St Louis, St Louis, MO, 63110, USA
| | - Eric H Kim
- Department of Surgery, Washington University at St Louis, St Louis, MO, 63110, USA
- Division of Urologic Surgery, Washington University at St Louis, St Louis, MO, 63110, USA
| | - Manish K Thakur
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Muhammad A Saeed
- Siteman Cancer Center, Washington University at St Louis, St Louis, MO, 63110, USA
| | - Russell K Pachynski
- Siteman Cancer Center, Washington University at St Louis, St Louis, MO, 63110, USA
- Division of Oncology, Department of Medicine, Washington University at St Louis, St Louis, MO, 63110, USA
| | - Markus A Seeliger
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, 11794, USA
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, NY, 11794, USA
| | - W Todd Miller
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, NY, 11794, USA
- Department of Veterans Affairs Medical Center, Northport, NY, 11768, USA
| | - Felix Y Feng
- Department of Radiation Oncology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, CA, USA
| | - Nupam P Mahajan
- Department of Surgery, Washington University at St Louis, St Louis, MO, 63110, USA.
- Division of Urologic Surgery, Washington University at St Louis, St Louis, MO, 63110, USA.
- Siteman Cancer Center, Washington University at St Louis, St Louis, MO, 63110, USA.
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11
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Kan Y, Miller WT. Activity of the nonreceptor tyrosine kinase Ack1 is regulated by tyrosine phosphorylation of its Mig6 homology region. FEBS Lett 2022; 596:2808-2820. [PMID: 36178070 PMCID: PMC9879303 DOI: 10.1002/1873-3468.14505] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/19/2022] [Indexed: 01/28/2023]
Abstract
Ack1 is a proto-oncogenic tyrosine kinase with homology to the tumour suppressor Mig6, an inhibitor of the epidermal growth factor receptor (EGFR). The residues critical for binding of Mig6 to EGFR are conserved within the Mig6 homology region (MHR) of Ack1. We tested whether intramolecular interactions between the Ack1 MHR and kinase domain (KD) are regulated by phosphorylation. We identified two Src phosphorylation sites within the MHR (Y859, Y860). Addition of Src-phosphorylated MHR to the Ack1 KD enhanced enzymatic activity. Co-expression of Src in cells led to increased Ack1 activity; mutation of Y859/Y860 blocked this increase. Collectively, the data suggest that phosphorylation of the Ack1 MHR regulates its kinase activity. Phosphorylation of Y859/Y860 occurs in cancers of the brain, breast, colon, and prostate, where genomic amplification or somatic mutations of Ack1 play a role in disease progression. Our findings suggest that MHR phosphorylation could contribute to Ack1 dysregulation in tumours.
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Affiliation(s)
- Yağmur Kan
- Department of Physiology and Biophysics, School of Medicine Stony Brook University NY USA
| | - W. Todd Miller
- Department of Physiology and Biophysics, School of Medicine Stony Brook University NY USA
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12
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Suresh P, Miller WT, London E. Effect of MαCD-mediated phospholipid exchange on plasma membrane ordered lipid domain stability. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.1866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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13
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Suresh P, Miller WT, London E. Phospholipid exchange shows insulin receptor activity is supported by both the propensity to form wide bilayers and ordered raft domains. J Biol Chem 2021; 297:101010. [PMID: 34324831 PMCID: PMC8379460 DOI: 10.1016/j.jbc.2021.101010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 11/29/2022] Open
Abstract
Insulin receptor (IR) is a membrane tyrosine kinase that mediates the response of cells to insulin. IR activity has been shown to be modulated by changes in plasma membrane lipid composition, but the properties and structural determinants of lipids mediating IR activity are poorly understood. Here, using efficient methyl-alpha-cyclodextrin mediated lipid exchange, we studied the effect of altering plasma membrane outer leaflet phospholipid composition upon the activity of IR in mammalian cells. After substitution of endogenous lipids with lipids having an ability to form liquid ordered (Lo) domains (sphingomyelins) or liquid disordered (Ld) domains (unsaturated phosphatidylcholines (PCs)), we found that the propensity of lipids to form ordered domains is required for high IR activity. Additional substitution experiments using a series of saturated PCs showed that IR activity increased substantially with increasing acyl chain length, which increases both bilayer width and the propensity to form ordered domains. Incorporating purified IR into alkyl maltoside micelles with increasing hydrocarbon lengths also increased IR activity, but more modestly than by increasing lipid acyl chain length in cells. These results suggest that the ability to form Lo domains as well as wide bilayer width contributes to increased IR activity. Inhibition of phosphatases showed that some of the lipid dependence of IR activity upon lipid structure reflected protection from phosphatases by lipids that support Lo domain formation. These results are consistent with a model in which a combination of bilayer width and ordered domain formation modulates IR activity via IR conformation and accessibility to phosphatases.
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Affiliation(s)
- Pavana Suresh
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, USA
| | - W Todd Miller
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York, USA; Department of Veterans Affairs Medical Center, Northport, New York, USA
| | - Erwin London
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, USA.
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14
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Tapia L, Solozabal N, Solà J, Pérez Y, Miller WT, Alfonso I. Cover Feature: Modulation of Src Kinase Activity by Selective Substrate Recognition with Pseudopeptidic Cages (Chem. Eur. J. 37/2021). Chemistry 2021. [DOI: 10.1002/chem.202101933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Lucía Tapia
- Department of Biological Chemistry Institute for Advanced Chemistry of Catalonia, IQAC-CSIC Jordi Girona 18–26 08034 Barcelona Spain
| | - Naiara Solozabal
- NMR Facility Institute for Advanced Chemistry of Catalonia, IQAC-CSIC Jordi Girona 18–26 08034 Barcelona Spain
| | - Jordi Solà
- Department of Biological Chemistry Institute for Advanced Chemistry of Catalonia, IQAC-CSIC Jordi Girona 18–26 08034 Barcelona Spain
| | - Yolanda Pérez
- NMR Facility Institute for Advanced Chemistry of Catalonia, IQAC-CSIC Jordi Girona 18–26 08034 Barcelona Spain
| | - W. Todd Miller
- Department of Physiology and Biophysics Stony Brook University and Department of Veterans Affairs Medical Center Stony Brook NY, 11794 USA
| | - Ignacio Alfonso
- Department of Biological Chemistry Institute for Advanced Chemistry of Catalonia, IQAC-CSIC Jordi Girona 18–26 08034 Barcelona Spain
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15
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Tapia L, Solozabal N, Solà J, Pérez Y, Miller WT, Alfonso I. Modulation of Src Kinase Activity by Selective Substrate Recognition with Pseudopeptidic Cages. Chemistry 2021; 27:9542-9549. [PMID: 33904620 PMCID: PMC8362067 DOI: 10.1002/chem.202100990] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Indexed: 12/15/2022]
Abstract
The selective recognition of tyrosine residues in peptides is an appealing approach to inhibiting their tyrosine kinase (TK)-mediated phosphorylation. Herein, we describe pseudopeptidic cages that efficiently protect substrates from the action of the Src TK enzyme, precluding the corresponding Tyr phosphorylation. Fluorescence emission titrations show that the most efficient cage inhibitors strongly bind the peptide substrates with a very good correlation between the binding constant and the inhibitory potency. Structural insights and additional control experiments further support the proposed mechanism of selective supramolecular protection of the substrates. Moreover, the approach also works in a completely different kinase-substrate system. These results illustrate the potential of supramolecular complexes for the efficient and selective modulation of TK signaling.
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Affiliation(s)
- Lucía Tapia
- Department of Biological ChemistryInstitute for Advanced Chemistry of Catalonia, IQAC-CSICJordi Girona 18–2608034BarcelonaSpain
| | - Naiara Solozabal
- NMR FacilityInstitute for Advanced Chemistry of Catalonia, IQAC-CSICJordi Girona 18–2608034BarcelonaSpain
| | - Jordi Solà
- Department of Biological ChemistryInstitute for Advanced Chemistry of Catalonia, IQAC-CSICJordi Girona 18–2608034BarcelonaSpain
| | - Yolanda Pérez
- NMR FacilityInstitute for Advanced Chemistry of Catalonia, IQAC-CSICJordi Girona 18–2608034BarcelonaSpain
| | - W. Todd Miller
- Department of Physiology and BiophysicsStony Brook University and Department of Veterans Affairs Medical CenterStony BrookNY, 11794USA
| | - Ignacio Alfonso
- Department of Biological ChemistryInstitute for Advanced Chemistry of Catalonia, IQAC-CSICJordi Girona 18–2608034BarcelonaSpain
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16
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Suresh P, Miller WT, London E. Modulation of Insulin Receptor Activity Upon Plasma Membrane Sterol and Phospholipid Substitutions to Alter Lipid Domain Formation. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.2059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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17
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Abstract
Homologous enzymes from different species display functional characteristics that correlate with the physiological and environmental temperatures encountered by the organisms. In this study, we have investigated the temperature sensitivity of the nonreceptor tyrosine kinase Src. We compared the temperature dependencies of c-Src and two Src kinases from single-celled eukaryotes, the choanoflagellate Monosiga brevicollis and the filasterean Capsaspora owczarzaki. Metazoan c-Src exhibits temperature sensitivity, with high activity at 30 °C and 37 °C. This sensitivity is driven by changes in substrate binding as well as maximal velocity, and it is dependent on the amino acid sequence surrounding tyrosine in the substrate. When tested with a peptide that displays temperature-dependent phosphorylation by c-Src, the enzymatic rates for the unicellular Src kinases show much less variation over the temperatures tested. The data demonstrate that unicellular Src kinases are temperature compensated relative to metazoan c-Src, consistent with an evolutionary adaptation to their environments.
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Affiliation(s)
- W. Todd Miller
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY, 11794, USA
- Department of Veterans Affairs Medical Center, Northport, NY, 11768, USA
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18
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Abstract
Src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristoylation sites (SRMS) is a tyrosine kinase that was discovered in 1994. It is a member of a family of nonreceptor tyrosine kinases that also includes Brk (PTK6) and Frk. Compared with other tyrosine kinases, there is relatively little information about the structure, function, and regulation of SRMS. In this review, we summarize the current state of knowledge regarding SRMS, including recent results aimed at identifying downstream signaling partners. We also present a structural model for the enzyme and discuss the potential involvement of SRMS in cancer cell signaling.
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Affiliation(s)
- Chakia J. McClendon
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY 11794-8661, USA;
| | - W. Todd Miller
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY 11794-8661, USA;
- Department of Veterans Affairs Medical Center, Northport, NY 11768, USA
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19
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Suresh P, London E, Miller WT. Modulation of Insulin Receptor Kinase Activity by Lipid Environment. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.1417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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20
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Joshi MK, Burton RA, Wu H, Lipchik AM, Craddock BP, Mo H, Parker LL, Miller WT, Post CB. Substrate binding to Src: A new perspective on tyrosine kinase substrate recognition from NMR and molecular dynamics. Protein Sci 2019; 29:350-359. [PMID: 31697410 DOI: 10.1002/pro.3777] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 11/04/2019] [Accepted: 11/05/2019] [Indexed: 01/01/2023]
Abstract
Most signal transduction pathways in humans are regulated by protein kinases through phosphorylation of their protein substrates. Typical eukaryotic protein kinases are of two major types: those that phosphorylate-specific sequences containing tyrosine (~90 kinases) and those that phosphorylate either serine or threonine (~395 kinases). The highly conserved catalytic domain of protein kinases comprises a smaller N lobe and a larger C lobe separated by a cleft region lined by the activation loop. Prior studies find that protein tyrosine kinases recognize peptide substrates by binding the polypeptide chain along the C-lobe on one side of the activation loop, while serine/threonine kinases bind their substrates in the cleft and on the side of the activation loop opposite to that of the tyrosine kinases. Substrate binding structural studies have been limited to four families of the tyrosine kinase group, and did not include Src tyrosine kinases. We examined peptide-substrate binding to Src using paramagnetic-relaxation-enhancement NMR combined with molecular dynamics simulations. The results suggest Src tyrosine kinase can bind substrate positioning residues C-terminal to the phosphoacceptor residue in an orientation similar to serine/threonine kinases, and unlike other tyrosine kinases. Mutagenesis corroborates this new perspective on tyrosine kinase substrate recognition. Rather than an evolutionary split between tyrosine and serine/threonine kinases, a change in substrate recognition may have occurred within the TK group of the human kinome. Protein tyrosine kinases have long been therapeutic targets, but many marketed drugs have deleterious off-target effects. More accurate knowledge of substrate interactions of tyrosine kinases has the potential for improving drug selectivity.
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Affiliation(s)
- Mehul K Joshi
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana
| | - Robert A Burton
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana.,Ancestry, Lehi, Utah
| | - Heng Wu
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana
| | - Andrew M Lipchik
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana
| | - Barbara P Craddock
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, New York
| | - Huaping Mo
- Purdue Interdepartmental NMR Facility PINMRF, Purdue University, West Lafayette, Indiana
| | - Laurie L Parker
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana
| | - W Todd Miller
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, New York.,Department of Veterans Affairs Medical Center, Northport, New York
| | - Carol Beth Post
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana
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21
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Delle Bovi RJ, Kim J, Suresh P, London E, Miller WT. Sterol structure dependence of insulin receptor and insulin-like growth factor 1 receptor activation. Biochim Biophys Acta Biomembr 2019; 1861:819-826. [PMID: 30682326 DOI: 10.1016/j.bbamem.2019.01.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 12/21/2018] [Accepted: 01/21/2019] [Indexed: 01/02/2023]
Abstract
The plasma membrane is a dynamic environment with a complex composition of lipids, proteins, and cholesterol. Areas enriched in cholesterol and sphingolipids are believed to form lipid rafts, domains of highly ordered lipids. The unique physical properties of these domains have been proposed to influence many cellular processes. Here, we demonstrate that the activation of insulin receptor (IR) and insulin-like growth factor 1 receptor (IGF1R) depends critically on the structures of membrane sterols. IR and IGF1R autophosphorylation in vivo was inhibited by cholesterol depletion, and autophosphorylation was restored by the replacement with exogenous cholesterol. We next screened a variety of sterols for effects on IR activation. The ability of sterols to support IR autophosphorylation was strongly correlated to the propensity of the sterols to form ordered domains. IR autophosphorylation was fully restored by the incorporation of ergosterol, dihydrocholesterol, 7-dehydrocholesterol, lathosterol, desmosterol, and allocholesterol, partially restored by epicholesterol, and not restored by lanosterol, coprostanol, and 4-cholesten-3-one. These data support the hypothesis that the ability to form ordered domains is sufficient for a sterol to support ligand-induced activation of IR and IGF1R in intact mammalian cells.
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Affiliation(s)
- Richard J Delle Bovi
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY 11794-8661, United States of America
| | - JiHyun Kim
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, United States of America
| | - Pavana Suresh
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, United States of America
| | - Erwin London
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, United States of America.
| | - W Todd Miller
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY 11794-8661, United States of America; Department of Veterans Affairs Medical Center, Northport, NY 11768, United States of America.
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22
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Hanson SM, Georghiou G, Thakur MK, Miller WT, Rest JS, Chodera JD, Seeliger MA. What Makes a Kinase Promiscuous for Inhibitors? Cell Chem Biol 2019; 26:390-399.e5. [PMID: 30612951 DOI: 10.1016/j.chembiol.2018.11.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 09/13/2018] [Accepted: 11/06/2018] [Indexed: 10/27/2022]
Abstract
ATP-competitive kinase inhibitors often bind several kinases due to the high conservation of the ATP binding pocket. Through clustering analysis of a large kinome profiling dataset, we found a cluster of eight promiscuous kinases that on average bind more than five times more kinase inhibitors than the other 398 kinases in the dataset. To understand the structural basis of promiscuous inhibitor binding, we determined the co-crystal structure of the receptor tyrosine kinase DDR1 with the type I inhibitors dasatinib and VX-680. Surprisingly, we find that DDR1 binds these type I inhibitors in an inactive conformation typically reserved for type II inhibitors. Our computational and biochemical studies show that DDR1 is unusually stable in this inactive conformation, giving a mechanistic explanation for inhibitor promiscuity. This phenotypic clustering analysis provides a strategy to obtain functional insights not available by sequence comparison alone.
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Affiliation(s)
- Sonya M Hanson
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794-8651, USA; Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065-1115, USA
| | - George Georghiou
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794-8651, USA
| | - Manish K Thakur
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794-8651, USA
| | - W Todd Miller
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY 11794-8651, USA
| | - Joshua S Rest
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245, USA
| | - John D Chodera
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065-1115, USA.
| | - Markus A Seeliger
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794-8651, USA.
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23
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Krishnan H, Miller WT, Blanco FJ, Goldberg GS. Src and podoplanin forge a path to destruction. Drug Discov Today 2019; 24:241-249. [DOI: 10.1016/j.drudis.2018.07.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 07/18/2018] [Accepted: 07/27/2018] [Indexed: 12/20/2022]
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24
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Guo J, Collins S, Miller WT, Rizzo RC. Identification of a Water-Coordinating HER2 Inhibitor by Virtual Screening Using Similarity-Based Scoring. Biochemistry 2018; 57:4934-4951. [PMID: 29975516 PMCID: PMC6110523 DOI: 10.1021/acs.biochem.8b00524] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
Human
epidermal growth factor receptor 2 (HER2) is a validated
breast cancer drug target for small molecule inhibitors that target
the ATP-binding pocket of the kinase domain. In this work, a large-scale
virtual screen was performed to a novel homology model of HER2, in
a hypothesized “fully active” state, that considered
water-mediated interactions during the prioritization of compounds
for experimental testing. This screen led to the identification of
a new inhibitor with micro molar affinity and potency (Kd = 7.0 μM, IC50 = 4.6 μM). Accompanying
molecular dynamics simulations showed that inhibitor binding likely
involves water coordination through an important water-mediated network
previously identified in our laboratory. The predicted binding geometry
also showed a remarkable overlap with the crystallographic poses for
two previously reported inhibitors of the related Chk1 kinase. Concurrent
with the HER2 studies, we developed formalized computational protocols
that leverage solvated footprints (per-residue interaction maps that
include bridging waters) to identify ligands that can “coordinate”
or “displace” key binding site waters. Proof-of-concept
screens targeting HIVPR and PARP1 demonstrate that molecules with
high footprint overlap can be effectively identified in terms of their
coordination or displacement patterns relative to a known reference.
Overall, the procedures developed as a result of this study should
be useful for researchers targeting HER2 and, more generally, for
any protein in which the identification of compounds that exploit
binding site waters is desirable.
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25
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Delle Bovi RJ, Miller WT. Expression and purification of functional insulin and insulin-like growth factor 1 holoreceptors from mammalian cells. Anal Biochem 2017; 536:69-77. [PMID: 28830678 PMCID: PMC5701837 DOI: 10.1016/j.ab.2017.08.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 08/16/2017] [Accepted: 08/17/2017] [Indexed: 12/25/2022]
Abstract
The insulin receptor (IR) and insulin-like growth factor 1 receptor (IGF1R) are receptor tyrosine kinases (RTKs) involved in the regulation of many important cellular processes. The current proposed models of activation are derived from structural studies using soluble extracellular domains and cytoplasmic tyrosine kinase domains. Preparations of full length IR and IGF1R have been hampered by the need for unconventional affinity chromatography resins and/or harsh eluting conditions. Here, we present a purification protocol to obtain full-length, detergent solubilized IR and IGF1R at quantities suitable for biochemical and structural characterization. We screened a panel of 24 structurally diverse detergents for optimal ligand activation. The receptors purified in n-dodecyl-β-D-maltoside showed ligand-stimulated autophosphorylation and kinase activity, suggesting an intact transmembrane signaling mechanism. This convenient purification protocol can be used to produce high quantities of IR, IGF1R, or other RTKs, and can be adapted for other challenging membrane proteins.
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MESH Headings
- Antigens, CD/genetics
- Antigens, CD/isolation & purification
- Antigens, CD/metabolism
- Chromatography, Affinity
- HEK293 Cells
- Humans
- Receptor, IGF Type 1
- Receptor, Insulin/genetics
- Receptor, Insulin/isolation & purification
- Receptor, Insulin/metabolism
- Receptors, Somatomedin/genetics
- Receptors, Somatomedin/isolation & purification
- Receptors, Somatomedin/metabolism
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Affiliation(s)
- Richard J Delle Bovi
- Department of Physiology and Biophysics, Stony Brook University, NY, United States.
| | - W Todd Miller
- Department of Physiology and Biophysics, Stony Brook University, NY, United States; Department of Veterans Affairs Medical Center, Northport, NY, United States.
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26
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George MD, Shah R, Kreider M, Miller WT, Merkel PA, Werth VP. Pulmonary function tests, interstitial lung disease and lung function decline in outpatients with classic and clinically amyopathic dermatomyositis. Br J Dermatol 2016; 176:262-264. [PMID: 27229750 DOI: 10.1111/bjd.14771] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- M D George
- Division of Rheumatology, University of Pennsylvania, Philadelphia, PA, U.S.A
| | - R Shah
- Division of Pulmonary & Critical Care Medicine, University of Pennsylvania, Philadelphia, PA, U.S.A.,Division of Pulmonary, Allergy, and Critical Care Medicine, University of California, San Francisco, CA, U.S.A
| | - M Kreider
- Division of Pulmonary & Critical Care Medicine, University of Pennsylvania, Philadelphia, PA, U.S.A
| | - W T Miller
- Department of Radiology, University of Pennsylvania, Philadelphia, PA, U.S.A
| | - P A Merkel
- Division of Rheumatology, University of Pennsylvania, Philadelphia, PA, U.S.A.,Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, PA, U.S.A
| | - V P Werth
- Department of Dermatology, University of Pennsylvania and Philadelphia Veterans Affairs Medical Center, Philadelphia, PA, U.S.A
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27
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Aleem S, Georghiou G, Kleiner RE, Guja K, Craddock BP, Lyczek A, Chan AI, Garcia-Diaz M, Miller WT, Liu DR, Seeliger MA. Structural and Biochemical Basis for Intracellular Kinase Inhibition by Src-specific Peptidic Macrocycles. Cell Chem Biol 2016; 23:1103-1112. [PMID: 27593110 DOI: 10.1016/j.chembiol.2016.07.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 07/04/2016] [Accepted: 07/14/2016] [Indexed: 12/12/2022]
Abstract
Protein kinases are attractive therapeutic targets because their dysregulation underlies many diseases, including cancer. The high conservation of the kinase domain and the evolution of drug resistance, however, pose major challenges to the development of specific kinase inhibitors. We recently discovered selective Src kinase inhibitors from a DNA-templated macrocycle library. Here, we reveal the structural basis for how these inhibitors retain activity against a disease-relevant, drug-resistant kinase mutant, while maintaining Src specificity. We find that these macrocycles display a degree of modularity: two of their three variable groups interact with sites on the kinase that confer selectivity, while the third group interacts with the universally conserved catalytic lysine and thereby retains the ability to inhibit the "gatekeeper" kinase mutant. We also show that these macrocycles inhibit migration of MDA-MB-231 breast tumor cells. Our findings establish intracellular kinase inhibition by peptidic macrocycles, and inform the development of potent and specific kinase inhibitors.
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Affiliation(s)
- Saadat Aleem
- Dept. of Physiology and Biophysics, Stony Brook University, Stony Brook, NY 11794-8661, USA
| | - George Georghiou
- Dept. of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794-8651, USA
| | - Ralph E Kleiner
- Dept. of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Kip Guja
- Dept. of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794-8651, USA
| | - Barbara P Craddock
- Dept. of Physiology and Biophysics, Stony Brook University, Stony Brook, NY 11794-8661, USA
| | - Agatha Lyczek
- Dept. of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794-8651, USA
| | - Alix I Chan
- Dept. of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Miguel Garcia-Diaz
- Dept. of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794-8651, USA
| | - W Todd Miller
- Dept. of Physiology and Biophysics, Stony Brook University, Stony Brook, NY 11794-8661, USA
| | - David R Liu
- Dept. of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Markus A Seeliger
- Dept. of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794-8651, USA
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28
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Touchette MH, Bommineni GR, Delle Bovi RJ, Gadbery JE, Nicora CD, Shukla AK, Kyle JE, Metz TO, Martin DW, Sampson NS, Miller WT, Tonge PJ, Seeliger JC. Diacyltransferase Activity and Chain Length Specificity of Mycobacterium tuberculosis PapA5 in the Synthesis of Alkyl β-Diol Lipids. Biochemistry 2015; 54:5457-68. [PMID: 26271001 DOI: 10.1021/acs.biochem.5b00455] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although they are classified as Gram-positive bacteria, Corynebacterineae possess an asymmetric outer membrane that imparts structural and thereby physiological similarity to more distantly related Gram-negative bacteria. Like lipopolysaccharide in Gram-negative bacteria, lipids in the outer membrane of Corynebacterineae have been associated with the virulence of pathogenic species such as Mycobacterium tuberculosis (Mtb). For example, Mtb strains that lack long, branched-chain alkyl esters known as dimycocerosates (DIMs) are significantly attenuated in model infections. The resultant interest in the biosynthetic pathway of these unusual virulence factors has led to the elucidation of many of the steps leading to the final esterification of the alkyl β-diol, phthiocerol, with branched-chain fatty acids known as mycocerosates. PapA5 is an acyltransferase implicated in these final reactions. Here, we show that PapA5 is indeed the terminal enzyme in DIM biosynthesis by demonstrating its dual esterification activity and chain-length preference using synthetic alkyl β-diol substrate analogues. By applying these analogues to a series of PapA5 mutants, we also revise a model for the substrate binding within PapA5. Finally, we demonstrate that the Mtb Ser/Thr kinases PknB and PknE modify PapA5 on three overlapping Thr residues and that a fourth Thr is unique to PknE phosphorylation. These results clarify the DIM biosynthetic pathway and indicate post-translational modifications that warrant further elucidation for their roles in the regulation of DIM biosynthesis.
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Affiliation(s)
| | | | | | | | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | - Anil K Shukla
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | - Jennifer E Kyle
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
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29
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Krishnan H, Ochoa-alvarez J, Shen Y, Nevel E, Kephart D, Nguyen A, Han M, Acharya N, Nagele R, Ramirez M, Miller WT, Kalyoussef E, Baredes S, Fatahzadeh M, Jensen L, Shienbaum A, Goldberg G. Abstract 4375: Podoplanin (PDPN): novel biomarker and chemotherapeutic target. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-4375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Cancer is a leading cause of death. In fact, cancer killed over 8 million people around the world in 2012. Over 90% of these cancer deaths are due to metastasis, which results from tumor cell migration and invasion. Specific cancer biomarkers need to be identified in order to effectively target these motile cells. The transmembrane glycoprotein receptor podoplanin (PDPN) promotes tumor cell motility and metastasis in many aggressive cancers. Indeed, PDPN has emerged as a prime cancer biomarker and chemotherapeutic target. Here, we describe how PDPN can be targeted to inhibit the growth and motility of melanoma and oral cancer cells. PDPN has a short intracellular domain of 9 amino acids which include two conserved serine residues. PDPN also has a large extracellular domain that is extensively O-glycosylated with α2,3-sialic acid linked to galactose. We are developing novel methods to target the intracellular and extracellular domains of PDPN to combat cancer progression. For example, we have found that some activators of protein kinase A can induce phosphorylation of the intracellular serine residues of PDPN to inhibit tumor cell migration. In addition, we have found that Maackia amurensis seed lectin (MASL) can target the extracellular domain of PDPN to inhibit tumor cell growth, migration, and tumor progression in cell culture and animal models. Furthermore, we utilized live cell imaging to find that PDPN expression can be modulated in cancer associated fibroblasts to inhibit neighboring tumor cell migration and survival. Thus, reagents can be used to target PDPN from inside of the cell and outside of the cell to inhibit tumor cell migration and combat cancer progression. This work illuminates novel strategies designed to exploit PDPN as a functionally relevant biomarker and chemotherapeutic target.
Citation Format: Harini Krishnan, Jhon Ochoa-alvarez, Yongquan Shen, Evan Nevel, David Kephart, Angels Nguyen, Min Han, Nimish Acharya, Robert Nagele, Maria Ramirez, W. Todd Miller, Evelyne Kalyoussef, Soly Baredes, Mahnaz Fatahzadeh, Lasse Jensen, Alan Shienbaum, Gary Goldberg. Podoplanin (PDPN): novel biomarker and chemotherapeutic target. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4375. doi:10.1158/1538-7445.AM2015-4375
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Affiliation(s)
| | | | | | | | | | | | - Min Han
- 1Rowan University, Stratford, NJ
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30
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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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31
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Krishnan H, Retzbach EP, Ramirez MI, Liu T, Li H, Miller WT, Goldberg GS. PKA and CDK5 can phosphorylate specific serines on the intracellular domain of podoplanin (PDPN) to inhibit cell motility. Exp Cell Res 2015; 335:115-22. [PMID: 25959509 DOI: 10.1016/j.yexcr.2015.04.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 04/26/2015] [Accepted: 04/28/2015] [Indexed: 12/12/2022]
Abstract
Podoplanin (PDPN) is a transmembrane glycoprotein that promotes tumor cell migration, invasion, and cancer metastasis. In fact, PDPN expression is induced in many types of cancer. Thus, PDPN has emerged as a functionally relevant cancer biomarker and chemotherapeutic target. PDPN contains 2 intracellular serine residues that are conserved between species ranging from mouse to humans. Recent studies indicate that protein kinase A (PKA) can phosphorylate PDPN in order to inhibit cell migration. However, the number and identification of specific residues phosphorylated by PKA have not been defined. In addition, roles of other kinases that may phosphorylate PDPN to control cell migration have not been investigated. We report here that cyclin dependent kinase 5 (CDK5) can phosphorylate PDPN in addition to PKA. Moreover, results from this study indicate that PKA and CDK5 cooperate to phosphorylate PDPN on both intracellular serine residues to decrease cell motility. These results provide new insight into PDPN phosphorylation dynamics and the role of PDPN in cell motility. Understanding novel mechanisms of PDPN intracellular signaling could assist with designing novel targeted chemotherapeutic agents and procedures.
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Affiliation(s)
- Harini Krishnan
- Graduate School of Biomedical Sciences and Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Science Center, 2 Medical Center Drive, Stratford, NJ 08084, USA
| | - Edward P Retzbach
- Graduate School of Biomedical Sciences and Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Science Center, 2 Medical Center Drive, Stratford, NJ 08084, USA
| | - Maria I Ramirez
- Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Tong Liu
- Center for Advanced Proteomics Research and Department of Biochemistry and Molecular Biology, Rutgers New Jersey Medical School Cancer Center,205 S. Orange Avenue, F-1226, Newark, NJ 07103, USA
| | - Hong Li
- Center for Advanced Proteomics Research and Department of Biochemistry and Molecular Biology, Rutgers New Jersey Medical School Cancer Center,205 S. Orange Avenue, F-1226, Newark, NJ 07103, USA
| | - W Todd Miller
- Department of Physiology and Biophysics, Basic Science Tower T-5, Stony Brook University, Stony Brook, NY 11794-8661, USA
| | - Gary S Goldberg
- Graduate School of Biomedical Sciences and Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Science Center, 2 Medical Center Drive, Stratford, NJ 08084, USA.
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32
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Fan G, Aleem S, Yang M, Miller WT, Tonks NK. Protein-tyrosine Phosphatase and Kinase Specificity in Regulation of SRC and Breast Tumor Kinase. J Biol Chem 2015; 290:15934-47. [PMID: 25897081 DOI: 10.1074/jbc.m115.651703] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Indexed: 11/06/2022] Open
Abstract
Despite significant evidence to the contrary, the view that phosphatases are "nonspecific" still pervades the field. Systems biology approaches to defining how signal transduction pathways are integrated at the level of whole organisms also often downplay the contribution of phosphatases, defining them as "erasers" that serve merely to restore the system to its basal state. Here, we present a study that counteracts the idea of "nonspecific phosphatases." We have characterized two structurally similar and functionally related kinases, BRK and SRC, which are regulated by combinations of activating autophosphorylation and inhibitory C-terminal sites of tyrosine phosphorylation. We demonstrated specificity at the level of the kinases in that SRMS phosphorylated the C terminus of BRK, but not SRC; in contrast, CSK is the kinase responsible for C-terminal phosphorylation of SRC, but not BRK. For the phosphatases, we observed that RNAi-mediated suppression of PTP1B resulted in opposing effects on the activity of BRK and SRC and have defined the mechanisms underlying this specificity. PTP1B inhibited BRK by directly dephosphorylating the Tyr-342 autophosphorylation site. In contrast, PTP1B potentiated SRC activity, but not by dephosphorylating SRC itself directly; instead, PTP1B regulated the interaction between CBP/PAG and CSK. SRC associated with, and phosphorylated, the transmembrane protein CBP/PAG at Tyr-317, resulting in CSK recruitment. We identified PAG as a substrate of PTP1B, and dephosphorylation abolished recruitment of the inhibitory kinase CSK. Overall, these findings illustrate how the combinatorial effects of PTKs and PTPs may be integrated to regulate signaling, with both classes of enzymes displaying exquisite specificity.
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Affiliation(s)
- Gaofeng Fan
- From the Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724-2208 and
| | - Saadat Aleem
- the Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York 11794-8661
| | - Ming Yang
- From the Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724-2208 and
| | - W Todd Miller
- the Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York 11794-8661
| | - Nicholas K Tonks
- From the Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724-2208 and
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33
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Cabail MZ, Li S, Lemmon E, Bowen ME, Hubbard SR, Miller WT. The insulin and IGF1 receptor kinase domains are functional dimers in the activated state. Nat Commun 2015; 6:6406. [PMID: 25758790 DOI: 10.1038/ncomms7406] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 01/26/2015] [Indexed: 12/31/2022] Open
Abstract
The insulin receptor (IR) and insulin-like growth factor-1 receptor (IGF1R) are highly related receptor tyrosine kinases with a disulfide-linked homodimeric architecture. Ligand binding to the receptor ectodomain triggers tyrosine autophosphorylation of the cytoplasmic domains, which stimulates catalytic activity and creates recruitment sites for downstream signalling proteins. Whether the two phosphorylated tyrosine kinase domains within the receptor dimer function independently or cooperatively to phosphorylate protein substrates is not known. Here we provide crystallographic, biophysical and biochemical evidence demonstrating that the phosphorylated kinase domains of IR and IGF1R form a specific dimeric arrangement involving an exchange of the juxtamembrane region proximal to the kinase domain. In this dimer, the active position of α-helix C in the kinase N lobe is stabilized, which promotes downstream substrate phosphorylation. These studies afford a novel strategy for the design of small-molecule IR agonists as potential therapeutic agents for type 2 diabetes.
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Affiliation(s)
- M Zulema Cabail
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York 11794, USA
| | - Shiqing Li
- Department of Biochemistry and Molecular Pharmacology, Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, New York 10016, USA
| | - Eric Lemmon
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York 11794, USA
| | - Mark E Bowen
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York 11794, USA
| | - Stevan R Hubbard
- Department of Biochemistry and Molecular Pharmacology, Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, New York 10016, USA
| | - W Todd Miller
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York 11794, USA
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34
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Yokoyama N, Miller WT. Molecular characterization of WDCP, a novel fusion partner for the anaplastic lymphoma tyrosine kinase ALK. Biomed Rep 2014; 3:9-13. [PMID: 25469238 DOI: 10.3892/br.2014.374] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 10/20/2014] [Indexed: 11/06/2022] Open
Abstract
Anaplastic lymphoma kinase (ALK) is a member of the receptor tyrosine kinase superfamily. The ALK gene is a site of frequent mutation and chromosomal rearrangement in various types of human cancers. A novel chromosomal translocation was recently identified in human colorectal cancer between the ALK gene and chromosome 2, open reading frame 44 (C2orf44), a gene of unknown function. As a first step in understanding the oncogenic properties of this fusion protein, C2orf44 cDNA was cloned and the encoded protein was characterized, which was designated as WD repeat and coiled coil containing protein (WDCP). A C-terminal proline-rich segment in WDCP was shown to mediate binding to the Src homology 3 domain of the Src family kinase hematopoietic cell kinase (Hck). Co-expression with Hck lead to tyrosine phosphorylation of WDCP. Chromatographic fractionation of WDCP-containing lysates indicates that the protein exists as an oligomer in mammalian cells. These results suggest that, in the context of the ALK-C2orf44 gene fusion, WDCP imposes an oligomeric structure on ALK that results in constitutive kinase activation and signaling.
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Affiliation(s)
- Noriko Yokoyama
- Department of Physiology and Biophysics, School of Medicine, State University of New York at Stony Brook, Stony Brook, NY 11794, USA
| | - W Todd Miller
- Department of Physiology and Biophysics, School of Medicine, State University of New York at Stony Brook, Stony Brook, NY 11794, USA
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35
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Abstract
When insulin-like growth factor-1 (IGF1) binds to its receptor, a physical constraint is released that allows the two transmembrane helices to come together to facilitate activation of the receptor.
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Affiliation(s)
- Stevan R Hubbard
- Stevan R Hubbard is in the Kimmel Center for Biology and Medicine at the Skirball Institute and the Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, United States
| | - W Todd Miller
- W Todd Miller is in the Department of Physiology and Biophysics, Stony Brook University, Stony Brook, United States
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36
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Abstract
The development of the phosphotyrosine-based signaling system predated the evolution of multicellular animals. Single-celled choanoflagellates, the closest living relatives to metazoans, possess numerous tyrosine kinases, including Src family nonreceptor tyrosine kinases. Choanoflagellates also have Csk (C-terminal Src kinase), the enzyme that regulates Src in metazoans; however, choanoflagellate Csk kinases fail to repress the cognate Src. Here, we have cloned and characterized Src and Csk kinases from Ministeria vibrans, a filasterean (the sister group to metazoans and choanoflagellates). The two Src kinases (MvSrc1 and MvSrc2) are enzymatically active Src kinases, although they have low activity toward mammalian cellular proteins. Unexpectedly, MvSrc2 has significant Ser/Thr kinase activity. The Csk homologue (MvCsk) is enzymatically inactive and fails to repress MvSrc activity. We suggest that the low activity of MvCsk is due to sequences in the SH2-kinase interface, and we show that a point mutation in this region partially restores MvCsk activity. The inactivity of filasterean Csk kinases is consistent with a model in which the stringent regulation of Src family kinases arose more recently in evolution, after the split between choanoflagellates and multicellular animals.
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Affiliation(s)
- Kira P Schultheiss
- Department of Physiology and Biophysics, Stony Brook University , Stony Brook, New York 11794, United States
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37
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Krishnan H, Ochoa-Alvarez JA, Shen Y, Nevel E, Lakshminarayanan M, Williams MC, Ramirez MI, Miller WT, Goldberg GS. Serines in the intracellular tail of podoplanin (PDPN) regulate cell motility. J Biol Chem 2013; 288:12215-21. [PMID: 23530051 DOI: 10.1074/jbc.c112.446823] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Podoplanin (PDPN) is a transmembrane receptor that affects the activities of Rho, ezrin, and other proteins to promote tumor cell motility, invasion, and metastasis. PDPN is found in many types of cancer and may serve as a tumor biomarker and chemotherapeutic target. The intracellular region of PDPN contains only two serines, and these are conserved in mammals including mice and humans. We generated cells from the embryos of homozygous null Pdpn knock-out mice to investigate the relevance of these serines to cell growth and migration on a clear (PDPN-free) background. We report here that one or both of these serines can be phosphorylated by PKA (protein kinase A). We also report that conversion of these serines to nonphosphorylatable alanine residues enhances cell migration, whereas their conversion to phosphomimetic aspartate residues decreases cell migration. These results indicate that PKA can phosphorylate PDPN to decrease cell migration. In addition, we report that PDPN expression in fibroblasts causes them to facilitate the motility and viability of neighboring melanoma cells in coculture. These findings shed new light on how PDPN promotes cell motility, its role in tumorigenesis, and its utility as a functionally relevant biomarker and chemotherapeutic target.
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Affiliation(s)
- Harini Krishnan
- Graduate School of Biomedical Sciences and Department of Molecular Biology, School of Osteopathic Medicine, University of Medicine and Dentistry of New Jersey, Stratford, New Jersey 08084, USA
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38
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Abstract
The role of Src in tumorigenesis has been extensively studied since the work of Peyton Rous over a hundred years ago. Src is a non-receptor tyrosine kinase that plays key roles in signaling pathways controlling tumor cell growth and migration. Src regulates the activities of numerous molecules to induce cell transformation. However, transformed cells do not always migrate and realize their tumorigenic potential. They can be normalized by surrounding nontransformed cells by a process called contact normalization. Tumor cells need to override contact normalization to become malignant or metastatic. In this review, we discuss the role of Src in cell migration and contact normalization, with emphasis on Cas and Abl pathways. This paradigm illuminates several chemotherapeutic targets and may lead to the identification of new biomarkers and the development of effective anticancer treatments.
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Affiliation(s)
- Harini Krishnan
- University of Medicine and Dentistry of New Jersey, Graduate School of Biomedical Sciences, School of Osteopathic Medicine, Stratford, NJ, USA
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39
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Abstract
Phosphotyrosine-based signaling plays a vital role in cellular communication in multicellular organisms. Unexpectedly, unicellular choanoflagellates (the closest phylogenetic group to metazoans) possess numbers of tyrosine kinases that are comparable to those in complex metazoans. Here, we have characterized tyrosine kinases from the filasterean Capsaspora owczarzaki, a unicellular protist representing the sister group to choanoflagellates and metazoans. Two Src-like tyrosine kinases have been identified in C. owczarzaki (CoSrc1 and CoSrc2), both of which have the arrangement of SH3, SH2, and catalytic domains seen in mammalian Src kinases. In Capsaspora cells, CoSrc1 and CoSrc2 localize to punctate structures in filopodia that may represent primordial focal adhesions. We have cloned, expressed, and purified both enzymes. CoSrc1 and CoSrc2 are active tyrosine kinases. Mammalian Src kinases are normally regulated in a reciprocal fashion by autophosphorylation in the activation loop (which increases activity) and by Csk-mediated phosphorylation of the C-terminal tail (which inhibits activity). Similar to mammalian Src kinases, the enzymatic activities of CoSrc1 and CoSrc2 are increased by autophosphorylation in the activation loop. We have identified a Csk-like kinase (CoCsk) in the genome of C. owczarzaki. We cloned, expressed, and purified CoCsk and found that it has no measurable tyrosine kinase activity. Furthermore, CoCsk does not phosphorylate or regulate CoSrc1 or CoSrc2 in cells or in vitro, and CoSrc1 and CoSrc2 are active in Capsaspora cell lysates. Thus, the function of Csk as a negative regulator of Src family kinases appears to have arisen with the emergence of metazoans.
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Affiliation(s)
- Kira P Schultheiss
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY 11794, USA
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40
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Miller WT. Tyrosine kinase signaling and the emergence of multicellularity. Biochim Biophys Acta 2012; 1823:1053-7. [PMID: 22480439 DOI: 10.1016/j.bbamcr.2012.03.009] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 03/19/2012] [Accepted: 03/20/2012] [Indexed: 11/30/2022]
Abstract
Tyrosine phosphorylation is an essential element of signal transduction in multicellular animals. Although tyrosine kinases were originally regarded as specific to the metazoan lineage, it is now clear that they evolved prior to the split between unicellular and multicellular eukaryotes (≈600million years ago). Genome analyses of choanoflagellates and other protists show an abundance of tyrosine kinases that rivals the most complex animals. Some of these kinases are orthologs of metazoan enzymes (e.g., Src), but others display unique domain compositions not seen in any metazoan. Biochemical experiments have highlighted similarities and differences between the unicellular and multicellular tyrosine kinases. In particular, it appears that the complex systems of kinase autoregulation may have evolved later in the metazoan lineage.
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Affiliation(s)
- W Todd Miller
- Department of Physiology and Biophysics, School of Medcine, Stony Brook University, Stony Brook, NY 11794-8661, USA.
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41
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Prieto-Echagüe V, Chan PM, Craddock BP, Manser E, Miller WT. PTB domain-directed substrate targeting in a tyrosine kinase from the unicellular choanoflagellate Monosiga brevicollis. PLoS One 2011; 6:e19296. [PMID: 21541291 PMCID: PMC3082566 DOI: 10.1371/journal.pone.0019296] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Accepted: 03/28/2011] [Indexed: 11/19/2022] Open
Abstract
Choanoflagellates are considered to be the closest living unicellular relatives of metazoans. The genome of the choanoflagellate Monosiga brevicollis contains a surprisingly high number and diversity of tyrosine kinases, tyrosine phosphatases, and phosphotyrosine-binding domains. Many of the tyrosine kinases possess combinations of domains that have not been observed in any multicellular organism. The role of these protein interaction domains in M. brevicollis kinase signaling is not clear. Here, we have carried out a biochemical characterization of Monosiga HMTK1, a protein containing a putative PTB domain linked to a tyrosine kinase catalytic domain. We cloned, expressed, and purified HMTK1, and we demonstrated that it possesses tyrosine kinase activity. We used immobilized peptide arrays to define a preferred ligand for the third PTB domain of HMTK1. Peptide sequences containing this ligand sequence are phosphorylated efficiently by recombinant HMTK1, suggesting that the PTB domain of HMTK1 has a role in substrate recognition analogous to the SH2 and SH3 domains of mammalian Src family kinases. We suggest that the substrate recruitment function of the noncatalytic domains of tyrosine kinases arose before their roles in autoinhibition.
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Affiliation(s)
- Victoria Prieto-Echagüe
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
| | - Perry M. Chan
- sGSK group, Neuroscience Research Partnership/A*Star, Singapore, Singapore
| | - Barbara P. Craddock
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
| | - Edward Manser
- sGSK group, Neuroscience Research Partnership/A*Star, Singapore, Singapore
| | - W. Todd Miller
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
- * E-mail:
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42
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Prieto-Echagüe V, Gucwa A, Brown DA, Miller WT. Regulation of Ack1 localization and activity by the amino-terminal SAM domain. BMC Biochem 2010; 11:42. [PMID: 20979614 PMCID: PMC2987765 DOI: 10.1186/1471-2091-11-42] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Accepted: 10/27/2010] [Indexed: 12/31/2022]
Abstract
Background The mechanisms that regulate the activity of the nonreceptor tyrosine kinase Ack1 (activated Cdc42-associated kinase) are poorly understood. The amino-terminal region of Ack1 is predicted to contain a sterile alpha motif (SAM) domain. SAM domains share a common fold and mediate protein-protein interactions in a wide variety of proteins. Here, we addressed the importance of the Ack1 SAM domain in kinase activity. Results We used immunofluorescence and Western blotting to show that Ack1 deletion mutants lacking the N-terminus displayed significantly reduced autophosphorylation in cells. A minimal construct comprising the N-terminus and kinase domain (NKD) was autophosphorylated, while the kinase domain alone (KD) was not. When expressed in mammalian cells, NKD localized to the plasma membrane, while KD showed a more diffuse cytosolic localization. Co-immunoprecipitation experiments showed a stronger interaction between full length Ack1 and NKD than between full length Ack1 and KD, indicating that the N-terminus was important for Ack1 dimerization. Increasing the local concentration of purified Ack1 kinase domain at the surface of lipid vesicles stimulated autophosphorylation and catalytic activity, consistent with a requirement for dimerization and trans-phosphorylation for activity. Conclusions Collectively, the data suggest that the N-terminus of Ack1 promotes membrane localization and dimerization to allow for autophosphorylation.
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Affiliation(s)
- Victoria Prieto-Echagüe
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, NY 11794-8661, USA
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43
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Prieto-Echagüe V, Gucwa A, Craddock BP, Brown DA, Miller WT. Cancer-associated mutations activate the nonreceptor tyrosine kinase Ack1. J Biol Chem 2010; 285:10605-15. [PMID: 20110370 DOI: 10.1074/jbc.m109.060459] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ack1 is a nonreceptor tyrosine kinase that participates in tumorigenesis, cell survival, and migration. Relatively little is known about the mechanisms that regulate Ack1 activity. Recently, four somatic missense mutations of Ack1 were identified in cancer tissue samples, but the effects on Ack1 activity, and function have not been described. These mutations occur in the N-terminal region, the C-lobe of the kinase domain, and the SH3 domain. Here, we show that the cancer-associated mutations increase Ack1 autophosphorylation in mammalian cells without affecting localization and increase Ack1 activity in immune complex kinase assays. The cancer-associated mutations potentiate the ability of Ack1 to promote proliferation and migration, suggesting that point mutation is a mechanism for Ack1 deregulation. We propose that the C-terminal Mig6 homology region (MHR) (residues 802-990) participates in inhibitory intramolecular interactions. The isolated kinase domain of Ack1 interacts directly with the MHR, and the cancer-associated E346K mutation prevents binding. Likewise, mutation of a key hydrophobic residue in the MHR (Phe(820)) prevents the MHR-kinase interaction, activates Ack1, and increases cell migration. Thus, the cancer-associated mutation E346K appears to destabilize an autoinhibited conformation of Ack1, leading to constitutively high Ack1 activity.
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Affiliation(s)
- Victoria Prieto-Echagüe
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, New York 11794, USA
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44
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Abstract
Src family kinases (SFKs) are modular signaling proteins possessing SH3, SH2, and tyrosine kinase domains. The SH3 and SH2 domains of SFKs have dual roles: they regulate the activity of the kinases, and they also target SFKs to their cellular substrates. We generated a series of novel SFKs by replacing the SH2 and SH3 domains of Hck with the syntrophin PDZ domain. In some constructs, the negative regulatory tyrosine in the C-terminal tail was also replaced with a PDZ ligand sequence. When expressed in mammalian cells, the substrate specificity of the PDZ-kinases was directed to a different group of proteins than wild-type Hck. The PDZ-kinases phosphorylate neuronal nitric oxide synthase (nNOS), a known binding partner of the syntrophin PDZ domain. We also introduced a PDZ ligand at the C-terminus of the adaptor protein Cas. PDZ-Hck kinases phosphorylate the engineered Cas protein in Cas(-/-) cells and restore the migration defect of these cells. A PDZ-kinase was also functional in rewiring MAPK signaling via an engineered ErbB2 construct containing a PDZ ligand sequence. Several of the PDZ-kinases show autoregulatory properties similar to natural SFKs. Thus, the PDZ-ligand interaction is able to functionally replace the normal SH2-pY527 interaction that regulates SFKs. Our data highlight the modularity and evolvability of signaling proteins.
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Affiliation(s)
- Shalini S Yadav
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, New York 11794-8661, USA
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45
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Miller WT. Making Sense of Signal TransductionReview and commentary on
Biochemistry of Signal Transduction and Regulation, 4th edition
, by Gerhard Krauss. Wiley-VCH, Weinheim, Germany, 2008, 646 pp. ISBN: 978-3-527-31397-6. Sci Signal 2009. [DOI: 10.1126/scisignal.2101pe79] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Textbook provides an overview of signaling concepts and models for teaching.
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Affiliation(s)
- W. Todd Miller
- Department of Physiology and Biophysics, Stony Brook University, Nicolls Road, BST T-6, Stony Brook, NY 11794–8661
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46
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Patwardhan P, Shiba K, Gordon C, Craddock BP, Tamiko M, Miller WT. Synthesis of functional signaling domains by combinatorial polymerization of phosphorylation motifs. ACS Chem Biol 2009; 4:751-8. [PMID: 19627099 DOI: 10.1021/cb900059f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The adaptor protein Cas contains a core substrate domain with multiple YXXP motifs that are phosphorylated by Src and other tyrosine kinases. Here, we used a synthetic strategy to determine the importance of the arrangement, spacing, and identity of the YXXP motifs. By polymerizing short DNA sequences encoding two phosphorylation motifs, we created a panel of Cas mutants in which the entire substrate domain was replaced by synthetic domains containing random numbers and arrangements of the motifs. Most of these synthetic Cas variants were recognized and phosphorylated by Src in vitro and in intact mammalian cells. The random polymer mutants also restored migration activity to Cas knockout cells; even artificial proteins containing a single motif retained some biological function. Our results suggest that the arrangement of Cas motifs is not critical for signaling. This method could be used to identify the minimal functional units in other signaling proteins.
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Affiliation(s)
- Parag Patwardhan
- Department of Physiology and Biophysics, School of Medicine, State University of New York at Stony Brook, Stony Brook, New York 11794
| | - Kiyotaka Shiba
- Department of Protein Engineering, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan
| | - Chris Gordon
- Department of Physiology and Biophysics, School of Medicine, State University of New York at Stony Brook, Stony Brook, New York 11794
| | - Barbara P. Craddock
- Department of Physiology and Biophysics, School of Medicine, State University of New York at Stony Brook, Stony Brook, New York 11794
| | - Minamisawa Tamiko
- Department of Protein Engineering, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan
| | - W. Todd Miller
- Department of Physiology and Biophysics, School of Medicine, State University of New York at Stony Brook, Stony Brook, New York 11794
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47
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Abstract
Until recently, phosphotyrosine signaling was thought to be restricted to multicellular animals. Surprisingly, the unicellular choanoflagellate Monosiga brevicollis contains a number and diversity of tyrosine kinases that exceeds that of any metazoan, including humans. Many of these M. brevicollis tyrosine kinases possess combinations of signaling domains that do not occur in metazoans. One such kinase, the Src-like protein MbSrc4, contains a lipid-binding C2 domain N-terminal to the conserved SH3-SH2-kinase domains. Here, we report that the enzyme is highly active as a tyrosine kinase and that the targeting functions of the C2, SH3, and SH2 domains are similar to the mammalian counterparts. The membrane-binding activity of the C2 domain is functionally equivalent to the myristoylation signal of c-Src, suggesting that it is an example of convergent evolution. When expressed in mammalian cells, full-length MbSrc4 displays low activity toward endogenous proteins, and it cannot functionally substitute for mammalian c-Src in a reporter gene assay. Removal of the MbSrc4 C2 domain leads to increased phosphorylation of cellular proteins. Thus, in contrast to the related M. brevicollis Src-like kinase MbSrc1, MbSrc4 is not targeted properly to mammalian Src substrates, suggesting that the C2 domain plays a specific role in M. brevicollis signaling.
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Affiliation(s)
- Wanqing Li
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, New York 11794, USA
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48
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Yadav SS, Miller WT. The evolutionarily conserved arrangement of domains in SRC family kinases is important for substrate recognition. Biochemistry 2008; 47:10871-80. [PMID: 18803405 DOI: 10.1021/bi800930e] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The SH3-SH2-kinase domain arrangement in nonreceptor tyrosine kinases has been conserved throughout evolution. For Src family kinases, the relative positions of the domains are important for enzyme regulation; they permit the assembly of Src kinases into autoinhibited conformations. The SH3 and SH2 domains of Src family kinases have an additional role in determining the substrate specificity of the kinase. We addressed the question of whether the domain arrangement of Src family kinases has a role in substrate specificity by producing mutants with alternative arrangements. Our results suggest that changes in the positions of domains can lead to specific changes in the phosphorylation of Sam68 and Cas by Src. Phosphorylation of Cas by several mutants triggers downstream signaling leading to cell migration. The placement of the SH2 domain with respect to the catalytic domain of Src appears to be especially important for proper substrate recognition, while the placement of the SH3 domain is more flexible. The results suggest that the involvement of the SH3 and SH2 domains in substrate recognition is one reason for the strict conservation of the SH3-SH2-kinase architecture.
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Affiliation(s)
- Shalini S Yadav
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, New York 11794-8661, USA
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49
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Abstract
The regulatory mechanism of Src tyrosine kinases includes conformational activation by a change in the catalytic domain tertiary structure and in domain-domain contacts between the catalytic domain and the SH2/SH3 regulatory domains. The kinase is activated when tyrosine phosphorylation occurs on the activation loop, but without phosphorylation of the C-terminal tail. Activation also occurs by allostery when contacts between the catalytic domain (CD) and the regulatory SH3 and SH2 domains are released as a result of exogenous protein binding. The aim of this work is to examine the proposed role of an electrostatic network in the conformational transition and to elucidate the molecular mechanism for long-range, allosteric conformational activation by using a combination of experimental enzyme kinetics and nonequilibrium molecular dynamics simulations. Salt dependence of the induction phase is observed in kinetic assays and supports the role of an electrostatic network in the transition. In addition, simulations provide evidence that allosteric activation involves a concerted motion coupling highly conserved residues, and spanning several nanometers from the catalytic site to the regulatory domain interface to communicate between the CD and the regulatory domains.
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Affiliation(s)
- Elif Ozkirimli
- 1Medicinal Chemistry and Molecular Pharmacology Department, Markey Center for Structural Biology and Purdue Cancer Center, Purdue University, West Lafayette, Indiana 47907-2091, USA
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50
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Wu J, Li W, Craddock BP, Foreman KW, Mulvihill MJ, Ji QS, Miller WT, Hubbard SR. Small-molecule inhibition and activation-loop trans-phosphorylation of the IGF1 receptor. EMBO J 2008; 27:1985-94. [PMID: 18566589 DOI: 10.1038/emboj.2008.116] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2008] [Accepted: 05/20/2008] [Indexed: 11/09/2022] Open
Abstract
The insulin-like growth factor-1 receptor (IGF1R) is a receptor tyrosine kinase (RTK) that has a critical role in mitogenic signalling during embryogenesis and an antiapoptotic role in the survival and progression of many human tumours. Here, we present the crystal structure of the tyrosine kinase domain of IGF1R (IGF1RK), in its unphosphorylated state, in complex with a novel compound, cis-3-[3-(4-methyl-piperazin-l-yl)-cyclobutyl]-1-(2-phenyl-quinolin-7-yl)-imidazo[1,5-a]pyrazin-8-ylamine (PQIP), which we show is a potent inhibitor of both the unphosphorylated (basal) and phosphorylated (activated) states of the kinase. PQIP interacts with residues in the ATP-binding pocket and in the activation loop, which confers specificity for IGF1RK and the highly related insulin receptor (IR) kinase. In this crystal structure, the IGF1RK active site is occupied by Tyr1135 from the activation loop of an symmetry (two-fold)-related molecule. This dimeric arrangement affords, for the first time, a visualization of the initial trans-phosphorylation event in the activation loop of an RTK, and provides a molecular rationale for a naturally occurring mutation in the activation loop of the IR that causes type II diabetes mellitus.
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Affiliation(s)
- Jinhua Wu
- Structural Biology Program, Kimmel Center for Biology and Medicine of the Skirball Institute of Biomolecular Medicine, Department of Pharmacology, New York University School of Medicine, New York, NY 10016, USA
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