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Shih YC, Chen HF, Wu CY, Ciou YR, Wang CW, Chuang HC, Tan TH. The phosphatase DUSP22 inhibits UBR2-mediated K63-ubiquitination and activation of Lck downstream of TCR signalling. Nat Commun 2024; 15:532. [PMID: 38225265 PMCID: PMC10789758 DOI: 10.1038/s41467-024-44843-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 01/08/2024] [Indexed: 01/17/2024] Open
Abstract
DUSP22 is a dual-specificity phosphatase that inhibits T cell activation by inactivating the kinase Lck. Here we show that the E3 ubiquitin ligase UBR2 is a positive upstream regulator of Lck during T-cell activation. DUSP22 dephosphorylates UBR2 at specific Serine residues, leading to ubiquitin-mediated UBR2 degradation. UBR2 is also modified by the SCF E3 ubiquitin ligase complex via Lys48-linked ubiquitination at multiple Lysine residues. Single-cell RNA sequencing analysis and UBR2 loss of function experiments showed that UBR2 is a positive regulator of proinflammatory cytokine expression. Mechanistically, UBR2 induces Lys63-linked ubiquitination of Lck at Lys99 and Lys276 residues, followed by Lck Tyr394 phosphorylation and activation as part of TCR signalling. Inflammatory phenotypes induced by TCR-triggered Lck activation or knocking out DUSP22, are attenuated by genomic deletion of UBR2. UBR2-Lck interaction and Lck Lys63-linked ubiquitination are induced in the peripheral blood T cells of human SLE patients, which demonstrate the relevance of the UBR2-mediated regulation of inflammation to human pathology. In summary, we show here an important regulatory mechanism of T cell activation, which finetunes the balance between T cell response and aggravated inflammation.
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Affiliation(s)
- Ying-Chun Shih
- Immunology Research Center, National Health Research Institutes, Zhunan, Taiwan
| | - Hsueh-Fen Chen
- Immunology Research Center, National Health Research Institutes, Zhunan, Taiwan
| | - Chia-Ying Wu
- Immunology Research Center, National Health Research Institutes, Zhunan, Taiwan
| | - Yi-Ru Ciou
- Immunology Research Center, National Health Research Institutes, Zhunan, Taiwan
| | - Chia-Wen Wang
- Immunology Research Center, National Health Research Institutes, Zhunan, Taiwan
| | - Huai-Chia Chuang
- Immunology Research Center, National Health Research Institutes, Zhunan, Taiwan.
| | - Tse-Hua Tan
- Immunology Research Center, National Health Research Institutes, Zhunan, Taiwan.
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2
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Groppe JC, Lu G, Tandang-Silvas MR, Pathi A, Konda S, Wu J, Le VQ, Culbert AL, Shore EM, Wharton KA, Kaplan FS. Polypeptide Substrate Accessibility Hypothesis: Gain-of-Function R206H Mutation Allosterically Affects Activin Receptor-like Protein Kinase Activity. Biomolecules 2023; 13:1129. [PMID: 37509165 PMCID: PMC10376983 DOI: 10.3390/biom13071129] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 07/10/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
Although structurally similar to type II counterparts, type I or activin receptor-like kinases (ALKs) are set apart by a metastable helix-loop-helix (HLH) element preceding the protein kinase domain that, according to a longstanding paradigm, serves passive albeit critical roles as an inhibitor-to-substrate-binding switch. A single recurrent mutation in the codon of the penultimate residue, directly adjacent the position of a constitutively activating substitution, causes milder activation of ACVR1/ALK2 leading to sporadic heterotopic bone deposition in patients presenting with fibrodysplasia ossificans progressiva, or FOP. To determine the protein structural-functional basis for the gain of function, R206H mutant, Q207D (aspartate-substituted caALK2) and HLH subdomain-truncated (208 Ntrunc) forms were compared to one another and the wild-type enzyme through in vitro kinase and protein-protein interaction analyses that were complemented by signaling read-out (p-Smad) in primary mouse embryonic fibroblasts and Drosophila S2 cells. Contrary to the paradigm, the HLH subdomain actively suppressed the phosphotransferase activity of the enzyme, even in the absence of FKBP12. Unexpectedly, perturbation of the HLH subdomain elevated kinase activity at a distance, i.e., allosterically, at the ATP-binding and polypeptide-interacting active site cleft. Accessibility to polypeptide substrate (BMP Smad C-terminal tails) due to allosterically altered conformations of type I active sites within heterohexameric cytoplasmic signaling complexes-assembled noncanonically by activin-type II receptors extracellularly-is hypothesized to produce a gain of function of the R206H mutant protein responsible for episodic heterotopic ossification in FOP.
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Affiliation(s)
- Jay C Groppe
- Department of Biomedical Sciences, Texas A&M University College of Dentistry, 3302 Gaston Ave, Dallas, TX 75246, USA
| | - Guorong Lu
- Department of Biomedical Sciences, Texas A&M University College of Dentistry, 3302 Gaston Ave, Dallas, TX 75246, USA
| | - Mary R Tandang-Silvas
- Department of Biomedical Sciences, Texas A&M University College of Dentistry, 3302 Gaston Ave, Dallas, TX 75246, USA
| | - Anupama Pathi
- Department of Biomedical Sciences, Texas A&M University College of Dentistry, 3302 Gaston Ave, Dallas, TX 75246, USA
| | - Shruti Konda
- Department of Biomedical Sciences, Texas A&M University College of Dentistry, 3302 Gaston Ave, Dallas, TX 75246, USA
| | - Jingfeng Wu
- Department of Biomedical Sciences, Texas A&M University College of Dentistry, 3302 Gaston Ave, Dallas, TX 75246, USA
| | - Viet Q Le
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
- Program in Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Andria L Culbert
- Department of Orthopaedics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Eileen M Shore
- Department of Orthopaedics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Kristi A Wharton
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Frederick S Kaplan
- Department of Orthopaedics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
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3
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Nguyen V, Ahler E, Sitko KA, Stephany JJ, Maly DJ, Fowler DM. Molecular determinants of Hsp90 dependence of Src kinase revealed by deep mutational scanning. Protein Sci 2023; 32:e4656. [PMID: 37167432 PMCID: PMC10273359 DOI: 10.1002/pro.4656] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 05/05/2023] [Accepted: 05/10/2023] [Indexed: 05/13/2023]
Abstract
Hsp90 is a molecular chaperone involved in the refolding and activation of numerous protein substrates referred to as clients. While the molecular determinants of Hsp90 client specificity are poorly understood and limited to a handful of client proteins, strong clients are thought to be destabilized and conformationally extended. Here, we measured the phosphotransferase activity of 3929 variants of the tyrosine kinase Src in both the presence and absence of an Hsp90 inhibitor. We identified 84 previously unknown functionally dependent client variants. Unexpectedly, many destabilized or extended variants were not functionally dependent on Hsp90. Instead, functionally dependent client variants were clustered in the αF pocket and β1-β2 strand regions of Src, which have yet to be described in driving Hsp90 dependence. Hsp90 dependence was also strongly correlated with kinase activity. We found that a combination of activation, global extension, and general conformational flexibility, primarily induced by variants at the αF pocket and β1-β2 strands, was necessary to render Src functionally dependent on Hsp90. Moreover, the degree of activation and flexibility required to transform Src into a functionally dependent client varied with variant location, suggesting that a combination of regulatory domain disengagement and catalytic domain flexibility are required for chaperone dependence. Thus, by studying the chaperone dependence of a massive number of variants, we highlight factors driving Hsp90 client specificity and propose a model of chaperone-kinase interactions.
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Affiliation(s)
- Vanessa Nguyen
- Department of BioengineeringUniversity of WashingtonSeattleWashingtonUSA
| | - Ethan Ahler
- Department of Genome SciencesUniversity of WashingtonSeattleWashingtonUSA
| | - Katherine A. Sitko
- Department of Genome SciencesUniversity of WashingtonSeattleWashingtonUSA
| | - Jason J. Stephany
- Department of Genome SciencesUniversity of WashingtonSeattleWashingtonUSA
| | - Dustin J. Maly
- Department of ChemistryUniversity of WashingtonSeattleWashingtonUSA
| | - Douglas M. Fowler
- Department of BioengineeringUniversity of WashingtonSeattleWashingtonUSA
- Department of Genome SciencesUniversity of WashingtonSeattleWashingtonUSA
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4
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Gurumoorthy V, Shrestha UR, Zhang Q, Pingali SV, Boder ET, Urban VS, Smith JC, Petridis L, O'Neill H. Disordered Domain Shifts the Conformational Ensemble of the Folded Regulatory Domain of the Multidomain Oncoprotein c-Src. Biomacromolecules 2023; 24:714-723. [PMID: 36692364 DOI: 10.1021/acs.biomac.2c01158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
c-Src kinase is a multidomain non-receptor tyrosine kinase that aberrantly phosphorylates several signaling proteins in cancers. Although the structural properties of the regulatory domains (SH3-SH2) and the catalytic kinase domain have been extensively characterized, there is less knowledge about the N-terminal disordered region (SH4UD) and its interactions with the other c-Src domains. Here, we used domain-selective isotopic labeling combined with the small-angle neutron scattering contrast matching technique to study SH4UD interactions with SH3-SH2. Our results show that in the presence of SH4UD, the radius of gyration (Rg) of SH3-SH2 increases, indicating that it has a more extended conformation. Hamiltonian replica exchange molecular dynamics simulations provide a detailed molecular description of the structural changes in SH4UD-SH3-SH2 and show that the regulatory loops of SH3 undergo significant conformational changes in the presence of SH4UD, while SH2 remains largely unchanged. Overall, this study highlights how a disordered region can drive a folded region of a multidomain protein to become flexible, which may be important for allosteric interactions with binding partners. This may help in the design of therapeutic interventions that target the regulatory domains of this important family of kinases.
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Affiliation(s)
- Viswanathan Gurumoorthy
- UT/ORNL Graduate School of Genome and Science Technology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Utsab R Shrestha
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Qiu Zhang
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Sai Venkatesh Pingali
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Eric T Boder
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Volker S Urban
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Loukas Petridis
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Hugh O'Neill
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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5
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Chen Q, Tesmer JJG. G protein-coupled receptor interactions with arrestins and GPCR kinases: the unresolved issue of signal bias. J Biol Chem 2022; 298:102279. [PMID: 35863432 PMCID: PMC9418498 DOI: 10.1016/j.jbc.2022.102279] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 07/05/2022] [Accepted: 07/08/2022] [Indexed: 12/25/2022] Open
Abstract
G protein–coupled receptor (GPCR) kinases (GRKs) and arrestins interact with agonist-bound GPCRs to promote receptor desensitization and downregulation. They also trigger signaling cascades distinct from those of heterotrimeric G proteins. Biased agonists for GPCRs that favor either heterotrimeric G protein or GRK/arrestin signaling are of profound pharmacological interest because they could usher in a new generation of drugs with greatly reduced side effects. One mechanism by which biased agonism might occur is by stabilizing receptor conformations that preferentially bind to GRKs and/or arrestins. In this review, we explore this idea by comparing structures of GPCRs bound to heterotrimeric G proteins with those of the same GPCRs in complex with arrestins and GRKs. The arrestin and GRK complexes all exhibit high conformational heterogeneity, which is likely a consequence of their unusual ability to adapt and bind to hundreds of different GPCRs. This dynamic behavior, along with the experimental tactics required to stabilize GPCR complexes for biophysical analysis, confounds these comparisons, but some possible molecular mechanisms of bias are beginning to emerge. We also examine if and how the recent structures advance our understanding of how arrestins parse the “phosphorylation barcodes” installed in the intracellular loops and tails of GPCRs by GRKs. In the future, structural analyses of arrestins in complex with intact receptors that have well-defined native phosphorylation barcodes, such as those installed by the two nonvisual subfamilies of GRKs, will be particularly illuminating.
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Affiliation(s)
- Qiuyan Chen
- Departments of Biological Sciences and of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - John J G Tesmer
- Departments of Biological Sciences and of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA.
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6
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Peng X, Wang K, Wang Y, Lu Y, Lv F, Cui Y, Wang Y, Si H. Exploration of the Mechanism of the Control of Coccidiosis in Chickens Based on Network Pharmacology and Molecular Docking With the Addition of Modified Gegen Qinlian Decoction. Front Vet Sci 2022; 9:849518. [PMID: 35372563 PMCID: PMC8968990 DOI: 10.3389/fvets.2022.849518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
Gegen Qinlian Decoction is a long-established Chinese herbal compound for the treatment of diarrhea and dysentery, while Magnolia officinalis has been demonstrated to have some anthelmintic activity. The preliminary screening of this study showed that the addition of Modified Gegen Qinlian Decoction has some effective on the prevention and treatment of coccidiosis in chickens. However, the mechanism of its treatment of chicken coccidiosis is not clear. The network pharmacology study was based on the screening of chemical components and related targets from TCMSP and PharmMapper server databases. Genes related to chicken coccidiosis were obtained from the SRA database, and those genes that intersected with the target genes of Modified Gegen Qinlian Decoction were screened. By exploring the target interactions through the String system and enrichment analysis by the Metascape system, the mechanism of action of Modified Gegen Qinlian Decoction in chicken coccidiosis was identified. Using real-time quantitative polymerase chain reaction (RT-qPCR) to analyze the mRNA levels of the relevant factors in chicken coccidiosis, molecular docking was used to reveal the extent of binding of the key target genes predicted in the network pharmacology by the action of Modified Gegen Qinlian Decoction. Compound and target screening suggested that the 99 chemical targets of Modified Gegen Qinlian Decoction were involved in chicken coccidiosis, and the enrichment results of KEGG pathway suggested that Modified Gegen Qinlian Decoction was significantly associated with PI3K/AKT signaling pathway in chicken coccidiosis. The Hubba gene module in Cytoscape_v3.7.1 software was used to analyze the network topology to obtain the Hubba gene SRC, STAT3, and PPARG, etc. The molecular docking results showed that SRC, STAT3, and PPARG were key targets in the treatment of coccidiosis in chickens by Modified Gegen Qinlian Decoction, which was in agreement with the RT-qPCR results. Through network pharmacology, molecular docking and in vitro experiments, it was confirmed that Modified Gegen Qinlian Decoction fights against chicken coccidiosis through key targets such as SRC, STAT3, and PPARG.
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7
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New Structural Perspectives in G Protein-Coupled Receptor-Mediated Src Family Kinase Activation. Int J Mol Sci 2021; 22:ijms22126489. [PMID: 34204297 PMCID: PMC8233884 DOI: 10.3390/ijms22126489] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 12/26/2022] Open
Abstract
Src family kinases (SFKs) are key regulators of cell proliferation, differentiation, and survival. The expression of these non-receptor tyrosine kinases is strongly correlated with cancer development and tumor progression. Thus, this family of proteins serves as an attractive drug target. The activation of SFKs can occur via multiple signaling pathways, yet many of them are poorly understood. Here, we summarize the current knowledge on G protein-coupled receptor (GPCR)-mediated regulation of SFKs, which is of considerable interest because GPCRs are among the most widely used pharmaceutical targets. This type of activation can occur through a direct interaction between the two proteins or be allosterically regulated by arrestins and G proteins. We postulate that a rearrangement of binding motifs within the active conformation of arrestin-3 mediates Src regulation by comparison of available crystal structures. Therefore, we hypothesize a potentially different activation mechanism compared to arrestin-2. Furthermore, we discuss the probable direct regulation of SFK by GPCRs and investigate the intracellular domains of exemplary GPCRs with conserved polyproline binding motifs that might serve as scaffolding domains to allow such a direct interaction. Large intracellular domains in GPCRs are often understudied and, in general, not much is known of their contribution to different signaling pathways. The suggested direct interaction between a GPCR and a SFK could allow for a potential immediate allosteric regulation of SFKs by GPCRs and thereby unravel a novel mechanism of SFK signaling. This overview will help to identify new GPCR-SFK interactions, which could serve to explain biological functions or be used to modulate downstream effectors.
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8
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Salinas-Garcia MC, Plaza-Garrido M, Camara-Artigas A. The impact of oncogenic mutations of the viral Src kinase on the structure and stability of the SH3 domain. Acta Crystallogr D Struct Biol 2021; 77:854-866. [PMID: 34076598 PMCID: PMC8171063 DOI: 10.1107/s2059798321004344] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/22/2021] [Indexed: 03/26/2023] Open
Abstract
Src kinase belongs to the family of Src-related nonreceptor tyrosine kinases. Because of its physiological role in cell growth and proliferation, its activity is strictly controlled by several mechanisms. Nevertheless, in viral Src kinase (v-Src) some of these mechanisms fail, and its uncontrolled activity is responsible for the occurrence of cancer. Here, the crystal structures of three SH3-domain mutants of v-Src were determined to unveil the effects of these oncogenic mutations in this regulatory domain. Mutations in the n-Src and distal loops have a low impact on the overall structure of the domain and its capacity to form intertwined dimers. However, mutations in the RT loop compromise the stability of the domain and make the protein very prone to aggregation. Additionally, these mutations prevent the formation of intertwined dimers. The results show a synergistic effect between mutations in the RT loop and those in the n-Src and distal loops. Analysis of the structures of the v-Src SH3-domain mutants and the closed inactive conformation of cellular Src kinase (c-Src) point to a loss of the interactions that are required to establish the compact inactive form of the kinase. Nevertheless, an analysis of structures of the c-Src SH3 domain complexed with class I and II peptides points to minor changes in the interactions between the v-Src SH3 domain and these peptides. In this way, the structures reported here indicate that mutations in the RT loop might impair the kinase regulation mechanism without affecting the recognition of short proline-rich motifs in the target proteins of the kinase, thus explaining the oncogenic behaviour of the protein.
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Affiliation(s)
- M. Carmen Salinas-Garcia
- Department of Chemistry and Physics, Agrifood Campus of International Excellence (ceiA3) and CIAMBITAL, University of Almeria, Carretera de Sacramento s/n, 04120 Almeria, Spain
| | - Marina Plaza-Garrido
- Department of Chemistry and Physics, Agrifood Campus of International Excellence (ceiA3) and CIAMBITAL, University of Almeria, Carretera de Sacramento s/n, 04120 Almeria, Spain
| | - Ana Camara-Artigas
- Department of Chemistry and Physics, Agrifood Campus of International Excellence (ceiA3) and CIAMBITAL, University of Almeria, Carretera de Sacramento s/n, 04120 Almeria, Spain
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9
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Chong Y, Liu G, Girmay S, Jiang X. Novel mutations in the signal transducer and activator of transcription 3 gene are associated with sheep body weight and fatness traits. Mamm Genome 2021; 32:38-49. [PMID: 33492461 DOI: 10.1007/s00335-020-09850-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 09/29/2020] [Indexed: 12/01/2022]
Abstract
The signal transducer and activator of transcription 3 (STAT3) gene plays a crucial role in leptin-mediated energy metabolism, upon which the growth and development of animals depend. Nevertheless, no studies have reported the effects of STAT3 gene polymorphisms on body weight and fatness modulation in sheep. This study aimed to illustrate STAT3 mRNA expression across tissues and various developmental stages of sheep and to highlight the association of STAT3 gene polymorphisms with body weight and fat-related traits in sheep, in order to identify a genetic marker that may conceivably be of value for marker-assisted selection (MAS). This study revealed that STAT3 was differentially expressed across age and sex (p < 0.05), with higher expression in the ram liver. The abundant expression of STAT3 in the liver of male sheep and increased expression in the hypothalamus and longissimus dorsi muscle from birth to six months of age may indicate the vital role of the STAT3 gene in animal growth and development. Moreover, SNP association analysis also revealed that the novel SNPs of the STAT3 gene detected in this study showed a significant association with body weight and fatness traits (p < 0.05). In conclusion, the significant genetic effects of the STAT3 gene polymorphisms on sheep growth and development revealed that STAT3 could be a marker gene for the selection of growth-related traits in sheep.
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Affiliation(s)
- Yuqing Chong
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, Huazhong Agricultural University, Wuhan, 430070, China.,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guiqiong Liu
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, Huazhong Agricultural University, Wuhan, 430070, China.,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shishay Girmay
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xunping Jiang
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, Huazhong Agricultural University, Wuhan, 430070, China. .,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.
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10
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Miller WT. Temperature sensitivities of metazoan and pre-metazoan Src kinases. Biochem Biophys Rep 2020; 23:100775. [PMID: 32566764 PMCID: PMC7298416 DOI: 10.1016/j.bbrep.2020.100775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/01/2020] [Accepted: 06/04/2020] [Indexed: 11/24/2022] Open
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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11
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Three-Dimensional Interactions Analysis of the Anticancer Target c-Src Kinase with Its Inhibitors. Cancers (Basel) 2020; 12:cancers12082327. [PMID: 32824733 PMCID: PMC7466017 DOI: 10.3390/cancers12082327] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/07/2020] [Accepted: 08/16/2020] [Indexed: 12/13/2022] Open
Abstract
Src family kinases (SFKs) constitute the biggest family of non-receptor tyrosine kinases considered as therapeutic targets for cancer therapy. An aberrant expression and/or activation of the proto-oncogene c-Src kinase, which is the oldest and most studied member of the family, has long been demonstrated to play a major role in the development, growth, progression and metastasis of numerous human cancers, including colon, breast, gastric, pancreatic, lung and brain carcinomas. For these reasons, the pharmacological inhibition of c-Src activity represents an effective anticancer strategy and a few compounds targeting c-Src, together with other kinases, have been approved as drugs for cancer therapy, while others are currently undergoing preclinical studies. Nevertheless, the development of potent and selective inhibitors of c-Src aimed at properly exploiting this biological target for the treatment of cancer still represents a growing field of study. In this review, the co-crystal structures of c-Src kinase in complex with inhibitors discovered in the past two decades have been described, highlighting the key ligand-protein interactions necessary to obtain high potency and the features to be exploited for addressing selectivity and drug resistance issues, thus providing useful information for the design of new and potent c-Src kinase inhibitors.
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12
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Berndt S, Gurevich VV, Iverson TM. Crystal structure of the SH3 domain of human Lyn non-receptor tyrosine kinase. PLoS One 2019; 14:e0215140. [PMID: 30969999 PMCID: PMC6457566 DOI: 10.1371/journal.pone.0215140] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 03/27/2019] [Indexed: 01/07/2023] Open
Abstract
Lyn kinase (Lck/Yes related novel protein tyrosine kinase) belongs to the family of Src-related non-receptor tyrosine kinases. Consistent with physiological roles in cell growth and proliferation, aberrant function of Lyn is associated with various forms of cancer, including leukemia, breast cancer and melanoma. Here, we determine a 1.3 Å resolution crystal structure of the polyproline-binding SH3 regulatory domain of human Lyn kinase, which adopts a five-stranded β-barrel fold. Mapping of cancer-associated point mutations onto this structure reveals that these amino acid substitutions are distributed throughout the SH3 domain and may affect Lyn kinase function distinctly.
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Affiliation(s)
- Sandra Berndt
- Department of Pharmacology, Vanderbilt University, Nashville, TN, United States of America
| | - Vsevolod V. Gurevich
- Department of Pharmacology, Vanderbilt University, Nashville, TN, United States of America
| | - T. M. Iverson
- Department of Pharmacology, Vanderbilt University, Nashville, TN, United States of America
- Department of Biochemistry, Vanderbilt University, Nashville, TN, United States of America
- Vanderbilt Institute of Chemical Biology, Nashville, TN, United States of America
- Center for Structural Biology, Nashville, TN, United States of America
- * E-mail:
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13
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Ouyang M, Wan R, Qin Q, Peng Q, Wang P, Wu J, Allen M, Shi Y, Laub S, Deng L, Lu S, Wang Y. Sensitive FRET Biosensor Reveals Fyn Kinase Regulation by Submembrane Localization. ACS Sens 2019; 4:76-86. [PMID: 30588803 DOI: 10.1021/acssensors.8b00896] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fyn kinase plays crucial roles in hematology and T cell signaling; however, there are currently limited tools to visualize the dynamic Fyn activity in live cells. Here we developed and characterized a highly sensitive Fyn biosensor based on fluorescence resonance energy transfer (FRET) to monitor Fyn kinase activity in live cells. Our results show that Fyn kinase activity can be induced in both mouse embryonic fibroblasts (MEFs) and T cells by ligand engagement. Two different motifs were further introduced to target the biosensor at the cellular membrane microdomains in MEFs, revealing that the Fyn-tagged biosensor had 70% greater response to growth factor stimulation than the Lyn-tagged version. This suggests that the plasma membrane microdomains can be categorized into different functional subdomains. Further experiments show that while the membrane accessibility is necessary for Fyn activation, the localization of Fyn outside of its microdomains causes its hyperactivity, indicating that membrane microdomains provide a suppressive microenvironment for Fyn regulation in MEFs. Interestingly, a relatively high Fyn activity can be observed at perinuclear regions, further supporting the notion that the membrane microenvironment has a significant impact on the local molecular functions. Our work hence highlights a novel Fyn FRET biosensor for live cell imaging and its application in revealing an intricate submembrane regulation of Fyn in live MEFs.
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Affiliation(s)
- Mingxing Ouyang
- Department of Bioengineering, University of California at San Diego, La Jolla, California 92093, United States
- Institute of Biomedical Engineering and Health Sciences, Changzhou University, Changzhou, Jiangsu Province 213164, China
| | - Rongxue Wan
- Department of Bioengineering, University of California at San Diego, La Jolla, California 92093, United States
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Qin Qin
- Department of Bioengineering, University of California at San Diego, La Jolla, California 92093, United States
| | - Qin Peng
- Department of Bioengineering, University of California at San Diego, La Jolla, California 92093, United States
| | - Pengzhi Wang
- Department of Bioengineering, University of California at San Diego, La Jolla, California 92093, United States
| | - Jenny Wu
- Department of Bioengineering, University of California at San Diego, La Jolla, California 92093, United States
| | - Molly Allen
- Department of Bioengineering, University of California at San Diego, La Jolla, California 92093, United States
| | - Yiwen Shi
- Department of Bioengineering, University of California at San Diego, La Jolla, California 92093, United States
| | - Shannon Laub
- Department of Bioengineering, University of California at San Diego, La Jolla, California 92093, United States
| | - Linhong Deng
- Institute of Biomedical Engineering and Health Sciences, Changzhou University, Changzhou, Jiangsu Province 213164, China
| | - Shaoying Lu
- Department of Bioengineering, University of California at San Diego, La Jolla, California 92093, United States
| | - Yingxiao Wang
- Department of Bioengineering, University of California at San Diego, La Jolla, California 92093, United States
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14
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Cui Y, Sun G. Structural versatility that serves the function of the HRD motif in the catalytic loop of protein tyrosine kinase, Src. Protein Sci 2018; 28:533-542. [PMID: 30461096 DOI: 10.1002/pro.3554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 11/07/2018] [Accepted: 11/08/2018] [Indexed: 12/19/2022]
Abstract
Site-directed mutagenesis is a traditional approach for structure-function analysis of protein tyrosine kinases, and it requires the generation, expression, purification, and analysis of each mutant enzyme. In this study, we report a versatile high throughput bacterial screening system that can identify functional kinase mutants by immunological detection of tyrosine phosphorylation. Two key features of this screening system are noteworthy. First, instead of blotting bacterial colonies directly from Agar plates to nitrocellulose membrane, the colonies were cultured in 96-well plates, and then spotted in duplicate onto the membrane with appropriate controls. This made the screening much more reliable compared with direct colony blotting transfer. A second feature is the parallel use of a protein tyrosine phosphatase (PTP)-expressing host and a non-PTP-expressing host. Because high activity Src mutants are toxic to the host, the PTP system allowed the identification of Src mutants with high activity, while the non-PTP system identified Src mutants with low activity. This approach was applied to Src mutant libraries randomized in the highly conserved HRD motif in the catalytic loop, and revealed that structurally diverse residues can replace the His and Arg residues, while the Asp residue is irreplaceable for catalytic activity.
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Affiliation(s)
- Yixin Cui
- Department of Cell and Molecular Biology, Center for Biotechnology and Life Science, University of Rhode Island, 120 Flagg Road, Kingston, Rhode Island, 02881
| | - Gongqin Sun
- Department of Cell and Molecular Biology, Center for Biotechnology and Life Science, University of Rhode Island, 120 Flagg Road, Kingston, Rhode Island, 02881
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15
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Wang L, Zheng G, Liu X, Ni D, He X, Cheng J, Lu S. Molecular dynamics simulations provide insights into the origin of gleevec's selectivity toward human tyrosine kinases. J Biomol Struct Dyn 2018; 37:2733-2744. [PMID: 30052122 DOI: 10.1080/07391102.2018.1496139] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Protein kinases are critical drug targets against cancer. Since the discovery of Gleevec, a specific inhibitor of Abl kinase, the capability of this drug to distinguish between Abl and other tyrosine kinases, such as Src, has been intensely investigated but the origin of Gleevec's selectivity to Abl against Src is less studied. Here, we performed molecular dynamics (MD) simulations, dynamical cross-correlation matrices (DCCM), dynamical network analysis, and binding free energy calculations to explore Gleevec's selectivity based on the crystal structures of Abl, Src, and their common ancestors (ANC-AS) and the two constructed mutation systems (AS→Abl and AS→Src). MD simulations revealed that the conformation of the phosphate-binding loop (P-loop) was altered significantly in the AS→Abl system. DCCM results unraveled that mutations increased anticorrelated motions in the AS→Abl system. Community network analysis suggested that the P-loop established special contacts in the AS→Abl system that are devoid in the AS→Src system. The binding free energy calculations unveiled that the affinity of Gleevec to AS→Abl increased to near the Abl level, whereas its affinity to AS→Src decreased to near the Src level. Analysis of individual residue contributions showed that the differences were located mainly at the P-loop. This study is valuable for understanding the sensitivity of Gleevec to human tyrosine kinases. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Lulu Wang
- a Department of Critical Care Medicine , Binzhou Medical University Hospital , Binzhou , Shandong , China
| | - Guodong Zheng
- b Department of VIP clinic , Changhai Hospital, Naval Military Medical University , Shanghai , China
| | - Xianxian Liu
- c Department of Infectious Diseases , Binzhou Medical University Hospital , Binzhou , Shandong , China
| | - Duan Ni
- d Department of Pathophysiology Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education , Shanghai Jiao Tong University, School of Medicine , Shanghai , China
| | - Xinheng He
- d Department of Pathophysiology Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education , Shanghai Jiao Tong University, School of Medicine , Shanghai , China
| | - Jinying Cheng
- c Department of Infectious Diseases , Binzhou Medical University Hospital , Binzhou , Shandong , China
| | - Shaoyong Lu
- d Department of Pathophysiology Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education , Shanghai Jiao Tong University, School of Medicine , Shanghai , China
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16
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Shah NH, Amacher JF, Nocka LM, Kuriyan J. The Src module: an ancient scaffold in the evolution of cytoplasmic tyrosine kinases. Crit Rev Biochem Mol Biol 2018; 53:535-563. [PMID: 30183386 PMCID: PMC6328253 DOI: 10.1080/10409238.2018.1495173] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Tyrosine kinases were first discovered as the protein products of viral oncogenes. We now know that this large family of metazoan enzymes includes nearly one hundred structurally diverse members. Tyrosine kinases are broadly classified into two groups: the transmembrane receptor tyrosine kinases, which sense extracellular stimuli, and the cytoplasmic tyrosine kinases, which contain modular ligand-binding domains and propagate intracellular signals. Several families of cytoplasmic tyrosine kinases have in common a core architecture, the "Src module," composed of a Src-homology 3 (SH3) domain, a Src-homology 2 (SH2) domain, and a kinase domain. Each of these families is defined by additional elaborations on this core architecture. Structural, functional, and evolutionary studies have revealed a unifying set of principles underlying the activity and regulation of tyrosine kinases built on the Src module. The discovery of these conserved properties has shaped our knowledge of the workings of protein kinases in general, and it has had important implications for our understanding of kinase dysregulation in disease and the development of effective kinase-targeted therapies.
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Affiliation(s)
- Neel H. Shah
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Jeanine F. Amacher
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Laura M. Nocka
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - John Kuriyan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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17
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Shah NH, Löbel M, Weiss A, Kuriyan J. Fine-tuning of substrate preferences of the Src-family kinase Lck revealed through a high-throughput specificity screen. eLife 2018; 7:35190. [PMID: 29547119 PMCID: PMC5889215 DOI: 10.7554/elife.35190] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 03/15/2018] [Indexed: 01/04/2023] Open
Abstract
The specificity of tyrosine kinases is attributed predominantly to localization effects dictated by non-catalytic domains. We developed a method to profile the specificities of tyrosine kinases by combining bacterial surface-display of peptide libraries with next-generation sequencing. Using this, we showed that the tyrosine kinase ZAP-70, which is critical for T cell signaling, discriminates substrates through an electrostatic selection mechanism encoded within its catalytic domain (Shah et al., 2016). Here, we expand this high-throughput platform to analyze the intrinsic specificity of any tyrosine kinase domain against thousands of peptides derived from human tyrosine phosphorylation sites. Using this approach, we find a difference in the electrostatic recognition of substrates between the closely related Src-family kinases Lck and c-Src. This divergence likely reflects the specialization of Lck to act in concert with ZAP-70 in T cell signaling. These results point to the importance of direct recognition at the kinase active site in fine-tuning specificity.
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Affiliation(s)
- Neel H Shah
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Mark Löbel
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Arthur Weiss
- Department of Medicine, Rosalind Russell/Ephraim P Engleman Rheumatology Research Center, University of California, San Francisco, San Francisco, United States.,Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| | - John Kuriyan
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
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18
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von Raußendorf F, de Ruiter A, Leonard TA. A switch in nucleotide affinity governs activation of the Src and Tec family kinases. Sci Rep 2017; 7:17405. [PMID: 29234112 PMCID: PMC5727165 DOI: 10.1038/s41598-017-17703-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 11/29/2017] [Indexed: 11/10/2022] Open
Abstract
The Tec kinases, closely related to Src family kinases, are essential for lymphocyte function in the adaptive immune system. Whilst the Src and Abl kinases are regulated by tail phosphorylation and N-terminal myristoylation respectively, the Tec kinases are notable for the absence of either regulatory element. We have found that the inactive conformations of the Tec kinase Itk and Src preferentially bind ADP over ATP, stabilising both proteins. We demonstrate that Itk adopts the same conformation as Src and that the autoinhibited conformation of Src is independent of its C-terminal tail. Allosteric activation of both Itk and Src depends critically on the disruption of a conserved hydrophobic stack that accompanies regulatory domain displacement. We show that a conformational switch permits the exchange of ADP for ATP, leading to efficient autophosphorylation and full activation. In summary, we propose a universal mechanism for the activation and autoinhibition of the Src and Tec kinases.
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Affiliation(s)
- Freia von Raußendorf
- Department of Structural and Computational Biology, Max F. Perutz Laboratories (MFPL), Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Anita de Ruiter
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences (BOKU), 1190, Vienna, Austria
| | - Thomas A Leonard
- Department of Structural and Computational Biology, Max F. Perutz Laboratories (MFPL), Campus Vienna Biocenter 5, 1030, Vienna, Austria.
- Department of Medical Biochemistry, Medical University of Vienna, 1090, Vienna, Austria.
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19
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Advani G, Lim YC, Catimel B, Lio DSS, Ng NLY, Chüeh AC, Tran M, Anasir MI, Verkade H, Zhu HJ, Turk BE, Smithgall TE, Ang CS, Griffin M, Cheng HC. Csk-homologous kinase (Chk) is an efficient inhibitor of Src-family kinases but a poor catalyst of phosphorylation of their C-terminal regulatory tyrosine. Cell Commun Signal 2017; 15:29. [PMID: 28784162 PMCID: PMC5547543 DOI: 10.1186/s12964-017-0186-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 07/28/2017] [Indexed: 11/10/2022] Open
Abstract
Background C-terminal Src kinase (Csk) and Csk-homologous kinase (Chk) are the major endogenous inhibitors of Src-family kinases (SFKs). They employ two mechanisms to inhibit SFKs. First, they phosphorylate the C-terminal tail tyrosine which stabilizes SFKs in a closed inactive conformation by engaging the SH2 domain in cis. Second, they employ a non-catalytic inhibitory mechanism involving direct binding of Csk and Chk to the active forms of SFKs that is independent of phosphorylation of their C-terminal tail. Csk and Chk are co-expressed in many cell types. Contributions of the two mechanisms towards the inhibitory activity of Csk and Chk are not fully clear. Furthermore, the determinants in Csk and Chk governing their inhibition of SFKs by the non-catalytic inhibitory mechanism are yet to be defined. Methods We determined the contributions of the two mechanisms towards the inhibitory activity of Csk and Chk both in vitro and in transduced colorectal cancer cells. Specifically, we assayed the catalytic activities of Csk and Chk in phosphorylating a specific peptide substrate and a recombinant SFK member Src. We employed surface plasmon resonance spectroscopy to measure the kinetic parameters of binding of Csk, Chk and their mutants to a constitutively active mutant of the SFK member Hck. Finally, we determined the effects of expression of recombinant Chk on anchorage-independent growth and SFK catalytic activity in Chk-deficient colorectal cancer cells. Results Our results revealed Csk as a robust enzyme catalysing phosphorylation of the C-terminal tail tyrosine of SFKs but a weak non-catalytic inhibitor of SFKs. In contrast, Chk is a poor catalyst of SFK tail phosphorylation but binds SFKs with high affinity, enabling it to efficiently inhibit SFKs with the non-catalytic inhibitory mechanism both in vitro and in transduced colorectal cancer cells. Further analyses mapped some of the determinants governing this non-catalytic inhibitory mechanism of Chk to its kinase domain. Conclusions SFKs are activated by different upstream signals to adopt multiple active conformations in cells. SFKs adopting these conformations can effectively be constrained by the two complementary inhibitory mechanisms of Csk and Chk. Furthermore, the lack of this non-catalytic inhibitory mechanism accounts for SFK overactivation in the Chk-deficient colorectal cancer cells. Electronic supplementary material The online version of this article (doi:10.1186/s12964-017-0186-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gahana Advani
- Department of Biochemistry & Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia.,Bio21 Biotechnology and Molecular Science Institute, University of Melbourne, Parkville, VIC, 3010, Australia.,Cell Signalling Research Laboratories, School of Biomedical Sciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Ya Chee Lim
- Department of Biochemistry & Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia.,PAP Rashidah Sa'adatul Bolkiah Institute of Health Sciences, Universiti Brunei Darussalam, Gadong, Brunei Darussalam
| | - Bruno Catimel
- Walter and Eliza Hall Institute for Medical Research and Department of Medical Biology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Daisy Sio Seng Lio
- Department of Biochemistry & Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia.,Bio21 Biotechnology and Molecular Science Institute, University of Melbourne, Parkville, VIC, 3010, Australia.,Cell Signalling Research Laboratories, School of Biomedical Sciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Nadia L Y Ng
- Department of Biochemistry & Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia.,Bio21 Biotechnology and Molecular Science Institute, University of Melbourne, Parkville, VIC, 3010, Australia.,Cell Signalling Research Laboratories, School of Biomedical Sciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Anderly C Chüeh
- Walter and Eliza Hall Institute for Medical Research and Department of Medical Biology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Mai Tran
- Department of Biochemistry & Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia.,Bio21 Biotechnology and Molecular Science Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Mohd Ishtiaq Anasir
- Department of Biochemistry & Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia.,Bio21 Biotechnology and Molecular Science Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Heather Verkade
- Department of Biochemistry & Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Hong-Jian Zhu
- Department of Surgery, University of Melbourne, Royal Melbourne Hospital, Parkville, VIC, 3052, Australia
| | - Benjamin E Turk
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
| | - Thomas E Smithgall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Ching-Seng Ang
- Bio21 Biotechnology and Molecular Science Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Michael Griffin
- Department of Biochemistry & Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia.,Bio21 Biotechnology and Molecular Science Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Heung-Chin Cheng
- Department of Biochemistry & Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia. .,Bio21 Biotechnology and Molecular Science Institute, University of Melbourne, Parkville, VIC, 3010, Australia. .,Cell Signalling Research Laboratories, School of Biomedical Sciences, University of Melbourne, Parkville, VIC, 3010, Australia.
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20
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78495111110.3390/cancers9050052" />
Abstract
The epidermal growth factor receptor (EGFR) is a receptor tyrosine kinase that is commonly upregulated in cancers such as in non-small-cell lung cancer, metastatic colorectal cancer, glioblastoma, head and neck cancer, pancreatic cancer, and breast cancer. Various mechanisms mediate the upregulation of EGFR activity, including common mutations and truncations to its extracellular domain, such as in the EGFRvIII truncations, as well as to its kinase domain, such as the L858R and T790M mutations, or the exon 19 truncation. These EGFR aberrations over-activate downstream pro-oncogenic signaling pathways, including the RAS-RAF-MEK-ERK MAPK and AKT-PI3K-mTOR pathways. These pathways then activate many biological outputs that are beneficial to cancer cell proliferation, including their chronic initiation and progression through the cell cycle. Here, we review the molecular mechanisms that regulate EGFR signal transduction, including the EGFR structure and its mutations, ligand binding and EGFR dimerization, as well as the signaling pathways that lead to G1 cell cycle progression. We focus on the induction of CYCLIN D expression, CDK4/6 activation, and the repression of cyclin-dependent kinase inhibitor proteins (CDKi) by EGFR signaling pathways. We also discuss the successes and challenges of EGFR-targeted therapies, and the potential for their use in combination with CDK4/6 inhibitors.
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21
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Wee P, Wang Z. Epidermal Growth Factor Receptor Cell Proliferation Signaling Pathways. Cancers (Basel) 2017; 9:cancers9050052. [PMID: 28513565 PMCID: PMC5447962 DOI: 10.3390/cancers9050052] [Citation(s) in RCA: 1001] [Impact Index Per Article: 143.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 05/10/2017] [Accepted: 05/10/2017] [Indexed: 12/12/2022] Open
Abstract
The epidermal growth factor receptor (EGFR) is a receptor tyrosine kinase that is commonly upregulated in cancers such as in non-small-cell lung cancer, metastatic colorectal cancer, glioblastoma, head and neck cancer, pancreatic cancer, and breast cancer. Various mechanisms mediate the upregulation of EGFR activity, including common mutations and truncations to its extracellular domain, such as in the EGFRvIII truncations, as well as to its kinase domain, such as the L858R and T790M mutations, or the exon 19 truncation. These EGFR aberrations over-activate downstream pro-oncogenic signaling pathways, including the RAS-RAF-MEK-ERK MAPK and AKT-PI3K-mTOR pathways. These pathways then activate many biological outputs that are beneficial to cancer cell proliferation, including their chronic initiation and progression through the cell cycle. Here, we review the molecular mechanisms that regulate EGFR signal transduction, including the EGFR structure and its mutations, ligand binding and EGFR dimerization, as well as the signaling pathways that lead to G1 cell cycle progression. We focus on the induction of CYCLIN D expression, CDK4/6 activation, and the repression of cyclin-dependent kinase inhibitor proteins (CDKi) by EGFR signaling pathways. We also discuss the successes and challenges of EGFR-targeted therapies, and the potential for their use in combination with CDK4/6 inhibitors.
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Affiliation(s)
- Ping Wee
- Department of Medical Genetics and Signal Transduction Research Group, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.
| | - Zhixiang Wang
- Department of Medical Genetics and Signal Transduction Research Group, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.
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22
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Musumeci F, Fallacara AL, Brullo C, Grossi G, Botta L, Calandro P, Chiariello M, Kissova M, Crespan E, Maga G, Schenone S. Identification of new pyrrolo[2,3-d]pyrimidines as Src tyrosine kinase inhibitors in vitro active against Glioblastoma. Eur J Med Chem 2016; 127:369-378. [PMID: 28076826 DOI: 10.1016/j.ejmech.2016.12.036] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 12/14/2016] [Accepted: 12/17/2016] [Indexed: 01/01/2023]
Abstract
In the last few years, several pyrrolo-pyrimidine derivatives have been either approved by the US FDA and in other countries for the treatment of different diseases or are currently in phase I/II clinical trials. Herein we present the synthesis and the characterization of a novel series of pyrrolo[2,3-d]pyrimidines, compounds 8a-j, and their activity against Glioblastoma multiforme (GBM). Docking studies and MM-GBSA analysis revealed the ability of such compounds to efficiently interact with the ATP binding site of Src. Enzymatic assays against a mini-panel of kinases (Src, Fyn, EGFR, Kit, Flt3, Abl, AblT315I) have been performed, showing an unexpected selectivity of our pyrrolo[2,3-d]pyrimidines for Src. Finally, the derivatives were tested for their antiproliferative potency on U87 GBM cell line. Compound 8h showed a considerable cytotoxicity effect against U87 cell line with an IC50 value of 7.1 μM.
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Affiliation(s)
- Francesca Musumeci
- Dipartimento di Farmacia, Università degli Studi di Genova, Viale Benedetto XV, 3, 16132 Genova, Italy
| | - Anna Lucia Fallacara
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Chiara Brullo
- Dipartimento di Farmacia, Università degli Studi di Genova, Viale Benedetto XV, 3, 16132 Genova, Italy
| | - Giancarlo Grossi
- Dipartimento di Farmacia, Università degli Studi di Genova, Viale Benedetto XV, 3, 16132 Genova, Italy
| | - Lorenzo Botta
- Dipartimento di Farmacia, Università"Federico II" di Napoli, Via D. Montesano 49, 80131 Napoli, Italy
| | - Pierpaolo Calandro
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Mario Chiariello
- Consiglio Nazionale delle Ricerche, Istituto di Fisiologia Clinica and Istituto Toscano Tumori, Core Research Laboratory, Via Fiorentina 1, 53100 Siena, Italy
| | - Miroslava Kissova
- Consiglio Nazionale delle Ricerche, Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Emmanuele Crespan
- Consiglio Nazionale delle Ricerche, Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Giovanni Maga
- Consiglio Nazionale delle Ricerche, Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Silvia Schenone
- Dipartimento di Farmacia, Università degli Studi di Genova, Viale Benedetto XV, 3, 16132 Genova, Italy.
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23
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Abstract
A new bioinformatics tool predicts natively disordered protein control elements that function in cis, opening the door to more systematic studies of this biomedically important class of protein modules.
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Affiliation(s)
- Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| | - Manjeet Kumar
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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24
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Zhang R, Zhang J, Wu Q, Meng F, Liu C. XB130: A novel adaptor protein in cancer signal transduction. Biomed Rep 2016; 4:300-306. [PMID: 26998266 DOI: 10.3892/br.2016.588] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 01/18/2016] [Indexed: 12/13/2022] Open
Abstract
Adaptor proteins are functional proteins that contain two or more protein-binding modules to link signaling proteins together, which affect cell growth and shape and have no enzymatic activity. The actin filament-associated protein (AFAP) family is an important member of the adaptor proteins, including AFAP1, AFAP1L1 and AFAP1L2/XB130. AFAP1 and AFAP1L1 share certain common characteristics and function as an actin-binding protein and a cSrc-activating protein. XB130 exhibits certain unique features in structure and function. The mRNA of XB130 is expressed in human spleen, thyroid, kidney, brain, lung, pancreas, liver, colon and stomach, and the most prominent disease associated with XB130 is cancer. XB130 has a controversial effect on cancer. Studies have shown that XB130 can promote cancer progression and downregulation of XB130-reduced growth of tumors derived from certain cell lines. A higher mRNA level of XB130 was shown to be associated with a better survival in non-small cell lung cancer. Previous studies have shown that XB130 can regulate cell growth, migration and invasion and possibly has the effect through the cAMP-cSrc-phosphoinositide 3-kinase/Akt pathway. Except for cancer, XB130 is also associated with other pathological or physiological procedures, such as airway repair and regeneration.
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Affiliation(s)
- Ruiyao Zhang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shannxi 710061, P.R. China
| | - Jingyao Zhang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shannxi 710061, P.R. China
| | - Qifei Wu
- Department of Thoracic Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shannxi 710061, P.R. China
| | - Fandi Meng
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shannxi 710061, P.R. China
| | - Chang Liu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shannxi 710061, P.R. China
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25
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Roskoski R. Src protein-tyrosine kinase structure, mechanism, and small molecule inhibitors. Pharmacol Res 2015; 94:9-25. [PMID: 25662515 DOI: 10.1016/j.phrs.2015.01.003] [Citation(s) in RCA: 369] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 01/26/2015] [Indexed: 12/13/2022]
Abstract
The physiological Src proto-oncogene is a protein-tyrosine kinase that plays key roles in cell growth, division, migration, and survival signaling pathways. From the N- to C-terminus, Src contains a unique domain, an SH3 domain, an SH2 domain, a protein-tyrosine kinase domain, and a regulatory tail. The chief phosphorylation sites of human Src include an activating pTyr419 that results from phosphorylation in the kinase domain by an adjacent Src molecule and an inhibitory pTyr530 in the regulatory tail that results from phosphorylation by C-terminal Src kinase (Csk) or Chk (Csk homologous kinase). The oncogenic Rous sarcoma viral protein lacks the equivalent of Tyr530 and is constitutively activated. Inactive Src is stabilized by SH2 and SH3 domains on the rear of the kinase domain where they form an immobilizing and inhibitory clamp. Protein kinases including Src contain hydrophobic regulatory and catalytic spines and collateral shell residues that are required to assemble the active enzyme. In the inactive enzyme, the regulatory spine contains a kink or a discontinuity with a structure that is incompatible with catalysis. The conversion of inactive to active Src is accompanied by electrostatic exchanges involving the breaking and making of distinct sets of kinase domain salt bridges and hydrogen bonds. Src-catalyzed protein phosphorylation requires the participation of two Mg(2+) ions. Although nearly all protein kinases possess a common K/E/D/D signature, each enzyme exhibits its unique variations of the protein-kinase reaction template. Bosutinib, dasatinib, and ponatinib are Src/multikinase inhibitors that are approved by the FDA for the treatment of chronic myelogenous leukemia and vandetanib is approved for the treatment of medullary thyroid cancer. The Src and BCR-Abl inhibitors saracatinib and AZD0424, along with the previous four drugs, are in clinical trials for a variety of solid tumors including breast and lung cancers. Both ATP and targeted therapeutic Src protein kinase inhibitors such as dasatinib and ponatinib make hydrophobic contacts with catalytic spine residues and form hydrogen bonds with hinge residues connecting the small and large kinase lobes.
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Affiliation(s)
- Robert Roskoski
- Blue Ridge Institute for Medical Research, 3754 Brevard Road, Suite 116, Box 19, Horse Shoe, NC 28742-8814, United States.
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26
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Energetic dissection of Gleevec's selectivity toward human tyrosine kinases. Nat Struct Mol Biol 2014; 21:848-53. [PMID: 25218445 PMCID: PMC4266587 DOI: 10.1038/nsmb.2891] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 08/20/2014] [Indexed: 01/16/2023]
Abstract
Protein kinases are obvious drug targets against cancer due to their central role in cellular regulation. Since the discovery of Gleevec, a potent and specific inhibitor of Abl kinase, as a highly successful cancer therapeutic, the ability of this drug to distinguish between Abl and other tyrosine kinases like Src has been intensely investigated, but without much success. Using NMR and fast kinetics, we establish a novel model that solves this longstanding question of two tyrosine kinases adopting almost identical structures when bound to Gleevec, yet having vastly different affinities. In contrast to all other proposed models we show that the origin of Abl’s high affinity lies predominantly in a conformational change after binding. An energy landscape that provides tight affinity via an induced-fit and binding plasticity via conformational selection mechanism is likely to be general for many inhibitors.
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27
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Chylek LA, Akimov V, Dengjel J, Rigbolt KTG, Hu B, Hlavacek WS, Blagoev B. Phosphorylation site dynamics of early T-cell receptor signaling. PLoS One 2014; 9:e104240. [PMID: 25147952 PMCID: PMC4141737 DOI: 10.1371/journal.pone.0104240] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 07/07/2014] [Indexed: 11/18/2022] Open
Abstract
In adaptive immune responses, T-cell receptor (TCR) signaling impacts multiple cellular processes and results in T-cell differentiation, proliferation, and cytokine production. Although individual protein-protein interactions and phosphorylation events have been studied extensively, we lack a systems-level understanding of how these components cooperate to control signaling dynamics, especially during the crucial first seconds of stimulation. Here, we used quantitative proteomics to characterize reshaping of the T-cell phosphoproteome in response to TCR/CD28 co-stimulation, and found that diverse dynamic patterns emerge within seconds. We detected phosphorylation dynamics as early as 5 s and observed widespread regulation of key TCR signaling proteins by 30 s. Development of a computational model pointed to the presence of novel regulatory mechanisms controlling phosphorylation of sites with central roles in TCR signaling. The model was used to generate predictions suggesting unexpected roles for the phosphatase PTPN6 (SHP-1) and shortcut recruitment of the actin regulator WAS. Predictions were validated experimentally. This integration of proteomics and modeling illustrates a novel, generalizable framework for solidifying quantitative understanding of a signaling network and for elucidating missing links.
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Affiliation(s)
- Lily A. Chylek
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, United States of America
| | - Vyacheslav Akimov
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Jörn Dengjel
- Department of Dermatology, Medical Center; Freiburg Institute for Advanced Studies (FRIAS); BIOSS Centre for Biological Signalling Studies; ZBSA Center for Biological Systems Analysis, University of Freiburg, Freiburg, Germany
| | - Kristoffer T. G. Rigbolt
- Department of Dermatology, Medical Center; Freiburg Institute for Advanced Studies (FRIAS); BIOSS Centre for Biological Signalling Studies; ZBSA Center for Biological Systems Analysis, University of Freiburg, Freiburg, Germany
| | - Bin Hu
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - William S. Hlavacek
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Blagoy Blagoev
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
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28
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Leonard SE, Register AC, Krishnamurty R, Brighty GJ, Maly DJ. Divergent modulation of Src-family kinase regulatory interactions with ATP-competitive inhibitors. ACS Chem Biol 2014; 9:1894-905. [PMID: 24946274 PMCID: PMC4136698 DOI: 10.1021/cb500371g] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
Multidomain protein kinases, central
controllers of signal transduction,
use regulatory domains to modulate catalytic activity in a complex
cellular environment. Additionally, these domains regulate noncatalytic
functions, including cellular localization and protein–protein
interactions. Src-family kinases (SFKs) are promising therapeutic
targets for a number of diseases and are an excellent model for studying
the regulation of multidomain kinases. Here, we demonstrate that the
regulatory domains of the SFKs Src and Hck are divergently affected
by ligands that stabilize two distinct inactive ATP-binding site conformations.
Conformation-selective, ATP-competitive inhibitors differentially
modulate the ability of the SH3 and SH2 domains of Src and Hck to
engage in intermolecular interactions and the ability of the kinase–inhibitor
complex to undergo post-translational modification by effector enzymes.
This surprising divergence in regulatory domain behavior by two classes
of inhibitors that each stabilize inactive ATP-binding site conformations
is found to occur through perturbation or stabilization of the αC
helix. These studies provide insight into how conformation-selective,
ATP-competitive inhibitors can be designed to modulate domain interactions
and post-translational modifications distal to the ATP-binding site
of kinases.
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Affiliation(s)
- Stephen E. Leonard
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - A. C. Register
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Ratika Krishnamurty
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Gabriel J. Brighty
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Dustin J. Maly
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
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29
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Alvarado JJ, Tarafdar S, Yeh JI, Smithgall TE. Interaction with the Src homology (SH3-SH2) region of the Src-family kinase Hck structures the HIV-1 Nef dimer for kinase activation and effector recruitment. J Biol Chem 2014; 289:28539-53. [PMID: 25122770 DOI: 10.1074/jbc.m114.600031] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
HIV-1 Nef supports high titer viral replication in vivo and is essential for AIDS progression. Nef function depends on interactions with multiple host cell effectors, including Hck and other Src-family kinases. Here we describe the x-ray crystal structure of Nef in complex with the Hck SH3-SH2 regulatory region to a resolution of 1.86 Å. The complex crystallized as a dimer of complexes, with the conserved Nef PXXPXR motif engaging the Hck SH3 domain. A new intercomplex contact was found between SH3 Glu-93, and Nef Arg-105. Mutagenesis of Hck SH3 Glu-93 interfered with Nef·Hck complex formation and kinase activation in cells. The Hck SH2 domains impinge on the N-terminal region of Nef to stabilize a dimer conformation that exposes Asp-123, a residue critical for Nef function. Our results suggest that in addition to serving as a kinase effector for Nef, Hck binding may reorganize the Nef dimer for functional interaction with other signaling partners.
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Affiliation(s)
- John Jeff Alvarado
- From the Departments of Microbiology and Molecular Genetics and Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15219 and
| | - Sreya Tarafdar
- From the Departments of Microbiology and Molecular Genetics and Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15261
| | - Joanne I Yeh
- Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15219 and
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30
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Bartolomé RA, Díaz-Martínez M, Coló GP, Arellano-Sánchez N, Torres-Ayuso P, Kleinovink JW, Mérida I, Teixidó J. A Blk-p190RhoGAP signaling module downstream of activated Gα13 functionally opposes CXCL12-stimulated RhoA activation and cell invasion. Cell Signal 2014; 26:2551-61. [PMID: 25025568 DOI: 10.1016/j.cellsig.2014.07.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 06/30/2014] [Accepted: 07/08/2014] [Indexed: 11/27/2022]
Abstract
Activation of the GTPase RhoA linked to cell invasion can be tightly regulated following Gα13 stimulation. We have used a cellular model displaying Gα13-dependent inhibition of RhoA activation associated with defective cell invasion to the chemokine CXCL12 to characterize the molecular players regulating these processes. Using both RNAi transfection approaches and protein overexpression experiments here we show that the Src kinase Blk is involved in Gα13-activated tyrosine phosphorylation of p190RhoGAP, which causes RhoA inactivation and ultimately leads to deficient cell invasion. Characterization of molecular interplays between Gα13, Blk and p190RhoGAP revealed that Blk binds Gα13, and that Blk-mediated p190RhoGAP phosphorylation upon Gα13 activation correlates with weakening of Gα13-Blk association connected to increased Blk-p190RhoGAP assembly. These results place Blk upstream of the p190RhoGAP-RhoA pathway in Gα13-activated cells, overall representing an opposing signaling module during CXCL12-triggered invasion. In addition, analyses with Blk- or Gα13-knockdown cells indicated that Blk can also mediate CXCL12-triggered phosphorylation of p190RhoGAP independently of Gα13. However, even if CXCL12 induces the Blk-mediated GAP phosphorylation, the simultaneous stimulation of the guanine-nucleotide exchange factor Vav1 by the chemokine, as earlier reported, leads to a net increase in RhoA activation. Therefore, when Gα13 is concurrently stimulated with CXCL12 there appears to be sufficient Blk activity to promote adequate levels of p190RhoGAP tyrosine phosphorylation to inactivate RhoA and to impair cell invasiveness.
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Affiliation(s)
- Rubén A Bartolomé
- Department of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas (CSIC), 28040 Madrid, Spain
| | - Marta Díaz-Martínez
- Department of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas (CSIC), 28040 Madrid, Spain
| | - Georgina P Coló
- Department of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas (CSIC), 28040 Madrid, Spain
| | - Nohemí Arellano-Sánchez
- Department of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas (CSIC), 28040 Madrid, Spain
| | - Pedro Torres-Ayuso
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CSIC), 28049 Madrid, Spain
| | - Jan Willem Kleinovink
- Department of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas (CSIC), 28040 Madrid, Spain
| | - Isabel Mérida
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CSIC), 28049 Madrid, Spain
| | - Joaquin Teixidó
- Department of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas (CSIC), 28040 Madrid, Spain.
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31
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Reynolds AB, Kanner SB, Bouton AH, Schaller MD, Weed SA, Flynn DC, Parsons JT. SRChing for the substrates of Src. Oncogene 2013; 33:4537-47. [PMID: 24121272 DOI: 10.1038/onc.2013.416] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 08/16/2013] [Accepted: 08/17/2013] [Indexed: 12/12/2022]
Abstract
By the mid 1980's, it was clear that the transforming activity of oncogenic Src was linked to the activity of its tyrosine kinase domain and attention turned to identifying substrates, the putative next level of control in the pathway to transformation. Among the first to recognize the potential of phosphotyrosine-specific antibodies, Parsons and colleagues launched a risky shotgun-based approach that led ultimately to the cDNA cloning and functional characterization of many of today's best-known Src substrates (for example, p85-Cortactin, p110-AFAP1, p130Cas, p125FAK and p120-catenin). Two decades and over 6000 citations later, the original goals of the project may be seen as secondary to the enormous impact of these protein substrates in many areas of biology. At the request of the editors, this review is not restricted to the current status of the substrates, but reflects also on the anatomy of the project itself and some of the challenges and decisions encountered along the way.
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Affiliation(s)
- A B Reynolds
- Department of Cancer Biology, Vanderbilt University, Nashville, TN, USA
| | - S B Kanner
- Arrowhead Research Corporation, Madison, WI, USA
| | - A H Bouton
- Departments of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - M D Schaller
- Department of Biochemistry, 3124 HSN, Robert C. Byrd Health Sciences Center, West Virginia University School of Medicine, Morgantown, WV, USA
| | - S A Weed
- Department of Neurobiology and Anatomy, 1833 Mary Babb Randolph Cancer Center, Robert C. Byrd Health Sciences Center, West Virginia University School of Medicine, Morgantown, WV, USA
| | - D C Flynn
- Department of Medical Lab Sciences, College of Health Sciences, University of Delaware, Newark, DE, USA
| | - J T Parsons
- Departments of Microbiology, Immunology and Cancer Biology, University of Virginia Cancer Center, Charlottesville, VA, USA
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32
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Bacarizo J, Camara-Artigas A. Atomic resolution structures of the c-Src SH3 domain in complex with two high-affinity peptides from classes I and II. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:756-66. [PMID: 23633584 DOI: 10.1107/s0907444913001522] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 01/15/2013] [Indexed: 12/20/2022]
Abstract
The atomic resolution crystal structures of complexes between the SH3 domain of the c-Src tyrosine kinase and two high-affinity peptides belonging to class I and class II have been solved. The crystals of the Thr98Asp and Thr98Glu mutants in complex with the APP12 peptide (APPLPPRNRPRL) belonged to the trigonal space group P3121 and in both cases the asymmetric unit was composed of one molecule of the SH3-APP12 complex. The crystals of the Thr98Glu mutant in complex with the VSL12 peptide (VSLARRPLPLP) belonged to the trigonal space group P3221 and the asymmetric unit was also composed of a single molecule of the SH3-VSL12 complex. All crystals were obtained in the presence of PEG 300 under the same conditions as reported for the intertwined dimeric structure of the c-Src SH3 domain, but the presence of the peptide stabilizes the monomeric form of the domain. These structures allow a detailed analysis of the role of salt bridges, cation-π interactions and hydrogen bonds in the binding of proline-rich motifs to the c-Src SH3 domain. Moreover, these crystallographic structures allow the role of water molecules in the binding of these motifs to the c-Src SH3 domain to be studied for the first time.
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Affiliation(s)
- Julio Bacarizo
- Department of Chemistry and Physics, University of Almería, Agrifood Campus of International Excellence, Carretera de Sacramento, 04120 Almería, Spain
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33
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Hossain S, Dubielecka PM, Sikorski AF, Birge RB, Kotula L. Crk and ABI1: binary molecular switches that regulate abl tyrosine kinase and signaling to the cytoskeleton. Genes Cancer 2012; 3:402-13. [PMID: 23226578 DOI: 10.1177/1947601912460051] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The nonreceptor tyrosine kinases Abl and Arg are among the most well-characterized tyrosine kinases in the human genome. The activation of Abl by N-terminal fusions with Bcr (Bcr-Abl) or Gag (v-Abl) is responsible for chronic myeloid leukemia or Ph+ acute lymphoblastic leukemia and mouse leukemia virus, respectively. In addition, aberrant Abl and Arg activation downstream of several oncogenic growth factor receptors contributes to the development and progression of a variety of human cancers, often associated with poor clinical outcome, drug resistance, and tumor invasion and metastasis. Abl activation can occur by a variety of mechanisms that include domain interactions involving structural remodeling of autoinhibited conformations as well as direct phosphorylation by upstream kinases and phosphatases. Constitutive activation of Abl plays a significant role in regulating the actin cytoskeleton by modulating cell adhesion, motility, and invadopodia. This review addresses the role of Abl and Arg in tumor progression with particular emphasis on the roles of Crk and Abi1 adapter proteins as distinct molecular switches for Abl transactivation. These insights, combined with new insights into the structure of these kinases, provide the rationale to envision that Crk and Abi1 fine-tune Abl regulation to control signaling to the cytoskeleton.
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Affiliation(s)
- Sajjad Hossain
- New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA ; Current address: Stony Brook University, Stony Brook, NY, USA
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34
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The role of Src kinase in macrophage-mediated inflammatory responses. Mediators Inflamm 2012; 2012:512926. [PMID: 23209344 PMCID: PMC3504478 DOI: 10.1155/2012/512926] [Citation(s) in RCA: 204] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2012] [Accepted: 09/28/2012] [Indexed: 12/28/2022] Open
Abstract
Src kinase (Src) is a tyrosine protein kinase that regulates cellular metabolism, survival, and proliferation. Many studies have shown that Src plays multiple roles in macrophage-mediated innate immunity, such as phagocytosis, the production of inflammatory cytokines/mediators, and the induction of cellular migration, which strongly implies that Src plays a pivotal role in the functional activation of macrophages. Macrophages are involved in a variety of immune responses and in inflammatory diseases including rheumatoid arthritis, atherosclerosis, diabetes, obesity, cancer, and osteoporosis. Previous studies have suggested roles for Src in macrophage-mediated inflammatory responses; however, recently, new functions for Src have been reported, implying that Src functions in macrophage-mediated inflammatory responses that have not been described. In this paper, we discuss recent studies regarding a number of these newly defined functions of Src in macrophage-mediated inflammatory responses. Moreover, we discuss the feasibility of Src as a target for the development of new pharmaceutical drugs to treat macrophage-mediated inflammatory diseases. We provide insights into recent reports regarding new functions for Src that are related to macrophage-related inflammatory responses and the development of novel Src inhibitors with strong immunosuppressive and anti-inflammatory properties, which could be applied to various macrophage-mediated inflammatory diseases.
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35
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Abstract
Abl kinases are prototypic cytoplasmic tyrosine kinases and are involved in a variety of chromosomal aberrations in different cancers. This causes the expression of Abl fusion proteins, such as Bcr-Abl, that are constitutively activated and drivers of tumorigenesis. Over the past decades, biochemical and functional studies on the molecular mechanisms of Abl regulation have gone hand in hand with progression of our structural understanding of autoinhibited and active Abl conformations. In parallel, Abl oncoproteins have become prime molecular targets for cancer therapy, using adenosine triphosphate (ATP)-competitive kinase inhibitors, such as imatinib. Abl-targeting drugs serve as a paradigm for our understanding of kinase inhibitor action, specificity, and resistance development. In this review article, I will review the molecular mechanisms that are responsible for the regulation of Abl kinase activity and how oncogenic Abl fusions signal. Furthermore, past and ongoing efforts to target Abl oncoproteins using ATP-competitive and allosteric inhibitors, as well as future possibilities using combination therapy, will be discussed.
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Affiliation(s)
- Oliver Hantschel
- École polytechnique fédérale de Lausanne (EPFL), School of Life Sciences, Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland
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36
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Huang R, Fang P, Kay BK. Isolation of monobodies that bind specifically to the SH3 domain of the Fyn tyrosine protein kinase. N Biotechnol 2011; 29:526-33. [PMID: 22155429 DOI: 10.1016/j.nbt.2011.11.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Revised: 10/24/2011] [Accepted: 11/27/2011] [Indexed: 11/15/2022]
Abstract
Fyn is a nonreceptor protein tyrosine kinase that belongs to a highly conserved kinase family, Src family kinases. Fyn plays an important role in inflammatory processes and neuronal functions. To generate a synthetic affinity reagent that can be used to probe Fyn, a phage-display library of fibronectin type III monobodies was affinity selected with the Src Homology 3 (SH3) domain of Fyn and three binders were isolated. One of the three binders, G9, is specific in binding to the SH3 domain of Fyn, but not to the other members of the Src family (i.e. Blk, Fgr, Hck, Lck, Lyn, Src and Yes), even though they share 51-81% amino acid identity. The other two bind principally to the Fyn SH3 domain, with some cross-reactivity to the Yes SH3 domain. The G9 binder has a dissociation constant of 166±6nM, as measured by isothermal titration calorimetry, and binds only to the Fyn SH3 domain out of 150 human SH3 domains examined in an array. Interestingly, although the G9 monobody lacks proline in its randomized BC and FG loops, it binds at the same site on the SH3 domain as proline-rich ligands, as revealed by competition assays. The G9 monobody, identified in this study, may be used as a highly selective probe for detecting and purifying cellular Fyn kinase.
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Affiliation(s)
- Renhua Huang
- Department of Biological Sciences, University of Illinois at Chicago, 845 W. Taylor St., 3240 SES - MC 066, Chicago, IL 60607-7060, USA
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37
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Martić S, Rains MK, Freeman D, Kraatz HB. Use of 5'-γ-ferrocenyl adenosine triphosphate (Fc-ATP) bioconjugates having poly(ethylene glycol) spacers in kinase-catalyzed phosphorylations. Bioconjug Chem 2011; 22:1663-72. [PMID: 21696155 DOI: 10.1021/bc200229y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The 5'-γ-ferrocenyl adenosine triphosphate (Fc-ATP) bioconjugates (3 and 4), containing the poly(ethylene glycol) spacers, were synthesized and compared to a hydrophobic analogue as co-substrates for the following protein kinases: sarcoma related kinase (Src), cyclin-dependent kinase (CDK), casein kinase II (CK2α), and protein kinase A (PKA). Electrochemical kinase assays indicate that the hydrophobic Fc-ATP analogue was an optimal co-substrate for which K(M) values were determined to be in the 30-200 μM range, depending on the particular protein kinase. The luminescence kinase assay demonstrated the kinase utility for all Fc-ATP conjugates, which is in line with the electrochemical data. Moreover, Fc-ATP bioconjugates exhibit competitive behavior with respect to ATP. Relatively poor performance of the polar Fc-ATP bioconjugates as co-substrates for protein kinases was presumably due to the additional H-bonding and electrostatic interactions of the poly(ethylene glycol) linkers of Fc-ATP with the kinase catalytic site and the target peptides. Phosphorylation of the full-length protein, His-tagged pro-caspase-3, was demonstrated through Fc-phosphoamide transfer to the Ser residues of the surface-bound protein by electrochemical means. These results suggest that electrochemical detection of the peptide and protein Fc-phosphorylation via tailored Fc-ATP co-substrates may be useful for probing protein-protein interactions.
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Affiliation(s)
- Sanela Martić
- Chemistry Department, The University of Western Ontario, London, Ontario, Canada
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Martić S, Labib M, Freeman D, Kraatz PHB. Probing the role of the linker in ferrocene-ATP conjugates: monitoring protein kinase catalyzed phosphorylations electrochemically. Chemistry 2011; 17:6744-52. [PMID: 21542035 DOI: 10.1002/chem.201003535] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Indexed: 11/08/2022]
Abstract
The synthesis and electrochemical properties of ferrocene conjugates are presented for the purpose of investigating adenosine 5'-[γ-ferrocenoylalkyl] triphosphate (1 a-4 a, ferrocene (Fc)-ATP) as co-substrates for phosphorylation reactions. Compounds 1 a-4 a were synthesized, purified by HPLC, and characterized by NMR spectroscopy and mass spectrometry. In solution, all Fc-ATP bioconjugates exhibit a reversible one-electron redox process with a half-wave potential (E(1/2)) in the 390-430 mV range, peak separations (ΔE(p)) in the 40-70 mV range, and the peak current ratio (i(pa)/i(pc)) near unity. The peptide-modified surface Glu-Gly-Ile-Tyr-Asp-Val-Pro was used to study the sarcoma-related protein (Src) kinase activity by employing the Fc-ATP bioconjugates as co-substrates. Subsequent kinase-catalyzed transfer of the γ-Fc-phosphate group to the tyrosine residues of the surface-bound peptides was characterized by a formal potential (E°) ≈390 mV (vs. Ag/AgCl). The Fc-coverage, estimated by time-of-flight secondary-ion mass spectrometry (TOF-SIMS) and cyclic voltammetry (CV), suggested validity of Fc-ATP conjugates as kinase co-substrates. Depending on the length of the alkyl spacer of the Fc-ATP conjugate, different current densities were obtained, pointing to a direct correlation between the two. Molecular modeling revealed that the structural constraint imposed by the short alkyl spacer (1 a) causes a steric congestion and negatively affects the outcome of phosphorylation reaction. An optimal analytical response was obtained with the Fc-ATP conjugates with linker lengths longer than six CH(2) groups.
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Affiliation(s)
- Sanela Martić
- Chemistry Department, The University of Western Ontario, London, Ontario, Canada
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Discovery and Characterization of a Cell-Permeable, Small-Molecule c-Abl Kinase Activator that Binds to the Myristoyl Binding Site. ACTA ACUST UNITED AC 2011; 18:177-86. [DOI: 10.1016/j.chembiol.2010.12.013] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Revised: 11/19/2010] [Accepted: 12/06/2010] [Indexed: 12/20/2022]
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Meiselbach H, Sticht H. Effect of the SH3-SH2 domain linker sequence on the structure of Hck kinase. J Mol Model 2010; 17:1927-34. [PMID: 21110053 DOI: 10.1007/s00894-010-0897-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Accepted: 11/03/2010] [Indexed: 11/25/2022]
Abstract
The coordination of activity in biological systems requires the existence of different signal transduction pathways that interact with one another and must be precisely regulated. The Src-family tyrosine kinases, which are found in many signaling pathways, differ in their physiological function despite their high overall structural similarity. In this context, the differences in the SH3-SH2 domain linkers might play a role for differential regulation, but the structural consequences of linker sequence remain poorly understood. We have therefore performed comparative molecular dynamics simulations of wildtype Hck and of a mutant Hck in which the SH3-SH2 domain linker is replaced by the corresponding sequence from the homologous kinase Lck. These simulations reveal that linker replacement not only affects the orientation of the SH3 domain itself, but also leads to an alternative conformation of the activation segment in the Hck kinase domain. The sequence of the SH3-SH2 domain linker thus exerts a remote effect on the active site geometry and might therefore play a role in modulating the structure of the inactive kinase or in fine-tuning the activation process itself.
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Affiliation(s)
- Heike Meiselbach
- Bioinformatik, Institut für Biochemie, Friedrich-Alexander-Universität, Fahrstraße 17, 91054 Erlangen-Nürnberg, Germany
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41
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DNA damage stress response in germ cells: role of c-Abl and clinical implications. Oncogene 2010; 29:6193-202. [PMID: 20818431 DOI: 10.1038/onc.2010.410] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cells experiencing DNA damage undergo a complex response entailing cell-cycle arrest, DNA repair and apoptosis, the relative importance of the three being modulated by the extent of the lesion. The observation that Abl interacts in the nucleus with several proteins involved in different aspects of DNA repair has led to the hypothesis that this kinase is part of the damage-sensing mechanism. However, the mechanistic details underlying the role of Abl in DNA repair remain unclear. Here, I will review the evidence supporting our current understanding of Abl activation following DNA insults, while focusing on the relevance of these mechanisms in protecting DNA-injured germ cells. Early studies have shown that Abl transcripts are highly expressed in the germ line. Abl-deficient mice exhibit multiple abnormalities, increased perinatal mortality and reduced fertility. Recent findings have implicated Abl in a cisplatin-induced signaling pathway eliciting death of immature oocytes. A p53-related protein, TAp63, is an important immediate downstream effector of this pathway. Of note, pharmacological inhibition of Abl protects the ovarian reserve from the toxic effects of cisplatin. This suggests that the extent of Abl catalytic outputs may shift the balance between survival (likely through DNA repair) and activation of a death response. Taken together, these observations are consistent with the evolutionary conserved relationship between DNA damage and activation of the p53 family of transcription factors, while shedding light on the key role of Abl in dictating the fate of germ cells upon genotoxic insults.
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Alvarado JJ, Betts L, Moroco JA, Smithgall TE, Yeh JI. Crystal structure of the Src family kinase Hck SH3-SH2 linker regulatory region supports an SH3-dominant activation mechanism. J Biol Chem 2010; 285:35455-61. [PMID: 20810664 DOI: 10.1074/jbc.m110.145102] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Most mammalian cell types depend on multiple Src family kinases (SFKs) to regulate diverse signaling pathways. Strict control of SFK activity is essential for normal cellular function, and loss of kinase regulation contributes to several forms of cancer and other diseases. Previous x-ray crystal structures of the SFKs c-Src and Hck revealed that intramolecular association of their Src homology (SH) 3 domains and SH2 kinase linker regions has a key role in down-regulation of kinase activity. However, the amino acid sequence of the Hck linker represents a suboptimal ligand for the isolated SH3 domain, suggesting that it may form the polyproline type II helical conformation required for SH3 docking only in the context of the intact structure. To test this hypothesis directly, we determined the crystal structure of a truncated Hck protein consisting of the SH2 and SH3 domains plus the linker. Despite the absence of the kinase domain, the structures and relative orientations of the SH2 and SH3 domains in this shorter protein were very similar to those observed in near full-length, down-regulated Hck. However, the SH2 kinase linker adopted a modified topology and failed to engage the SH3 domain. This new structure supports the idea that these noncatalytic regions work together as a "conformational switch" that modulates kinase activity in a manner unique to the SH3 domain and linker topologies present in the intact Hck protein. Our results also provide fresh structural insight into the facile induction of Hck activity by HIV-1 Nef and other Hck SH3 domain binding proteins and implicate the existence of innate conformational states unique to individual Src family members that "fine-tune" their sensitivities to activation by SH3-based ligands.
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Affiliation(s)
- John J Alvarado
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260, USA
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43
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Jamros MA, Oliveira LC, Whitford PC, Onuchic JN, Adams JA, Blumenthal DK, Jennings PA. Proteins at work: a combined small angle X-RAY scattering and theoretical determination of the multiple structures involved on the protein kinase functional landscape. J Biol Chem 2010; 285:36121-8. [PMID: 20801888 DOI: 10.1074/jbc.m110.116947] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
C-terminal Src kinase (Csk) phosphorylates and down-regulates the Src family tyrosine kinases (SFKs). Crystallographic studies of Csk found an unusual arrangement of the SH2 and SH3 regulatory domains about the kinase core, forming a compact structure. However, recent structural studies of mutant Csk in the presence of an inhibitor indicate that the enzyme accesses an expanded structure. To investigate whether wt-Csk may also access open conformations we applied small angle x-ray scattering (SAXS). We find wt-Csk frequently occupies an extended conformation where the regulatory domains are removed from the kinase core. In addition, all-atom structure-based simulations indicate Csk occupies two free energy basins. These basins correspond to ensembles of distinct global conformations of Csk: a compact structure and an extended structure. The transitions between these structures are entropically driven and accessible via thermal fluctuations that break local interactions. We further characterized the ensemble by generating theoretical scattering curves for mixed populations of conformations from both basins and compared the predicted scattering curves to the experimental profile. This population-combination analysis is more consistent with the experimental data than any rigid model. It suggests that Csk adopts a broad ensemble of conformations in solution, populating extended conformations not observed in the crystal structure that may play an important role in the regulation of Csk. The methodology developed here is broadly applicable to biological macromolecules and will provide useful information about what ensembles of conformations are consistent with the experimental data as well as the ubiquitous dynamic reversible assembly processes inherent in biology.
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Affiliation(s)
- Michael A Jamros
- Department of Chemistry and Biochemistry, University of California, La Jolla, California 92093, USA
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Dusa A, Mouton C, Pecquet C, Herman M, Constantinescu SN. JAK2 V617F constitutive activation requires JH2 residue F595: a pseudokinase domain target for specific inhibitors. PLoS One 2010; 5:e11157. [PMID: 20585391 PMCID: PMC2886835 DOI: 10.1371/journal.pone.0011157] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Accepted: 05/21/2010] [Indexed: 12/29/2022] Open
Abstract
The JAK2 V617F mutation present in over 95% of Polycythemia Vera patients and in 50% of Essential Thrombocythemia and Primary Myelofibrosis patients renders the kinase constitutively active. In the absence of a three-dimensional structure for the full-length protein, the mechanism of activation of JAK2 V617F has remained elusive. In this study, we used functional mutagenesis to investigate the involvement of the JH2 αC helix in the constitutive activation of JAK2 V617F. We show that residue F595, located in the middle of the αC helix of JH2, is indispensable for the constitutive activity of JAK2 V617F. Mutation of F595 to Ala, Lys, Val or Ile significantly decreases the constitutive activity of JAK2 V617F, but F595W and F595Y are able to restore it, implying an aromaticity requirement at position 595. Substitution of F595 to Ala was also able to decrease the constitutive activity of two other JAK2 mutants, T875N and R683G, as well as JAK2 K539L, albeit to a lower extent. In contrast, the F595 mutants are activated by erythropoietin-bound EpoR. We also explored the relationship between the dimeric conformation of EpoR and several JAK2 mutants. Since residue F595 is crucial to the constitutive activation of JAK2 V617F but not to initiation of JAK2 activation by cytokines, we suggest that small molecules that target the region around this residue might specifically block oncogenic JAK2 and spare JAK2 wild-type.
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Affiliation(s)
- Alexandra Dusa
- Ludwig Institute for Cancer Research Ltd., Brussels, Belgium
- de Duve Institute, Université catholique de Louvain, Brussels, Belgium
| | - Céline Mouton
- Ludwig Institute for Cancer Research Ltd., Brussels, Belgium
- de Duve Institute, Université catholique de Louvain, Brussels, Belgium
| | - Christian Pecquet
- Ludwig Institute for Cancer Research Ltd., Brussels, Belgium
- de Duve Institute, Université catholique de Louvain, Brussels, Belgium
| | - Murielle Herman
- Ludwig Institute for Cancer Research Ltd., Brussels, Belgium
- de Duve Institute, Université catholique de Louvain, Brussels, Belgium
| | - Stefan N. Constantinescu
- Ludwig Institute for Cancer Research Ltd., Brussels, Belgium
- de Duve Institute, Université catholique de Louvain, Brussels, Belgium
- * E-mail:
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Reciprocally coupled residues crucial for protein kinase Pak2 activity calculated by statistical coupling analysis. PLoS One 2010; 5:e9455. [PMID: 20209159 PMCID: PMC2830475 DOI: 10.1371/journal.pone.0009455] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2009] [Accepted: 02/09/2010] [Indexed: 12/01/2022] Open
Abstract
Regulation of Pak2 activity involves at least two mechanisms: (i) phosphorylation of the conserved Thr402 in the activation loop and (ii) interaction of the autoinhibitory domain (AID) with the catalytic domain. We collected 482 human protein kinase sequences from the kinome database and globally mapped the evolutionary interactions of the residues in the catalytic domain with Thr402 by sequence-based statistical coupling analysis (SCA). Perturbation of Thr402 (34.6%) suggests a communication pathway between Thr402 in the activation loop, and Phe387 (ΔΔE387F,402T = 2.80) in the magnesium positioning loop, Trp427 (ΔΔE427W,402T = 3.12) in the F-helix, and Val404 (ΔΔE404V,402T = 4.43) and Gly405 (ΔΔE405G,402T = 2.95) in the peptide positioning loop. When compared to the cAMP-dependent protein kinase (PKA) and Src, the perturbation pattern of threonine phosphorylation in the activation loop of Pak2 is similar to that of PKA, and different from the tyrosine phosphorylation pattern of Src. Reciprocal coupling analysis by SCA showed the residues perturbed by Thr402 and the reciprocal coupling pairs formed a network centered at Trp427 in the F-helix. Nine pairs of reciprocal coupling residues crucial for enzymatic activity and structural stabilization were identified. Pak2, PKA and Src share four pairs. Reciprocal coupling residues exposed to the solvent line up as an activation groove. This is the inhibitor (PKI) binding region in PKA and the activation groove for Pak2. This indicates these evolutionary conserved residues are crucial for the catalytic activity of PKA and Pak2.
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Lyn-mediated mitochondrial tyrosine phosphorylation is required to preserve mitochondrial integrity in early liver regeneration. Biochem J 2009; 425:401-12. [PMID: 19832701 DOI: 10.1042/bj20090902] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Functional alterations in mitochondria such as overproduction of ROS (reactive oxygen species) and overloading of calcium, with subsequent change in the membrane potential, are traditionally regarded as pro-apoptotic conditions. Although such events occur in the early phases of LR (liver regeneration) after two-thirds PH (partial hepatectomy), hepatocytes do not undergo apoptosis but continue to proliferate until the mass of the liver is restored. The aim of the present study was to establish whether tyrosine phosphorylation, an emerging mechanism of regulation of mitochondrial function, participates in the response to liver injury following PH and is involved in contrasting mitochondrial pro-apoptotic signalling. Mitochondrial tyrosine phosphorylation, negligible in the quiescent liver, was detected in the early phases of LR with a trend similar to the events heralding mitochondrial apoptosis and was attributed to the tyrosine kinase Lyn, a member of the Src family. Lyn was shown to accumulate in an active form in the mitochondrial intermembrane space, where it was found to be associated with a multiprotein complex. Our results highlight a role for tyrosine phosphorylation in accompanying, and ultimately counteracting, mitochondrial events otherwise leading to apoptosis, hence conveying information required to preserve the mitochondrial integrity during LR.
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Yokoyama N, Malbon CC. Dishevelled-2 docks and activates Src in a Wnt-dependent manner. J Cell Sci 2009; 122:4439-51. [PMID: 19920076 DOI: 10.1242/jcs.051847] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Wnt3a activates the ;canonical' signaling pathway, stimulating the nuclear accumulation of beta-catenin and activation of Lef/Tcf-sensitive transcription of developmentally important genes. Using totipotent mouse F9 teratocarcinoma cells expressing frizzled-1 (Fz1), we investigated roles of tyrosine kinase activity in Wnt/beta-catenin signaling. Treatment with either genistein or Src family kinase inhibitor PP2 attenuates Wnt3a-stimulated Lef/Tcf transcription activation and primitive endoderm formation. siRNA-induced knockdown of Src likewise attenuates Lef/Tcf transcription and primitive endoderm formation in response to Wnt3a, implicating Src as a positive regulator of Wnt/beta-catenin signaling. We discovered that Src binds dishevelled-2 (Dvl2), a key phosphoprotein in Wnt signaling, at two positions: an SH3-binding domain and a C-terminal domain. The Y18F mutant of Dvl2 attenuates the Wnt3a-stimulated Lef/Tcf-sensitive transcriptional response. Wnt3a stimulates Src docking to Dvl2 and activation of this tyrosine kinase. Activated Src, in turn, enhances Wnt activation of the canonical pathway. We show that Dvl2 and beta-catenin are crucially important substrates for tyrosine phosphorylation in the canonical Wnt/beta-catenin pathway.
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Affiliation(s)
- Noriko Yokoyama
- Department of Pharmacology, Health Sciences Center, State University of New York at Stony Brook, Stony Brook, NY 11794-8651, USA.
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Zhao J, Zhang Y, Ithychanda SS, Tu Y, Chen K, Qin J, Wu C. Migfilin interacts with Src and contributes to cell-matrix adhesion-mediated survival signaling. J Biol Chem 2009; 284:34308-20. [PMID: 19833732 DOI: 10.1074/jbc.m109.045021] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Integrin-mediated cell-extracellular matrix (ECM) adhesion is essential for protection of epithelial cells against apoptosis, but the underlying mechanism is incompletely understood. Here we show that migfilin, an integrin-proximal adaptor protein, interacts with Src and contributes to cell-ECM-mediated survival signaling. Loss of cell-ECM adhesion markedly reduces the migfilin level in untransformed epithelial cells and concomitantly induces apoptosis. Overexpression of migfilin substantially desensitizes cell detachment-induced apoptosis. Conversely, depletion of migfilin promotes apoptosis despite the presence of cell-ECM adhesion. At the molecular level migfilin directly interacts with Src, and the migfilin binding surface overlaps with the inhibitory intramolecular interaction sites in Src. Consequently, the binding of migfilin activates Src, resulting in suppression of apoptosis. Our results reveal a novel mechanism by which cell-ECM adhesion regulates Src activation and survival signaling. This migfilin-mediated signaling pathway is dysfunctional in multiple types of carcinoma cells, which likely contributes to aberrant Src activation and anoikis resistance in the cancerous cells.
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Affiliation(s)
- Jianping Zhao
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, USA
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Tesmer JJG. Structure and function of regulator of G protein signaling homology domains. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2009; 86:75-113. [PMID: 20374714 DOI: 10.1016/s1877-1173(09)86004-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
All regulator of G protein signaling (RGS) proteins contain a conserved domain of approximately 130 amino acids that binds to activated heterotrimeric G protein α subunits (Gα) and accelerates their rate of GTP hydrolysis. Homologous domains are found in at least six other protein families, including a family of Rho guanine nucleotide exchange factors (RhoGEFs) and the G protein-coupled receptor kinases (GRKs). Although some of the RhoGEF and GRK RGS-like domains can also bind to activated Gα subunits, they do so in distinct ways and with much lower levels of GTPase activation. In other protein families, the domains have as of yet no obvious relationship to heterotrimeric G protein signaling. These RGS homology (RH) domains are now recognized as mediators of extraordinarily diverse protein-protein interactions. Through these interactions, they play roles that range from enzyme to molecular scaffold to signal transducing module. In this review, the atomic structures of RH domains from RGS proteins, Axins, RhoGEFs, and GRKs are compared in light of what is currently known about their functional roles.
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Affiliation(s)
- John J G Tesmer
- Department of Pharmacology, Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109‐2216, USA
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50
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Alternative splicing modulates autoinhibition and SH3 accessibility in the Src kinase Fyn. Mol Cell Biol 2009; 29:6438-48. [PMID: 19805512 DOI: 10.1128/mcb.00398-09] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Src family kinases are central regulators of a large number of signaling pathways. To adapt to the idiosyncrasies of different cell types, these kinases may need a fine-tuning of their intrinsic molecular control mechanisms. Here, we describe on a molecular level how the Fyn kinase uses alternative splicing to adapt to different cellular environments. Using structural analysis, site-directed mutagenesis, and functional analysis, we show how the inclusion of either exon 7A or 7B affects the autoinhibition of Fyn and how this changes the SH3-dependent interaction and tyrosine phosphorylation of Sam68, with functional consequences for the Sam68-regulated survival of epithelial cells. Our results illustrate a novel mechanism of evolution that may contribute to the complexity of Src kinase regulation.
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