1
|
Wang M, Sun J, Yan X, Yang W, Wang W, Li Y, Wang L, Song L. CgSHIP2 negatively regulates the mRNA expressions of CgIL-17s in response to Vibrio splendidus stimulation in Crassostrea gigas. FISH & SHELLFISH IMMUNOLOGY 2024; 149:109612. [PMID: 38705548 DOI: 10.1016/j.fsi.2024.109612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/29/2024] [Accepted: 05/03/2024] [Indexed: 05/07/2024]
Abstract
SH2 domain containing inositol polyphosphate5-phosphatase-2 (SHIP2) is a member of the 5-phosphatase family, acting as a vital negative regulator of immune response in vertebrates. In the present study, a SHIP2 homologue (designed as CgSHIP2) was identified from Pacific oyster, Crassostrea gigas. There was a SH2 domain, an IPPc domain and a SAM domain in CgSHIP2. The mRNA transcripts of CgSHIP2 were widely expressed in all the tested tissues with the highest expression in haemolymph. The mRNA expressions of CgSHIP2 in haemocytes increased significantly at 6, 12, 48 and 72 h after Vibrio splendidus stimulation. The positive green signals of CgSHIP2 protein were mainly located in cytoplasm of haemocytes. After the expression of CgSHIP2 was inhibited by RNA interference, the mRNA transcripts of interleukin 17s (CgIL-17-1, CgIL-17-2, CgIL-17-3 and CgIL-17-6) in the haemocytes increased significantly at 24 h after V. splendidus stimulation, which were 8.15-fold (p < 0.001), 3.44-fold (p < 0.05), 2.15-fold (p < 0.01) and 4.63-fold (p < 0.05) compared with that in NC-RNAi group, respectively. Obvious branchial swelling and cilium shedding in gills were observed in CgSHIP2-RNAi group at 24 h after V. splendidus stimulation. The results suggested that CgSHIP2 played an important role in controlling inflammatory response induced by bacteria in oysters.
Collapse
Affiliation(s)
- Mengjia Wang
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Jiejie Sun
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China.
| | - Xiaoxue Yan
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Wenwen Yang
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Wei Wang
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Yinan Li
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Lingling Wang
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Laboratory of Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Linsheng Song
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Laboratory of Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China.
| |
Collapse
|
2
|
Vincenzi M, Mercurio FA, Autiero I, Leone M. Cancer-Related Mutations in the Sam Domains of EphA2 Receptor and Ship2 Lipid Phosphatase: A Computational Study. Molecules 2024; 29:1024. [PMID: 38474536 DOI: 10.3390/molecules29051024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/09/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024] Open
Abstract
The lipid phosphatase Ship2 interacts with the EphA2 receptor by forming a heterotypic Sam (sterile alpha motif)-Sam complex. Ship2 works as a negative regulator of receptor endocytosis and consequent degradation, and anti-oncogenic effects in cancer cells should be induced by hindering its association with EphA2. Herein, a computational approach is presented to investigate the relationship between Ship2-Sam/EphA2-Sam interaction and cancer onset and further progression. A search was first conducted through the COSMIC (Catalogue of Somatic Mutations in Cancer) database to identify cancer-related missense mutations positioned inside or close to the EphA2-Sam and Ship2-Sam reciprocal binding interfaces. Next, potential differences in the chemical-physical properties of mutant and wild-type Sam domains were evaluated by bioinformatics tools based on analyses of primary sequences. Three-dimensional (3D) structural models of mutated EphA2-Sam and Ship2-Sam domains were built as well and deeply analysed with diverse computational instruments, including molecular dynamics, to classify potentially stabilizing and destabilizing mutations. In the end, the influence of mutations on the EphA2-Sam/Ship2-Sam interaction was studied through docking techniques. This in silico approach contributes to understanding, at the molecular level, the mutation/cancer relationship by predicting if amino acid substitutions could modulate EphA2 receptor endocytosis.
Collapse
Affiliation(s)
- Marian Vincenzi
- Institute of Biostructures and Bioimaging, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Flavia Anna Mercurio
- Institute of Biostructures and Bioimaging, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Ida Autiero
- Institute of Biostructures and Bioimaging, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging, Via Pietro Castellino 111, 80131 Naples, Italy
| |
Collapse
|
3
|
Hunting for Novel Routes in Anticancer Drug Discovery: Peptides against Sam-Sam Interactions. Int J Mol Sci 2022; 23:ijms231810397. [PMID: 36142306 PMCID: PMC9499636 DOI: 10.3390/ijms231810397] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/02/2022] [Accepted: 09/02/2022] [Indexed: 01/10/2023] Open
Abstract
Among the diverse protein binding modules, Sam (Sterile alpha motif) domains attract attention due to their versatility. They are present in different organisms and play many functions in physiological and pathological processes by binding multiple partners. The EphA2 receptor contains a Sam domain at the C-terminus (EphA2-Sam) that is able to engage protein regulators of receptor stability (including the lipid phosphatase Ship2 and the adaptor Odin). Ship2 and Odin are recruited by EphA2-Sam through heterotypic Sam-Sam interactions. Ship2 decreases EphA2 endocytosis and consequent degradation, producing chiefly pro-oncogenic outcomes in a cellular milieu. Odin, through its Sam domains, contributes to receptor stability by possibly interfering with ubiquitination. As EphA2 is upregulated in many types of tumors, peptide inhibitors of Sam-Sam interactions by hindering receptor stability could function as anticancer therapeutics. This review describes EphA2-Sam and its interactome from a structural and functional perspective. The diverse design strategies that have thus far been employed to obtain peptides targeting EphA2-mediated Sam-Sam interactions are summarized as well. The generated peptides represent good initial lead compounds, but surely many efforts need to be devoted in the close future to improve interaction affinities towards Sam domains and consequently validate their anticancer properties.
Collapse
|
4
|
Vincenzi M, Anna Mercurio F, Di Natale C, Palumbo R, Pirone L, La Manna S, Marasco D, Maria Pedone E, Leone M. Targeting Ship2-Sam with peptide ligands: Novel insights from a multidisciplinary approach. Bioorg Chem 2022; 122:105680. [DOI: 10.1016/j.bioorg.2022.105680] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/24/2022] [Accepted: 02/09/2022] [Indexed: 01/06/2023]
|
5
|
Vincenzi M, Mercurio FA, Leone M. NMR Spectroscopy in the Conformational Analysis of Peptides: An Overview. Curr Med Chem 2021; 28:2729-2782. [PMID: 32614739 DOI: 10.2174/0929867327666200702131032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/21/2020] [Accepted: 05/28/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND NMR spectroscopy is one of the most powerful tools to study the structure and interaction properties of peptides and proteins from a dynamic perspective. Knowing the bioactive conformations of peptides is crucial in the drug discovery field to design more efficient analogue ligands and inhibitors of protein-protein interactions targeting therapeutically relevant systems. OBJECTIVE This review provides a toolkit to investigate peptide conformational properties by NMR. METHODS Articles cited herein, related to NMR studies of peptides and proteins were mainly searched through PubMed and the web. More recent and old books on NMR spectroscopy written by eminent scientists in the field were consulted as well. RESULTS The review is mainly focused on NMR tools to gain the 3D structure of small unlabeled peptides. It is more application-oriented as it is beyond its goal to deliver a profound theoretical background. However, the basic principles of 2D homonuclear and heteronuclear experiments are briefly described. Protocols to obtain isotopically labeled peptides and principal triple resonance experiments needed to study them, are discussed as well. CONCLUSION NMR is a leading technique in the study of conformational preferences of small flexible peptides whose structure can be often only described by an ensemble of conformations. Although NMR studies of peptides can be easily and fast performed by canonical protocols established a few decades ago, more recently we have assisted to tremendous improvements of NMR spectroscopy to investigate instead large systems and overcome its molecular weight limit.
Collapse
Affiliation(s)
- Marian Vincenzi
- Institute of Biostructures and Bioimaging, National Research Council of Italy, Via Mezzocannone 16, 80134, Naples, Italy
| | - Flavia Anna Mercurio
- Institute of Biostructures and Bioimaging, National Research Council of Italy, Via Mezzocannone 16, 80134, Naples, Italy
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging, National Research Council of Italy, Via Mezzocannone 16, 80134, Naples, Italy
| |
Collapse
|
6
|
Neira JL, Rizzuti B, Ortega-Alarcón D, Giudici AM, Abián O, Fárez-Vidal ME, Velázquez-Campoy A. The armadillo-repeat domain of plakophilin 1 binds the C-terminal sterile alpha motif (SAM) of p73. Biochim Biophys Acta Gen Subj 2021; 1865:129914. [PMID: 33872756 DOI: 10.1016/j.bbagen.2021.129914] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 04/13/2021] [Accepted: 04/13/2021] [Indexed: 12/31/2022]
Abstract
BACKGROUND Plakophilin 1 (PKP1) is a component of desmosomes, which are key structural components for cell-cell adhesion, and can also be found in other cell locations. The p53, p63 and p73 proteins belong to the p53 family of transcription factors, playing crucial roles in tumour suppression. The α-splice variant of p73 (p73α) has at its C terminus a sterile alpha motif (SAM); such domain, SAMp73, is involved in the interaction with other macromolecules. METHODS We studied the binding of SAMp73 with the armadillo domain of PKP1 (ARM-PKP1) in the absence and the presence of 100 mM NaCl, by using several biophysical techniques, namely fluorescence, far-ultraviolet circular dichroism (CD), nuclear magnetic resonance (NMR), isothermal titration calorimetry (ITC), and molecular docking and simulations. RESULTS Association was observed between the two proteins, with a dissociation constant of ~5 μM measured by ITC and fluorescence in the absence of NaCl. The binding region of SAMp73 involved residues of the so-called "middle-loop-end-helix" binding region (i.e., comprising the third helix, together with the C terminus of the second one, and the N-cap of the fourth), as shown by 15N, 1H- HSQC-NMR spectra. Molecular modelling provided additional information on the possible structure of the binding complex. CONCLUSIONS This newly-observed interaction could have potential therapeutic relevance in the tumour pathways where PKP1 is involved, and under conditions when there is a possible inactivation of p53. GENERAL SIGNIFICANCE The discovery of the binding between SAMp73 and ARM-PKP1 suggests a functional role for their interaction, including the possibility that SAMp73 could assist PKP1 in signalling pathways.
Collapse
Affiliation(s)
- José L Neira
- IDIBE, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Joint Units IQFR-CSIC-BIFI, GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain.
| | - Bruno Rizzuti
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Joint Units IQFR-CSIC-BIFI, GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain; CNR-NANOTEC, Licryl-UOS Cosenza and CEMIF.Cal, Department of Physics, University of Calabria, 87036 Rende, Italy.
| | - David Ortega-Alarcón
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Joint Units IQFR-CSIC-BIFI, GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | | | - Olga Abián
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Joint Units IQFR-CSIC-BIFI, GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain; Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain; Instituto Aragonés de Ciencias de la Salud (IACS), 50009 Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - María Esther Fárez-Vidal
- Departamento de Bioquímica y Biología Molecular III e Inmunología, Facultad de Medicina, Universidad de Granada, 18016 Granada, Spain; Instituto de Investigación Biomédica IBS, Complejo Hospitalario Universitario de Granada, Universidad de Granada, 18071 Granada, Spain
| | - Adrián Velázquez-Campoy
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Joint Units IQFR-CSIC-BIFI, GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain; Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain; Fundacion ARAID, Government of Aragon, 50009 Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| |
Collapse
|
7
|
Vincenzi M, Mercurio FA, Leone M. Protein Interaction Domains: Structural Features and Drug Discovery Applications (Part 2). Curr Med Chem 2021; 28:854-892. [PMID: 31942846 DOI: 10.2174/0929867327666200114114142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/28/2019] [Accepted: 11/04/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Proteins present a modular organization made up of several domains. Apart from the domains playing catalytic functions, many others are crucial to recruit interactors. The latter domains can be defined as "PIDs" (Protein Interaction Domains) and are responsible for pivotal outcomes in signal transduction and a certain array of normal physiological and disease-related pathways. Targeting such PIDs with small molecules and peptides able to modulate their interaction networks, may represent a valuable route to discover novel therapeutics. OBJECTIVE This work represents a continuation of a very recent review describing PIDs able to recognize post-translationally modified peptide segments. On the contrary, the second part concerns with PIDs that interact with simple peptide sequences provided with standard amino acids. METHODS Crucial structural information on different domain subfamilies and their interactomes was gained by a wide search in different online available databases (including the PDB (Protein Data Bank), the Pfam (Protein family), and the SMART (Simple Modular Architecture Research Tool)). Pubmed was also searched to explore the most recent literature related to the topic. RESULTS AND CONCLUSION PIDs are multifaceted: they have all diverse structural features and can recognize several consensus sequences. PIDs can be linked to different diseases onset and progression, like cancer or viral infections and find applications in the personalized medicine field. Many efforts have been centered on peptide/peptidomimetic inhibitors of PIDs mediated interactions but much more work needs to be conducted to improve drug-likeness and interaction affinities of identified compounds.
Collapse
Affiliation(s)
- Marian Vincenzi
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy
| | - Flavia Anna Mercurio
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy
| |
Collapse
|
8
|
Arthur A, Gronthos S. Eph-Ephrin Signaling Mediates Cross-Talk Within the Bone Microenvironment. Front Cell Dev Biol 2021; 9:598612. [PMID: 33634116 PMCID: PMC7902060 DOI: 10.3389/fcell.2021.598612] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 01/15/2021] [Indexed: 12/18/2022] Open
Abstract
Skeletal integrity is maintained through the tightly regulated bone remodeling process that occurs continuously throughout postnatal life to replace old bone and to repair skeletal damage. This is maintained primarily through complex interactions between bone resorbing osteoclasts and bone forming osteoblasts. Other elements within the bone microenvironment, including stromal, osteogenic, hematopoietic, endothelial and neural cells, also contribute to maintaining skeletal integrity. Disruption of the dynamic interactions between these diverse cellular systems can lead to poor bone health and an increased susceptibility to skeletal diseases including osteopenia, osteoporosis, osteoarthritis, osteomalacia, and major fractures. Recent reports have implicated a direct role for the Eph tyrosine kinase receptors and their ephrin ligands during bone development, homeostasis and skeletal repair. These membrane-bound molecules mediate contact-dependent signaling through both the Eph receptors, termed forward signaling, and through the ephrin ligands, referred to as reverse signaling. This review will focus on Eph/ ephrin cross-talk as mediators of hematopoietic and stromal cell communication, and how these interactions contribute to blood/ bone marrow function and skeletal integrity during normal steady state or pathological conditions.
Collapse
Affiliation(s)
- Agnieszka Arthur
- Mesenchymal Stem Cell Laboratory, Faculty of Health and Medical Sciences, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia.,Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Stan Gronthos
- Mesenchymal Stem Cell Laboratory, Faculty of Health and Medical Sciences, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia.,Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| |
Collapse
|
9
|
Zhou H, Yue X, Wang Z, Li S, Zhu J, Yang Y, Liu M. Expression, purification and characterization of the RhoA-binding domain of human SHIP2 in E.coli. Protein Expr Purif 2021; 180:105821. [PMID: 33421554 DOI: 10.1016/j.pep.2021.105821] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/02/2020] [Accepted: 01/03/2021] [Indexed: 11/26/2022]
Abstract
Human SH2-containing inositol 5-phosphatase 2 (SHIP2) is a multi-domain protein playing essential roles in various physiological and pathological processes. In cell polarization and migration, SHIP2 serves as a RhoA effector for manipulating the level of phosphatidylinositol 3,4,5-trisphosphate. The domain between SH2 and a potential PH-R domain of SHIP2 was suggested to bind with GTP-bound form of RhoA. However, the structure of this RhoA-binding domain (RBD) of SHIP2 and the mechanism for its binding with RhoA remain unknown. In this study, SHIP2118-298 and SHIP2176-298, two truncated proteins harboring the RBD were designed, expressed, and purified successfully in E. coli. Unexpectedly, both SHIP2118-298 and SHIP2176-298 were determined to exist as homo-dimers in solution by multi-angle light scattering. Circular dichroism spectra indicated that both proteins predominantly consisted of α-helix structure. Moreover, in pull-down experiments, both proteins could bind with GTP-bound RhoA and RhoAQ63L, a mutant mimicing the state of GTP-bound RhoA. Importantly, in silico analysis showed that the shorter truncation, SHIP2176-298, contained all ordered residues between the SH2 and the PH-R domain, and matched the RhoA effector motif 1 of PKN1 well in sequence alignment, suggesting that SHIP2176-298 is sufficient for further studies on the structure and RhoA binding of SHIP2. This work shortens and confirms the main region of SHIP2 interacting with RhoA, provides the method for sample preparation, and presents preliminary information for SHIP2-RBD structure, which will facilitate the comprehensive understanding of the structure and function of SHIP2.
Collapse
Affiliation(s)
- Heng Zhou
- Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan, 430070, China; State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan, 430071, China
| | - Xiali Yue
- Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Zi Wang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuangli Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan, 430071, China
| | - Jiang Zhu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan, 430071, China.
| | - Yunhuang Yang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan, 430071, China
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| |
Collapse
|
10
|
Baudet S, Bécret J, Nicol X. Approaches to Manipulate Ephrin-A:EphA Forward Signaling Pathway. Pharmaceuticals (Basel) 2020; 13:ph13070140. [PMID: 32629797 PMCID: PMC7407804 DOI: 10.3390/ph13070140] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/19/2020] [Accepted: 06/28/2020] [Indexed: 02/07/2023] Open
Abstract
Erythropoietin-producing hepatocellular carcinoma A (EphA) receptors and their ephrin-A ligands are key players of developmental events shaping the mature organism. Their expression is mostly restricted to stem cell niches in adults but is reactivated in pathological conditions including lesions in the heart, lung, or nervous system. They are also often misregulated in tumors. A wide range of molecular tools enabling the manipulation of the ephrin-A:EphA system are available, ranging from small molecules to peptides and genetically-encoded strategies. Their mechanism is either direct, targeting EphA receptors, or indirect through the modification of intracellular downstream pathways. Approaches enabling manipulation of ephrin-A:EphA forward signaling for the dissection of its signaling cascade, the investigation of its physiological roles or the development of therapeutic strategies are summarized here.
Collapse
|
11
|
Ray S, Chee L, Matson DR, Palermo NY, Bresnick EH, Hewitt KJ. Sterile α-motif domain requirement for cellular signaling and survival. J Biol Chem 2020; 295:7113-7125. [PMID: 32241909 PMCID: PMC7242717 DOI: 10.1074/jbc.ra119.011895] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 04/01/2020] [Indexed: 01/21/2023] Open
Abstract
Hundreds of sterile α-motif (SAM) domains have predicted structural similarities and are reported to bind proteins, lipids, or RNAs. However, the majority of these domains have not been analyzed functionally. Previously, we demonstrated that a SAM domain-containing protein, SAMD14, promotes SCF/proto-oncogene c-Kit (c-Kit) signaling, erythroid progenitor function, and erythrocyte regeneration. Deletion of a Samd14 enhancer (Samd14-Enh), occupied by GATA2 and SCL/TAL1 transcription factors, reduces SAMD14 expression in bone marrow and spleen and is lethal in a hemolytic anemia mouse model. To rigorously establish whether Samd14-Enh deletion reduces anemia-dependent c-Kit signaling by lowering SAMD14 levels, we developed a genetic rescue assay in murine Samd14-Enh-/- primary erythroid precursor cells. SAMD14 expression at endogenous levels rescued c-Kit signaling. The conserved SAM domain was required for SAMD14 to increase colony-forming activity, c-Kit signaling, and progenitor survival. To elucidate the molecular determinants of SAM domain function in SAMD14, we substituted its SAM domain with distinct SAM domains predicted to be structurally similar. The chimeras were less effective than SAMD14 itself in rescuing signaling, survival, and colony-forming activities. Thus, the SAMD14 SAM domain has attributes that are distinct from other SAM domains and underlie SAMD14 function as a regulator of cellular signaling and erythrocyte regeneration.
Collapse
Affiliation(s)
- Suhita Ray
- Department of Genetics, Cell Biology and Anatomy, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska 68198
| | - Linda Chee
- Department of Genetics, Cell Biology and Anatomy, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska 68198
| | - Daniel R Matson
- University of Wisconsin-Madison Blood Research Program, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53705
| | - Nick Y Palermo
- Holland Computing Center, University of Nebraska-Lincoln, Lincoln, Nebraska 68588
| | - Emery H Bresnick
- University of Wisconsin-Madison Blood Research Program, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53705
| | - Kyle J Hewitt
- Department of Genetics, Cell Biology and Anatomy, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska 68198
| |
Collapse
|
12
|
Vincenzi M, Mercurio FA, Leone M. Sam Domains in Multiple Diseases. Curr Med Chem 2020; 27:450-476. [PMID: 30306850 DOI: 10.2174/0929867325666181009114445] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Revised: 07/26/2018] [Accepted: 08/27/2018] [Indexed: 12/13/2022]
Abstract
BACKGROUND The sterile alpha motif (Sam) domain is a small helical protein module, able to undergo homo- and hetero-oligomerization, as well as polymerization, thus forming different types of protein architectures. A few Sam domains are involved in pathological processes and consequently, they represent valuable targets for the development of new potential therapeutic routes. This study intends to collect state-of-the-art knowledge on the different modes by which Sam domains can favor disease onset and progression. METHODS This review was build up by searching throughout the literature, for: a) the structural properties of Sam domains, b) interactions mediated by a Sam module, c) presence of a Sam domain in proteins relevant for a specific disease. RESULTS Sam domains appear crucial in many diseases including cancer, renal disorders, cataracts. Often pathologies are linked to mutations directly positioned in the Sam domains that alter their stability and/or affect interactions that are crucial for proper protein functions. In only a few diseases, the Sam motif plays a kind of "side role" and cooperates to the pathological event by enhancing the action of a different protein domain. CONCLUSION Considering the many roles of the Sam domain into a significant variety of diseases, more efforts and novel drug discovery campaigns need to be engaged to find out small molecules and/or peptides targeting Sam domains. Such compounds may represent the pillars on which to build novel therapeutic strategies to cure different pathologies.
Collapse
Affiliation(s)
- Marian Vincenzi
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy
| | - Flavia Anna Mercurio
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy.,Cirpeb, InterUniversity Research Centre on Bioactive Peptides, University of Naples "Federico II", Via Mezzocannone, 16, 80134 Naples, Italy
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy.,Cirpeb, InterUniversity Research Centre on Bioactive Peptides, University of Naples "Federico II", Via Mezzocannone, 16, 80134 Naples, Italy
| |
Collapse
|
13
|
Murakami C, Hoshino F, Sakai H, Hayashi Y, Yamashita A, Sakane F. Diacylglycerol kinase δ and sphingomyelin synthase-related protein functionally interact via their sterile α motif domains. J Biol Chem 2020; 295:2932-2947. [PMID: 31980461 DOI: 10.1074/jbc.ra119.012369] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/23/2020] [Indexed: 12/27/2022] Open
Abstract
The δ isozyme of diacylglycerol kinase (DGKδ) plays critical roles in lipid signaling by converting diacylglycerol (DG) to phosphatidic acid (PA). We previously demonstrated that DGKδ preferably phosphorylates palmitic acid (16:0)- and/or palmitoleic acid (16:1)-containing DG molecular species, but not arachidonic acid (20:4)-containing DG species, which are recognized as DGK substrates derived from phosphatidylinositol turnover, in high glucose-stimulated myoblasts. However, little is known about the origin of these DG molecular species. DGKδ and two DG-generating enzymes, sphingomyelin synthase (SMS) 1 and SMS-related protein (SMSr), contain a sterile α motif domain (SAMD). In this study, we found that SMSr-SAMD, but not SMS1-SAMD, co-immunoprecipitates with DGKδ-SAMD. Full-length DGKδ co-precipitated with full-length SMSr more strongly than with SMS1. However, SAMD-deleted variants of SMSr and DGKδ interacted only weakly with full-length DGKδ and SMSr, respectively. These results strongly suggested that DGKδ interacts with SMSr through their respective SAMDs. To determine the functional outcomes of the relationship between DGKδ and SMSr, we used LC-MS/MS to investigate whether overexpression of DGKδ and/or SMSr in COS-7 cells alters the levels of PA species. We found that SMSr overexpression significantly enhances the production of 16:0- or 16:1-containing PA species such as 14:0/16:0-, 16:0/16:0-, 16:0/18:1-, and/or 16:1/18:1-PA in DGKδ-overexpressing COS-7 cells. Moreover, SMSr enhanced DGKδ activity via their SAMDs in vitro Taken together, these results strongly suggest that SMSr is a candidate DG-providing enzyme upstream of DGKδ and that the two enzymes represent a new pathway independent of phosphatidylinositol turnover.
Collapse
Affiliation(s)
- Chiaki Murakami
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba 263-8522, Japan
| | - Fumi Hoshino
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba 263-8522, Japan
| | - Hiromichi Sakai
- Department of Biosignaling and Radioisotope Experiment, Interdisciplinary Center for Science Research, Organization for Research and Academic Information, Shimane University, Izumo 693-8501, Japan
| | - Yasuhiro Hayashi
- Faculty of Pharma Sciences, Teikyo University, Kaga 2-11-1, Itabashi-ku, Tokyo 173-8605, Japan
| | - Atsushi Yamashita
- Faculty of Pharma Sciences, Teikyo University, Kaga 2-11-1, Itabashi-ku, Tokyo 173-8605, Japan
| | - Fumio Sakane
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba 263-8522, Japan.
| |
Collapse
|
14
|
Joshi R, Qin L, Cao X, Zhong S, Voss C, Min W, Li SSC. DLC1 SAM domain-binding peptides inhibit cancer cell growth and migration by inactivating RhoA. J Biol Chem 2019; 295:645-656. [PMID: 31806702 DOI: 10.1074/jbc.ra119.011929] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Indexed: 12/25/2022] Open
Abstract
Deleted-in-liver cancer 1 (DLC1) exerts its tumor suppressive function mainly through the Rho-GTPase-activating protein (RhoGAP) domain. When activated, the domain promotes the hydrolysis of RhoA-GTP, leading to reduced cell migration. DLC1 is kept in an inactive state by an intramolecular interaction between its RhoGAP domain and the DLC1 sterile α motif (SAM) domain. We have shown previously that this autoinhibited state of DLC1 may be alleviated by tensin-3 (TNS3) or PTEN. We show here that the TNS3/PTEN-DLC1 interactions are mediated by the C2 domains of the former and the SAM domain of the latter. Intriguingly, the DLC1 SAM domain was capable of binding to specific peptide motifs within the C2 domains. Indeed, peptides containing the binding motifs were highly effective in blocking the C2-SAM domain-domain interaction. Importantly, when fused to the tat protein-transduction sequence and subsequently introduced into cells, the C2 peptides potently promoted the RhoGAP function in DLC1, leading to decreased RhoA activation and reduced tumor cell growth in soft agar and migration in response to growth factor stimulation. To facilitate the development of the C2 peptides as potential therapeutic agents, we created a cyclic version of the TNS3 C2 domain-derived peptide and showed that this peptide readily entered the MDA-MB-231 breast cancer cells and effectively inhibited their migration. Our work shows, for the first time, that the SAM domain is a peptide-binding module and establishes the framework on which to explore DLC1 SAM domain-binding peptides as potential therapeutic agents for cancer treatment.
Collapse
Affiliation(s)
- Rakesh Joshi
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada; Departments of Surgery, Pathology and Oncology, Western University, London, Ontario N6A 5A5, Canada
| | - Lyugao Qin
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - Xuan Cao
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shanshan Zhong
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - Courtney Voss
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - Weiping Min
- Departments of Surgery, Pathology and Oncology, Western University, London, Ontario N6A 5A5, Canada.
| | - Shawn S C Li
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada.
| |
Collapse
|
15
|
Mercurio FA, Di Natale C, Pirone L, Vincenzi M, Marasco D, De Luca S, Pedone EM, Leone M. Exploring the Ability of Cyclic Peptides to Target SAM Domains: A Computational and Experimental Study. Chembiochem 2019; 21:702-711. [DOI: 10.1002/cbic.201900444] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Flavia A. Mercurio
- Institute of Biostructures and BioimagingNational Research Council Via Mezzocannone 16 80134 Naples Italy
| | - Concetta Di Natale
- Department of PharmacyUniversity of Naples “Federico II” Via Mezzocannone 16 80134 Naples Italy
| | - Luciano Pirone
- Institute of Biostructures and BioimagingNational Research Council Via Mezzocannone 16 80134 Naples Italy
| | - Marian Vincenzi
- Institute of Biostructures and BioimagingNational Research Council Via Mezzocannone 16 80134 Naples Italy
| | - Daniela Marasco
- Institute of Biostructures and BioimagingNational Research Council Via Mezzocannone 16 80134 Naples Italy
- Department of PharmacyUniversity of Naples “Federico II” Via Mezzocannone 16 80134 Naples Italy
| | - Stefania De Luca
- Institute of Biostructures and BioimagingNational Research Council Via Mezzocannone 16 80134 Naples Italy
| | - Emilia M. Pedone
- Institute of Biostructures and BioimagingNational Research Council Via Mezzocannone 16 80134 Naples Italy
| | - Marilisa Leone
- Institute of Biostructures and BioimagingNational Research Council Via Mezzocannone 16 80134 Naples Italy
| |
Collapse
|
16
|
Vincenzi M, Mercurio FA, Leone M. About TFE: Old and New Findings. Curr Protein Pept Sci 2019; 20:425-451. [PMID: 30767740 DOI: 10.2174/1389203720666190214152439] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 07/16/2018] [Accepted: 07/18/2018] [Indexed: 01/28/2023]
Abstract
The fluorinated alcohol 2,2,2-Trifluoroethanol (TFE) has been implemented for many decades now in conformational studies of proteins and peptides. In peptides, which are often disordered in aqueous solutions, TFE acts as secondary structure stabilizer and primarily induces an α -helical conformation. The exact mechanism through which TFE plays its stabilizing roles is still debated and direct and indirect routes, relying either on straight interaction between TFE and molecules or indirect pathways based on perturbation of solvation sphere, have been proposed. Another still unanswered question is the capacity of TFE to favor in peptides a bioactive or a native-like conformation rather than simply stimulate the raise of secondary structure elements that reflect only the inherent propensity of a specific amino-acid sequence. In protein studies, TFE destroys unique protein tertiary structure and often leads to the formation of non-native secondary structure elements, but, interestingly, gives some hints about early folding intermediates. In this review, we will summarize proposed mechanisms of TFE actions. We will also describe several examples, in which TFE has been successfully used to reveal structural properties of different molecular systems, including antimicrobial and aggregation-prone peptides, as well as globular folded and intrinsically disordered proteins.
Collapse
Affiliation(s)
- Marian Vincenzi
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy
| | - Flavia A Mercurio
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy.,Cirpeb, InterUniversity Research Centre on Bioactive Peptides, University of Naples "Federico II", Via Mezzocannone 16, 80134 Naples, Italy
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy.,Cirpeb, InterUniversity Research Centre on Bioactive Peptides, University of Naples "Federico II", Via Mezzocannone 16, 80134 Naples, Italy
| |
Collapse
|
17
|
Neira JL, Díaz-García C, Prieto M, Coutinho A. The C-terminal SAM domain of p73 binds to the N terminus of MDM2. Biochim Biophys Acta Gen Subj 2019; 1863:760-770. [DOI: 10.1016/j.bbagen.2019.01.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/25/2019] [Accepted: 01/31/2019] [Indexed: 01/10/2023]
|
18
|
Design and analysis of EphA2-SAM peptide ligands: A multi-disciplinary screening approach. Bioorg Chem 2019; 84:434-443. [DOI: 10.1016/j.bioorg.2018.12.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 11/22/2018] [Accepted: 12/06/2018] [Indexed: 01/28/2023]
|
19
|
Kukuk L, Dingley AJ, Granzin J, Nagel-Steger L, Thiagarajan-Rosenkranz P, Ciupka D, Hänel K, Batra-Safferling R, Pacheco V, Stoldt M, Pfeffer K, Beer-Hammer S, Willbold D, Koenig BW. Structure of the SLy1 SAM homodimer reveals a new interface for SAM domain self-association. Sci Rep 2019; 9:54. [PMID: 30631134 PMCID: PMC6328559 DOI: 10.1038/s41598-018-37185-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 11/30/2018] [Indexed: 11/08/2022] Open
Abstract
Sterile alpha motif (SAM) domains are protein interaction modules that are involved in a diverse range of biological functions such as transcriptional and translational regulation, cellular signalling, and regulation of developmental processes. SH3 domain-containing protein expressed in lymphocytes 1 (SLy1) is involved in immune regulation and contains a SAM domain of unknown function. In this report, the structure of the SLy1 SAM domain was solved and revealed that this SAM domain forms a symmetric homodimer through a novel interface. The interface consists primarily of the two long C-terminal helices, α5 and α5', of the domains packing against each other. The dimerization is characterized by a dissociation constant in the lower micromolar range. A SLy1 SAM domain construct with an extended N-terminus containing five additional amino acids of the SLy1 sequence further increases the stability of the homodimer, making the SLy1 SAM dimer two orders of magnitude more stable than previously studied SAM homodimers, suggesting that the SLy1 SAM dimerization is of functional significance. The SLy1 SAM homodimer contains an exposed mid-loop surface on each monomer, which may provide a scaffold for mediating interactions with other SAM domain-containing proteins via a typical mid-loop-end-helix interface.
Collapse
Affiliation(s)
- Laura Kukuk
- Institute of Complex Systems, Strukturbiochemie (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Andrew J Dingley
- Institute of Complex Systems, Strukturbiochemie (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Joachim Granzin
- Institute of Complex Systems, Strukturbiochemie (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Luitgard Nagel-Steger
- Institute of Complex Systems, Strukturbiochemie (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Pallavi Thiagarajan-Rosenkranz
- Institute of Complex Systems, Strukturbiochemie (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Daniel Ciupka
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Karen Hänel
- Institute of Complex Systems, Strukturbiochemie (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Renu Batra-Safferling
- Institute of Complex Systems, Strukturbiochemie (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Victor Pacheco
- Institute of Complex Systems, Strukturbiochemie (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany
- Institut für Makromolekulare Chemie, Albert-Ludwigs-Universität Freiburg, Stefan-Meier-Straße 31, 79104, Freiburg, Germany
| | - Matthias Stoldt
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Klaus Pfeffer
- Institut für Medizinische Mikrobiologie und Krankenhaushygiene, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Sandra Beer-Hammer
- Institut für Medizinische Mikrobiologie und Krankenhaushygiene, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
- Institut für Experimentelle und Klinische Pharmakologie und Toxikologie, und Interfakultäres Zentrum für Pharmakogenomik und Arzneimittelforschung (ICePhA), Eberhard-Karls-Universität Tübingen, Wilhelmstraße 56, 72074, Tübingen, Germany
| | - Dieter Willbold
- Institute of Complex Systems, Strukturbiochemie (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany.
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany.
| | - Bernd W Koenig
- Institute of Complex Systems, Strukturbiochemie (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany.
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany.
| |
Collapse
|
20
|
Wang Z, Nie Y, Zhang K, Xu H, Ramelot TA, Kennedy MA, Liu M, Zhu J, Yang Y. Solution structure of SHIP2 SH2 domain and its interaction with a phosphotyrosine peptide from c-MET. Arch Biochem Biophys 2018; 656:31-37. [PMID: 30165040 DOI: 10.1016/j.abb.2018.08.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/10/2018] [Accepted: 08/26/2018] [Indexed: 12/12/2022]
Abstract
SH2 domain-containing inositol 5-phosphatase 2 (SHIP2) binds with the Y1356-phosphorylated hepatocyte growth factor (HGF) receptor, c-MET, through its SH2 domain, which is essential for the role of SHIP2 in HGF-induced cell scattering and cell spreading. Previously, the experimental structure of the SH2 domain from SHIP2 (SHIP2-SH2) had not been reported, and its interaction with the Y1356-phosphorylated c-MET had not been investigated from a structural point of view. In this study, the solution structure of SHIP2-SH2 was determined by NMR spectroscopy, where it was found to adopt a typical SH2-domain fold that contains a positively-charged pocket for binding to phosphotyrosine (pY). The interaction between SHIP2-SH2 and a pY-containing peptide from c-MET (Y1356 phosphorylated) was investigated through NMR titrations. The results showed that the binding affinity of SHIP2-SH2 with the phosphopeptide is at low micromolar level, and the binding interface consists of the positively-charged pocket and its surrounding regions. Furthermore, R28, S49 and R70 were identified as key residues for the binding and may directly interact with the pY. Taken together, these findings provide structural insights into the binding of SHIP2-SH2 with the Y1356-phosphorylated c-MET, and lay a foundation for further studies of the interactions between SHIP2-SH2 and its various binding partners.
Collapse
Affiliation(s)
- Zi Wang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yao Nie
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kunxiao Zhang
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Huaihai Institute of Technology, Lianyungang, 222005, China
| | - Henghao Xu
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Huaihai Institute of Technology, Lianyungang, 222005, China
| | - Theresa A Ramelot
- Department of Chemistry and Biochemistry, The Northeast Structural Genomics Consortium, Miami University, Oxford, OH, 45056, United States
| | - Michael A Kennedy
- Department of Chemistry and Biochemistry, The Northeast Structural Genomics Consortium, Miami University, Oxford, OH, 45056, United States
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Jiang Zhu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China.
| | - Yunhuang Yang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China.
| |
Collapse
|
21
|
Mercurio FA, Pirone L, Di Natale C, Marasco D, Pedone EM, Leone M. Sam domain-based stapled peptides: Structural analysis and interaction studies with the Sam domains from the EphA2 receptor and the lipid phosphatase Ship2. Bioorg Chem 2018; 80:602-610. [PMID: 30036816 DOI: 10.1016/j.bioorg.2018.07.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 07/06/2018] [Accepted: 07/12/2018] [Indexed: 12/27/2022]
Abstract
Sam (Sterile alpha motif) domains represent small helical protein-protein interaction modules which play versatile functions in different cellular processes. The Sam domain from the EphA2 receptor binds the Sam domain of the lipid phosphatase Ship2 and this interaction modulates receptor endocytosis and degradation primarily generating pro-oncogenic effects in cell. To identify molecule antagonists of the EphA2-Sam/Ship2-Sam complex with anti-cancer activity, we focused on hydrocarbon helical stapled peptides. EphA2-Sam and one of its interactors (i.e., the first Sam domain of the adaptor protein Odin) were used as model systems for peptide design. Increase in helicity in the stapled peptides, with respect to the corresponding linear/native-like regions, was proved by structural studies conducted through CD (Circular Dichroism) and NMR (Nuclear Magnetic Resonance). Interestingly, interaction assays by means of NMR, SPR (Surface Plasmon Resonance) and MST (MicroScale Thermophoresis) techniques led to the discovery of a novel ligand of Ship2-Sam.
Collapse
Affiliation(s)
- Flavia Anna Mercurio
- Institute of Biostructures and Bioimaging (CNR), Naples, Italy; InterUniversity Research Centre on Bioactive Peptides (CIRPEB), University of Naples Federico II, Naples, Italy
| | - Luciano Pirone
- Institute of Biostructures and Bioimaging (CNR), Naples, Italy; InterUniversity Research Centre on Bioactive Peptides (CIRPEB), University of Naples Federico II, Naples, Italy
| | | | - Daniela Marasco
- Institute of Biostructures and Bioimaging (CNR), Naples, Italy; InterUniversity Research Centre on Bioactive Peptides (CIRPEB), University of Naples Federico II, Naples, Italy; University of Naples Federico II, Department of Pharmacy, Naples, Italy
| | - Emilia Maria Pedone
- Institute of Biostructures and Bioimaging (CNR), Naples, Italy; InterUniversity Research Centre on Bioactive Peptides (CIRPEB), University of Naples Federico II, Naples, Italy
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging (CNR), Naples, Italy; InterUniversity Research Centre on Bioactive Peptides (CIRPEB), University of Naples Federico II, Naples, Italy.
| |
Collapse
|
22
|
Mercurio FA, Di Natale C, Pirone L, Iannitti R, Marasco D, Pedone EM, Palumbo R, Leone M. The Sam-Sam interaction between Ship2 and the EphA2 receptor: design and analysis of peptide inhibitors. Sci Rep 2017; 7:17474. [PMID: 29234063 PMCID: PMC5727260 DOI: 10.1038/s41598-017-17684-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 11/21/2017] [Indexed: 12/21/2022] Open
Abstract
The lipid phosphatase Ship2 represents a drug discovery target for the treatment of different diseases, including cancer. Its C-terminal sterile alpha motif domain (Ship2-Sam) associates with the Sam domain from the EphA2 receptor (EphA2-Sam). This interaction is expected to mainly induce pro-oncogenic effects in cells therefore, inhibition of the Ship2-Sam/EphA2-Sam complex may represent an innovative route to discover anti-cancer therapeutics. In the present work, we designed and analyzed several peptide sequences encompassing the interaction interface of EphA2-Sam for Ship2-Sam. Peptide conformational analyses and interaction assays with Ship2-Sam conducted through diverse techniques (CD, NMR, SPR and MST), identified a positively charged penta-amino acid native motif in EphA2-Sam, that once repeated three times in tandem, binds Ship2-Sam. NMR experiments show that the peptide targets the negatively charged binding site of Ship2-Sam for EphA2-Sam. Preliminary in vitro cell-based assays indicate that -at 50 µM concentration- it induces necrosis of PC-3 prostate cancer cells with more cytotoxic effect on cancer cells than on normal dermal fibroblasts. This work represents a pioneering study that opens further opportunities for the development of inhibitors of the Ship2-Sam/EphA2-Sam complex for therapeutic applications.
Collapse
Affiliation(s)
- Flavia Anna Mercurio
- Institute of Biostructures and Bioimaging (IBB), CNR, via Mezzocannone 16, 80134, Naples, Italy
| | - Concetta Di Natale
- Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples "Federico II", Via Mezzocannone 16, 80134, Naples, Italy
| | - Luciano Pirone
- Institute of Biostructures and Bioimaging (IBB), CNR, via Mezzocannone 16, 80134, Naples, Italy
| | - Roberta Iannitti
- Institute of Biostructures and Bioimaging (IBB), CNR, via Mezzocannone 16, 80134, Naples, Italy
| | - Daniela Marasco
- Institute of Biostructures and Bioimaging (IBB), CNR, via Mezzocannone 16, 80134, Naples, Italy.,Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples "Federico II", Via Mezzocannone 16, 80134, Naples, Italy
| | - Emilia Maria Pedone
- Institute of Biostructures and Bioimaging (IBB), CNR, via Mezzocannone 16, 80134, Naples, Italy
| | - Rosanna Palumbo
- Institute of Biostructures and Bioimaging (IBB), CNR, via Mezzocannone 16, 80134, Naples, Italy
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging (IBB), CNR, via Mezzocannone 16, 80134, Naples, Italy.
| |
Collapse
|
23
|
Mercurio FA, Costantini S, Di Natale C, Pirone L, Guariniello S, Scognamiglio PL, Marasco D, Pedone EM, Leone M. Structural investigation of a C-terminal EphA2 receptor mutant: Does mutation affect the structure and interaction properties of the Sam domain? BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1095-1104. [DOI: 10.1016/j.bbapap.2017.06.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 05/03/2017] [Accepted: 06/05/2017] [Indexed: 12/25/2022]
|
24
|
Medina-Carmona E, Neira JL, Salido E, Fuchs JE, Palomino-Morales R, Timson DJ, Pey AL. Site-to-site interdomain communication may mediate different loss-of-function mechanisms in a cancer-associated NQO1 polymorphism. Sci Rep 2017; 7:44532. [PMID: 28291250 PMCID: PMC5349528 DOI: 10.1038/srep44532] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 02/10/2017] [Indexed: 12/27/2022] Open
Abstract
Disease associated genetic variations often cause intracellular enzyme inactivation, dysregulation and instability. However, allosteric communication of mutational effects to distant functional sites leading to loss-of-function remains poorly understood. We characterize here interdomain site-to-site communication by which a common cancer-associated single nucleotide polymorphism (c.C609T/p.P187S) reduces the activity and stability in vivo of NAD(P)H:quinone oxidoreductase 1 (NQO1). NQO1 is a FAD-dependent, two-domain multifunctional stress protein acting as a Phase II enzyme, activating cancer pro-drugs and stabilizing p53 and p73α oncosuppressors. We show that p.P187S causes structural and dynamic changes communicated to functional sites far from the mutated site, affecting the FAD binding site located at the N-terminal domain (NTD) and accelerating proteasomal degradation through dynamic effects on the C-terminal domain (CTD). Structural protein:protein interaction studies reveal that the cancer-associated polymorphism does not abolish the interaction with p73α, indicating that oncosuppressor destabilization largely mirrors the low intracellular stability of p.P187S. In conclusion, we show how a single disease associated amino acid change may allosterically perturb several functional sites in an oligomeric and multidomain protein. These results have important implications for the understanding of loss-of-function genetic diseases and the identification of novel structural hot spots as targets for pharmacological intervention.
Collapse
Affiliation(s)
- Encarnación Medina-Carmona
- Department of Physical Chemistry, Faculty of Sciences, University of Granada, Av. Fuentenueva s/n, 18071, Granada, Spain
| | - Jose L. Neira
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Avda. del Ferrocarril s/n, 03202, Elche, Alicante, Spain
- Instituto de Biocomputación y Física de los Sistemas Complejos (BIFI), 50009, Zaragoza, Spain
| | - Eduardo Salido
- Hospital Universitario de Canarias, Centre for Biomedical Research on Rare Diseases (CIBERER), Tenerife, Spain
| | - Julian E. Fuchs
- Institute of General, Inorganic and Theoretical Chemistry, Faculty of Chemistry and Pharmacy, University of Innsbruck, Innsbruck, Austria
| | - Rogelio Palomino-Morales
- Department of Biochemistry and Molecular Biology I, Faculty of Sciences, University of Granada, Av. Fuentenueva s/n, 18071, Granada, Spain
| | - David J. Timson
- School of Pharmacy and Biomolecular Sciences, The University of Brighton, Brighton, UK
| | - Angel L. Pey
- Department of Physical Chemistry, Faculty of Sciences, University of Granada, Av. Fuentenueva s/n, 18071, Granada, Spain
| |
Collapse
|
25
|
Thomas MP, Erneux C, Potter BVL. SHIP2: Structure, Function and Inhibition. Chembiochem 2017; 18:233-247. [DOI: 10.1002/cbic.201600541] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Mark P. Thomas
- Department of Pharmacy and Pharmacology; University of Bath; Claverton Down Bath BA2 7AY UK
| | - Christophe Erneux
- I.R.I.B.H.M.; Université Libre de Bruxelles; Campus Erasme 808 Route de Lennik 1070 Brussels Belgium
| | - Barry V. L. Potter
- Drug Discovery and Medicinal Chemistry; Department of Pharmacology; University of Oxford; Mansfield Road Oxford OX1 3QT UK
| |
Collapse
|
26
|
Singh DR, Ahmed F, Paul MD, Gedam M, Pasquale EB, Hristova K. The SAM domain inhibits EphA2 interactions in the plasma membrane. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1864:31-38. [PMID: 27776928 DOI: 10.1016/j.bbamcr.2016.10.011] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 09/26/2016] [Accepted: 10/18/2016] [Indexed: 11/18/2022]
Abstract
All members of the Eph receptor family of tyrosine kinases contain a SAM domain near the C terminus, which has been proposed to play a role in receptor homotypic interactions and/or interactions with binding partners. The SAM domain of EphA2 is known to be important for receptor function, but its contribution to EphA2 lateral interactions in the plasma membrane has not been determined. Here we use a FRET-based approach to directly measure the effect of the SAM domain on the stability of EphA2 dimers on the cell surface in the absence of ligand binding. We also investigate the functional consequences of EphA2 SAM domain deletion. Surprisingly, we find that the EphA2 SAM domain inhibits receptor dimerization and decreases EphA2 tyrosine phosphorylation. This role is dramatically different from the role of the SAM domain of the related EphA3 receptor, which we previously found to stabilize EphA3 dimers and increase EphA3 tyrosine phosphorylation in cells in the absence of ligand. Thus, the EphA2 SAM domain likely contributes to a unique mode of EphA2 interaction that leads to distinct signaling outputs.
Collapse
Affiliation(s)
- Deo R Singh
- Department of Materials Science and Engineering, Johns Hopkins University, 3400 Charles Street, Baltimore, MD 21218, United States
| | - Fozia Ahmed
- Department of Materials Science and Engineering, Johns Hopkins University, 3400 Charles Street, Baltimore, MD 21218, United States
| | - Michael D Paul
- Program in Molecular Biophysics, Johns Hopkins University, 3400 Charles street, Baltimore, MD 21218, United States
| | - Manasee Gedam
- Department of Materials Science and Engineering, Johns Hopkins University, 3400 Charles Street, Baltimore, MD 21218, United States
| | - Elena B Pasquale
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Road, La Jolla, San Diego, CA 92037, United States
| | - Kalina Hristova
- Department of Materials Science and Engineering, Johns Hopkins University, 3400 Charles Street, Baltimore, MD 21218, United States; Program in Molecular Biophysics, Johns Hopkins University, 3400 Charles street, Baltimore, MD 21218, United States.
| |
Collapse
|
27
|
Mercurio FA, Marasco D, Di Natale C, Pirone L, Costantini S, Pedone EM, Leone M. Targeting EphA2-Sam and Its Interactome: Design and Evaluation of Helical Peptides Enriched in Charged Residues. Chembiochem 2016; 17:2179-2188. [DOI: 10.1002/cbic.201600413] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Flavia A. Mercurio
- Institute of Biostructures and Bioimaging; National Research Council; Via Mezzocannone 16 80134 Naples Italy
| | - Daniela Marasco
- Institute of Biostructures and Bioimaging; National Research Council; Via Mezzocannone 16 80134 Naples Italy
- Department of Pharmacy; University of Naples “Federico II”; Via Mezzocannone 16 80134 Naples Italy
| | - Concetta Di Natale
- Department of Biology; University of Naples “Federico II”; Via Cinthia 4 80126 Naples Italy
| | - Luciano Pirone
- Institute of Biostructures and Bioimaging; National Research Council; Via Mezzocannone 16 80134 Naples Italy
| | - Susan Costantini
- CROM; IRCCS-Istituto Nazionale Tumori “Fondazione G. Pascale”; Via Mariano Semmola 52 80131 Naples Italy
| | - Emilia M. Pedone
- Institute of Biostructures and Bioimaging; National Research Council; Via Mezzocannone 16 80134 Naples Italy
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging; National Research Council; Via Mezzocannone 16 80134 Naples Italy
| |
Collapse
|
28
|
Smirnova E, Kwan JJ, Siu R, Gao X, Zoidl G, Demeler B, Saridakis V, Donaldson LW. A new mode of SAM domain mediated oligomerization observed in the CASKIN2 neuronal scaffolding protein. Cell Commun Signal 2016; 14:17. [PMID: 27549312 PMCID: PMC4994250 DOI: 10.1186/s12964-016-0140-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 08/12/2016] [Indexed: 11/18/2022] Open
Abstract
Background CASKIN2 is a homolog of CASKIN1, a scaffolding protein that participates in a signaling network with CASK (calcium/calmodulin-dependent serine kinase). Despite a high level of homology between CASKIN2 and CASKIN1, CASKIN2 cannot bind CASK due to the absence of a CASK Interaction Domain and consequently, may have evolved undiscovered structural and functional distinctions. Results We demonstrate that the crystal structure of the Sterile Alpha Motif (SAM) domain tandem (SAM1-SAM2) oligomer from CASKIN2 is different than CASKIN1, with the minimal repeating unit being a dimer, rather than a monomer. Analytical ultracentrifugation sedimentation velocity methods revealed differences in monomer/dimer equilibria across a range of concentrations and ionic strengths for the wild type CASKIN2 SAM tandem and a structure-directed double mutant that could not oligomerize. Further distinguishing CASKIN2 from CASKIN1, EGFP-tagged SAM tandem proteins expressed in Neuro2a cells produced punctae that were distinct both in shape and size. Conclusions This study illustrates a new way in which neuronal SAM domains can assemble into large macromolecular assemblies that might concentrate and amplify synaptic responses. Electronic supplementary material The online version of this article (doi:10.1186/s12964-016-0140-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Ekaterina Smirnova
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Jamie J Kwan
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Ryan Siu
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Xin Gao
- Division of Computer, Computational Bioscience Research Center, Electrical and Mathematical Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Georg Zoidl
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada.,Department of Psychology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Borries Demeler
- Department of Biochemistry, University of Texas Health Science Center at San Antonio, 7760 Floyd Curl Drive, San Antonio, TX, 78229-3900, USA
| | - Vivian Saridakis
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Logan W Donaldson
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada.
| |
Collapse
|
29
|
DaRosa PA, Ovchinnikov S, Xu W, Klevit RE. Structural insights into SAM domain-mediated tankyrase oligomerization. Protein Sci 2016; 25:1744-52. [PMID: 27328430 DOI: 10.1002/pro.2968] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 06/16/2016] [Indexed: 12/28/2022]
Abstract
Tankyrase 1 (TNKS1; a.k.a. ARTD5) and tankyrase 2 (TNKS2; a.k.a ARTD6) are highly homologous poly(ADP-ribose) polymerases (PARPs) that function in a wide variety of cellular processes including Wnt signaling, Src signaling, Akt signaling, Glut4 vesicle translocation, telomere length regulation, and centriole and spindle pole maturation. Tankyrase proteins include a sterile alpha motif (SAM) domain that undergoes oligomerization in vitro and in vivo. However, the SAM domains of TNKS1 and TNKS2 have not been structurally characterized and the mode of oligomerization is not yet defined. Here we model the SAM domain-mediated oligomerization of tankyrase. The structural model, supported by mutagenesis and NMR analysis, demonstrates a helical, homotypic head-to-tail polymer that facilitates TNKS self-association. Furthermore, we show that TNKS1 and TNKS2 can form (TNKS1 SAM-TNKS2 SAM) hetero-oligomeric structures mediated by their SAM domains. Though wild-type tankyrase proteins have very low solubility, model-based mutations of the SAM oligomerization interface residues allowed us to obtain soluble TNKS proteins. These structural insights will be invaluable for the functional and biophysical characterization of TNKS1/2, including the role of TNKS oligomerization in protein poly(ADP-ribosyl)ation (PARylation) and PARylation-dependent ubiquitylation.
Collapse
Affiliation(s)
- Paul A DaRosa
- Department of Biochemistry, University of Washington, Seattle, Washington, 98195.,Department of Biological Structure, University of Washington, Seattle, Washington, 98195
| | - Sergey Ovchinnikov
- Department of Biochemistry, University of Washington, Seattle, Washington, 98195.,Howard Hughes Medical Institute, University of Washington, Seattle, Washington, 98195
| | - Wenqing Xu
- Department of Biological Structure, University of Washington, Seattle, Washington, 98195
| | - Rachel E Klevit
- Department of Biochemistry, University of Washington, Seattle, Washington, 98195
| |
Collapse
|
30
|
Taylor EB, Nayak DK, Quiniou SMA, Bengten E, Wilson M. Identification of SHIP-1 and SHIP-2 homologs in channel catfish, Ictalurus punctatus. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2015; 51:79-87. [PMID: 25743379 DOI: 10.1016/j.dci.2015.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 02/23/2015] [Accepted: 02/24/2015] [Indexed: 06/04/2023]
Abstract
Src homology domain 2 (SH2) domain-containing inositol 5'-phosphatases (SHIP) proteins have diverse roles in signal transduction. SHIP-1 and SHIP-2 homologs were identified in channel catfish, Ictalurus punctatus, based on sequence homology to murine and human SHIP sequences. Full-length cDNAs for catfish SHIP-1 and SHIP-2 (IpSHIP-1 and IpSHIP-2) were obtained using 5' and 3' RACE protocols. Catfish SHIP molecules share a high degree of sequence identity to their respective SHIP sequences from diverse taxa and both are encoded by single copy genes. IpSHIP-1 and IpSHIP-2 transcripts were expressed in all catfish tissues analyzed except for skin, and IpSHIP-1 message was more abundant than IpSHIP-2 message in lymphoid tissues. Catfish clonal B, cytotoxic T, and macrophage cell lines also expressed message for both molecules. IpSHIP-1 and IpSHIP-2 SH2 domains were expressed as recombinant proteins and were both found to be bound by cross-reacting rabbit anti-mouse SHIP-1 pAb. The anti-mouse SHIP-1 pAb also reacted with cell lysates from the cytotoxic T cell lines, macrophages and stimulated PBL. SHIP-1 is also phosphorylated at a conserved tyrosine residue, as shown by immunoprecipitation studies.
Collapse
Affiliation(s)
- Erin B Taylor
- Department of Microbiology, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Deepak K Nayak
- Department of Microbiology, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Sylvie M A Quiniou
- Warmwater Aquaculture Research Unit, USDA-ARS, Stoneville, MS 38776, USA
| | - Eva Bengten
- Department of Microbiology, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Melanie Wilson
- Department of Microbiology, University of Mississippi Medical Center, Jackson, MS 39216, USA.
| |
Collapse
|
31
|
Mercurio FA, Di Natale C, Pirone L, Scognamiglio PL, Marasco D, Pedone EM, Saviano M, Leone M. Peptide Fragments of Odin-Sam1: Conformational Analysis and Interaction Studies with EphA2-Sam. Chembiochem 2015; 16:1629-36. [DOI: 10.1002/cbic.201500197] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Indexed: 11/09/2022]
|
32
|
Chien W, Sun QY, Lee KL, Ding LW, Wuensche P, Torres-Fernandez LA, Tan SZ, Tokatly I, Zaiden N, Poellinger L, Mori S, Yang H, Tyner JW, Koeffler HP. Activation of protein phosphatase 2A tumor suppressor as potential treatment of pancreatic cancer. Mol Oncol 2015; 9:889-905. [PMID: 25637283 PMCID: PMC4387089 DOI: 10.1016/j.molonc.2015.01.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 01/07/2015] [Accepted: 01/07/2015] [Indexed: 12/28/2022] Open
Abstract
We utilized three tiers of screening to identify novel therapeutic agents for pancreatic cancers. First, we analyzed 14 pancreatic cancer cell lines against a panel of 66 small-molecule kinase inhibitors and dasatinib was the most potent. Second, we performed RNA expression analysis on 3 dasatinib-resistant and 3 dasatinib-sensitive pancreatic cancer cell lines to profile their gene expression. Third, gene profiling data was integrated with the Connectivity Map database to search for potential drugs. Thioridazine was one of the top ranking small molecules with highly negative enrichment. Thioridazine and its family members of phenothiazine including penfluridol caused pancreatic cancer cell death and affected protein expression levels of molecules involved in cell cycle regulation, apoptosis, and multiple kinase activities. This family of drugs causes activation of protein phosphatase 2 (PP2A). The drug FTY-720 (activator of PP2A) induced apoptosis of pancreatic cancer cells. Silencing catalytic unit of PP2A rendered pancreatic cancer cells resistant to penfluridol. Our observations suggest potential therapeutic use of penfluridol or similar agent associated with activation of PP2A in pancreatic cancers.
Collapse
Affiliation(s)
- Wenwen Chien
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.
| | - Qiao-Yang Sun
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Kian Leong Lee
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Ling-Wen Ding
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Peer Wuensche
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | | | - Siew Zhuan Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Itay Tokatly
- Cancer Research Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer 52621, Israel
| | - Norazean Zaiden
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Lorenz Poellinger
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Seiichi Mori
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Jeffrey W Tyner
- Department of Cell & Developmental Biology, Oregon Health & Science University, Portland, OR 97239, USA
| | - H Phillip Koeffler
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; Cedars-Sinai Medical Center, UCLA School of Medicine, Los Angeles, CA, USA; National University Cancer Institute, Singapore
| |
Collapse
|
33
|
Abstract
Eph receptor tyrosine kinases control cell-cell interactions during normal and oncogenic development, and are implicated in a range of processes including angiogenesis, stem cell maintenance and metastasis. They are thus of great interest as targets for cancer therapy. EphA3, originally isolated from leukemic and melanoma cells, is presently one of the most promising therapeutic targets, with multiple tumor-promoting roles in a variety of cancer types. This review focuses on EphA3, its functions in controlling cellular behavior, both in normal and pathological development, and most particularly in cancer.
Collapse
Affiliation(s)
- Peter W Janes
- Department of Biochemistry and Molecular Biology, Monash University , Victoria , Australia and
| | | | | | | | | | | |
Collapse
|
34
|
Neira JL. Structural dissection of the C-terminal sterile alpha motif (SAM) of human p73. Arch Biochem Biophys 2014; 558:133-42. [DOI: 10.1016/j.abb.2014.07.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 07/01/2014] [Accepted: 07/06/2014] [Indexed: 10/25/2022]
|
35
|
Mercurio FA, Scognamiglio PL, Di Natale C, Marasco D, Pellecchia M, Leone M. CD and NMR conformational studies of a peptide encompassing the Mid Loop interface of Ship2-Sam. Biopolymers 2014; 101:1088-98. [DOI: 10.1002/bip.22512] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 05/23/2014] [Accepted: 05/23/2014] [Indexed: 11/07/2022]
Affiliation(s)
| | - Pasqualina L. Scognamiglio
- Department of Pharmacy; University "Federico II"; Naples Italy
- Centro Interuniversitario di Ricerca sui Peptidi Bioattivi (CIRPEB); Naples Italy
- IIT Italian Institute of Technology; Naples Italy
| | - Concetta Di Natale
- Department of Pharmacy; University "Federico II"; Naples Italy
- IIT Italian Institute of Technology; Naples Italy
| | - Daniela Marasco
- Institute of Biostructures and Bioimaging (CNR); Naples Italy
- Department of Pharmacy; University "Federico II"; Naples Italy
- Centro Interuniversitario di Ricerca sui Peptidi Bioattivi (CIRPEB); Naples Italy
| | | | - Marilisa Leone
- Institute of Biostructures and Bioimaging (CNR); Naples Italy
- Centro Interuniversitario di Ricerca sui Peptidi Bioattivi (CIRPEB); Naples Italy
| |
Collapse
|
36
|
Fu CH, Lin RJ, Yu J, Chang WW, Liao GS, Chang WY, Tseng LM, Tsai YF, Yu JC, Yu AL. A Novel Oncogenic Role of Inositol Phosphatase SHIP2 in ER-Negative Breast Cancer Stem Cells: Involvement of JNK/Vimentin Activation. Stem Cells 2014; 32:2048-60. [DOI: 10.1002/stem.1735] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 03/19/2014] [Accepted: 04/09/2014] [Indexed: 12/26/2022]
Affiliation(s)
- Chiung-Hui Fu
- Graduate Institute of Life Sciences, National Defense Medical Center; Taipei Taiwan
- Genomics Research Center, Academia Sinica; Taipei Taiwan
- Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou; Taoyuan Taiwan
| | - Ruey-Jen Lin
- Genomics Research Center, Academia Sinica; Taipei Taiwan
- Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou; Taoyuan Taiwan
| | - John Yu
- Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou; Taoyuan Taiwan
- Institute of Cellular and Organismic Biology, Academia Sinica; Taipei Taiwan
| | - Wen-Wei Chang
- Genomics Research Center, Academia Sinica; Taipei Taiwan
- School of Biomedical Sciences; Chung Shan Medical University; Taichung Taiwan
- Department of Medical Research; Chung Shan Medical University Hospital; Taichung Taiwan
| | - Guo-Shiou Liao
- Division of General Surgery, Department of Surgery; Tri-Service General Hospital; Taipei Taiwan
| | - Wen-Ying Chang
- Genomics Research Center, Academia Sinica; Taipei Taiwan
- Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou; Taoyuan Taiwan
| | - Ling-Ming Tseng
- Division of General Surgery, Department of Surgery; Taipei-Veterans General Hospital; Taipei Taiwan
- National Yang Ming University; Taipei Taiwan
| | - Yi-Fang Tsai
- Division of General Surgery, Department of Surgery; Taipei-Veterans General Hospital; Taipei Taiwan
| | - Jyh-Cherng Yu
- Graduate Institute of Life Sciences, National Defense Medical Center; Taipei Taiwan
- Division of General Surgery, Department of Surgery; Tri-Service General Hospital; Taipei Taiwan
| | - Alice L. Yu
- Graduate Institute of Life Sciences, National Defense Medical Center; Taipei Taiwan
- Genomics Research Center, Academia Sinica; Taipei Taiwan
- Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou; Taoyuan Taiwan
- Department of Pediatrics; University of California in San Diego; San Diego California USA
| |
Collapse
|
37
|
Zhang L, Buck M. Molecular simulations of a dynamic protein complex: role of salt-bridges and polar interactions in configurational transitions. Biophys J 2014; 105:2412-7. [PMID: 24268153 DOI: 10.1016/j.bpj.2013.09.052] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 08/23/2013] [Accepted: 09/24/2013] [Indexed: 12/29/2022] Open
Abstract
Ion charge pairs and hydrogen bonds have been extensively studied for their roles in stabilizing protein complexes and in steering the process of protein association. Recently, it has become clear that some protein complexes are dynamic in that they interconvert between several alternate configurations. We have previously characterized one such system: the EphA2:SHIP2 SAM-SAM heterodimer by solution NMR. Here we carried out extensive all-atom molecular-dynamics simulations on a microsecond time-scale starting with different NMR-derived structures for the complex. Transitions are observed between several discernible configurations at average time intervals of 50-100 ns. The domains reorient relative to one another by substantial rotation and a slight shifting of the interfaces. Bifurcated and intermediary salt-bridge and hydrogen-bond interactions play a role in the transitions in a process that can be described as moving along a "monkey-bar". We notice an increased density of salt bridges near protein interaction surfaces that appear to enable these transitions, also suggesting why the trajectories can become kinetically hindered in regions where fewer of such interactions are possible. In this context, even microsecond molecular-dynamics simulations are not sufficient to sample the energy landscape unless the structures remain close to their experimentally derived low-energy configurations.
Collapse
Affiliation(s)
- Liqun Zhang
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, Cleveland, Ohio
| | | |
Collapse
|
38
|
Characterization of the SAM domain of the PKD-related protein ANKS6 and its interaction with ANKS3. BMC STRUCTURAL BIOLOGY 2014; 14:17. [PMID: 24998259 PMCID: PMC4105859 DOI: 10.1186/1472-6807-14-17] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Accepted: 06/30/2014] [Indexed: 11/10/2022]
Abstract
BACKGROUND Autosomal dominant polycystic kidney disease (ADPKD) is the most common genetic disorder leading to end-stage renal failure in humans. In the PKD/Mhm(cy/+) rat model of ADPKD, the point mutation R823W in the sterile alpha motif (SAM) domain of the protein ANKS6 is responsible for disease. SAM domains are known protein-protein interaction domains, capable of binding each other to form polymers and heterodimers. Despite its physiological importance, little is known about the function of ANKS6 and how the R823W point mutation leads to PKD. Recent work has revealed that ANKS6 interacts with a related protein called ANKS3. Both ANKS6 and ANKS3 have a similar domain structure, with ankyrin repeats at the N-terminus and a SAM domain at the C-terminus. RESULTS The SAM domain of ANKS3 is identified as a direct binding partner of the ANKS6 SAM domain. We find that ANKS3-SAM polymerizes and ANKS6-SAM can bind to one end of the polymer. We present crystal structures of both the ANKS3-SAM polymer and the ANKS3-SAM/ANKS6-SAM complex, revealing the molecular details of their association. We also learn how the R823W mutation disrupts ANKS6 function by dramatically destabilizing the SAM domain such that the interaction with ANKS3-SAM is lost. CONCLUSIONS ANKS3 is a direct interacting partner of ANKS6. By structurally and biochemically characterizing the interaction between the ANKS3 and ANKS6 SAM domains, our work provides a basis for future investigation of how the interaction between these proteins mediates kidney function.
Collapse
|
39
|
Borthakur S, Lee H, Kim S, Wang BC, Buck M. Binding and function of phosphotyrosines of the Ephrin A2 (EphA2) receptor using synthetic sterile α motif (SAM) domains. J Biol Chem 2014; 289:19694-703. [PMID: 24825902 DOI: 10.1074/jbc.m114.567602] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The sterile α motif (SAM) domain of the ephrin receptor tyrosine kinase, EphA2, undergoes tyrosine phosphorylation, but the effect of phosphorylation on the structure and interactions of the receptor is unknown. Studies to address these questions have been hindered by the difficulty of obtaining site-specifically phosphorylated proteins in adequate amounts. Here, we describe the use of chemically synthesized and specifically modified domain-length peptides to study the behavior of phosphorylated EphA2 SAM domains. We show that tyrosine phosphorylation of any of the three tyrosines, Tyr(921), Tyr(930), and Tyr(960), has a surprisingly small effect on the EphA2 SAM structure and stability. However, phosphorylation at Tyr(921) and Tyr(930) enables differential binding to the Src homology 2 domain of the adaptor protein Grb7, which we propose will lead to distinct functional outcomes. Setting up different signaling platforms defined by selective interactions with adaptor proteins thus adds another level of regulation to EphA2 signaling.
Collapse
Affiliation(s)
| | - HyeongJu Lee
- From the Departments of Physiology and Biophysics
| | | | - Bing-Cheng Wang
- From the Departments of Physiology and Biophysics, Pharmacology, and the Rammelkamp Center for Research, MetroHealth Medical Center, Cleveland, Ohio 44109the Case Comprehensive Cancer Center, and
| | - Matthias Buck
- From the Departments of Physiology and Biophysics, the Case Comprehensive Cancer Center, and Neurosciences, the Case Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, Ohio 44106 and
| |
Collapse
|
40
|
Xie J, Erneux C, Pirson I. How does SHIP1/2 balance PtdIns(3,4)P2 and does it signal independently of its phosphatase activity? Bioessays 2013; 35:733-43. [PMID: 23650141 DOI: 10.1002/bies.201200168] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The number of cellular events identified as being directly or indirectly modulated by phosphoinositides dramatically increased in the recent years. Part of the complexity results from the fact that the seven phosphoinositides play second messenger functions in many different areas of growth factors and insulin signaling, cytoskeletal organization, membrane dynamics, trafficking, or nuclear signaling. PtdIns(3,4)P2 is commonly reported as a product of the SH2 domain-containing inositol 5-phosphatases 1/2 (SHIP1 and SHIP2) that dephosphorylate PtdIns(3,4,5)P3 at the 5-position. Here we discuss recent interest in PtdIns(3,4)P2 signaling highlighting its involvement in key cellular mechanisms such as cell adhesion, migration, and cytoskeletal regulation. We question and discuss the involvement of SHIP2 either as a PI 5-phosphatase or as a scaffold protein in insulin signaling, cytoskeletal dynamics, and endocytosis of growth factor receptors.
Collapse
Affiliation(s)
- Jingwei Xie
- Department of Pathophysiology, China Medical University, Heping District, Shenyang Liaoning Province, China
| | | | | |
Collapse
|
41
|
Abstract
Phosphoinositide signalling molecules interact with a plethora of effector proteins to regulate cell proliferation and survival, vesicular trafficking, metabolism, actin dynamics and many other cellular functions. The generation of specific phosphoinositide species is achieved by the activity of phosphoinositide kinases and phosphatases, which phosphorylate and dephosphorylate, respectively, the inositol headgroup of phosphoinositide molecules. The phosphoinositide phosphatases can be classified as 3-, 4- and 5-phosphatases based on their specificity for dephosphorylating phosphates from specific positions on the inositol head group. The SAC phosphatases show less specificity for the position of the phosphate on the inositol ring. The phosphoinositide phosphatases regulate PI3K/Akt signalling, insulin signalling, endocytosis, vesicle trafficking, cell migration, proliferation and apoptosis. Mouse knockout models of several of the phosphoinositide phosphatases have revealed significant physiological roles for these enzymes, including the regulation of embryonic development, fertility, neurological function, the immune system and insulin sensitivity. Importantly, several phosphoinositide phosphatases have been directly associated with a range of human diseases. Genetic mutations in the 5-phosphatase INPP5E are causative of the ciliopathy syndromes Joubert and MORM, and mutations in the 5-phosphatase OCRL result in Lowe's syndrome and Dent 2 disease. Additionally, polymorphisms in the 5-phosphatase SHIP2 confer diabetes susceptibility in specific populations, whereas reduced protein expression of SHIP1 is reported in several human leukaemias. The 4-phosphatase, INPP4B, has recently been identified as a tumour suppressor in human breast and prostate cancer. Mutations in one SAC phosphatase, SAC3/FIG4, results in the degenerative neuropathy, Charcot-Marie-Tooth disease. Indeed, an understanding of the precise functions of phosphoinositide phosphatases is not only important in the context of normal human physiology, but to reveal the mechanisms by which these enzyme families are implicated in an increasing repertoire of human diseases.
Collapse
|
42
|
Mercurio FA, Marasco D, Pirone L, Scognamiglio PL, Pedone EM, Pellecchia M, Leone M. Heterotypic Sam-Sam association between Odin-Sam1 and Arap3-Sam: binding affinity and structural insights. Chembiochem 2012; 14:100-6. [PMID: 23239578 DOI: 10.1002/cbic.201200592] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Indexed: 11/07/2022]
Abstract
Arap3 is a phosphatidylinositol 3 kinase effector protein that plays a role as GTPase activator (GAP) for Arf6 and RhoA. Arap3 contains a sterile alpha motif (Sam) domain that has high sequence homology with the Sam domain of the EphA2-receptor (EphA2-Sam). Both Arap3-Sam and EphA2-Sam are able to associate with the Sam domain of the lipid phosphatase Ship2 (Ship2-Sam). Recently, we reported a novel interaction between the first Sam domain of Odin (Odin-Sam1), a protein belonging to the ANKS (ANKyrin repeat and Sam domain containing) family, and EphA2-Sam. In our latest work, we applied NMR spectroscopy, surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) to characterize the association between Arap3-Sam and Odin-Sam1. We show that these two Sam domains interact with low micromolar affinity. Moreover, by means of molecular docking techniques, supported by NMR data, we demonstrate that Odin-Sam1 and Arap3-Sam might bind with a topology that is common to several Sam-Sam complexes. The revealed structural details form the basis for the design of potential peptide antagonists that could be used as chemical tools to investigate functional aspects related to heterotypic Arap3-Sam associations.
Collapse
Affiliation(s)
- Flavia A Mercurio
- Department of Biological Sciences, University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy
| | | | | | | | | | | | | |
Collapse
|
43
|
Nievergall E, Lackmann M, Janes PW. Eph-dependent cell-cell adhesion and segregation in development and cancer. Cell Mol Life Sci 2012; 69:1813-42. [PMID: 22204021 PMCID: PMC11114713 DOI: 10.1007/s00018-011-0900-6] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Revised: 11/06/2011] [Accepted: 11/28/2011] [Indexed: 01/23/2023]
Abstract
Numerous studies attest to essential roles for Eph receptors and their ephrin ligands in controlling cell positioning and tissue patterning during normal and oncogenic development. These studies suggest multiple, sometimes contradictory, functions of Eph-ephrin signalling, which under different conditions can promote either spreading and cell-cell adhesion or cytoskeletal collapse, cell rounding, de-adhesion and cell-cell segregation. A principle determinant of the balance between these two opposing responses is the degree of receptor/ligand clustering and activation. This equilibrium is likely altered in cancers and modulated by somatic mutations of key Eph family members that have emerged as candidate cancer markers in recent profiling studies. In addition, cross-talk amongst Ephs and with other signalling pathways significantly modulates cell-cell adhesion, both between and within Eph- and ephrin-expressing cell populations. This review summarises our current understanding of how Eph receptors control cell adhesion and morphology, and presents examples demonstrating the importance of these events in normal development and cancer.
Collapse
Affiliation(s)
- Eva Nievergall
- Department of Biochemistry and Molecular Biology, Monash University, Wellington Road, Clayton, VIC 3800 Australia
- Present Address: Haematology Department, SA Pathology, Frome Road, Adelaide, SA 5000 Australia
| | - Martin Lackmann
- Department of Biochemistry and Molecular Biology, Monash University, Wellington Road, Clayton, VIC 3800 Australia
| | - Peter W. Janes
- Department of Biochemistry and Molecular Biology, Monash University, Wellington Road, Clayton, VIC 3800 Australia
| |
Collapse
|
44
|
Lee HJ, Hota PK, Chugha P, Guo H, Miao H, Zhang L, Kim SJ, Stetzik L, Wang BC, Buck M. NMR structure of a heterodimeric SAM:SAM complex: characterization and manipulation of EphA2 binding reveal new cellular functions of SHIP2. Structure 2012; 20:41-55. [PMID: 22244754 DOI: 10.1016/j.str.2011.11.013] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Revised: 11/08/2011] [Accepted: 11/10/2011] [Indexed: 02/06/2023]
Abstract
The sterile alpha motif (SAM) for protein-protein interactions is encountered in over 200 proteins, but the structural basis for its interactions is just becoming clear. Here we solved the structure of the EphA2-SHIP2 SAM:SAM heterodimeric complex by use of NMR restraints from chemical shift perturbations, NOE and RDC experiments. Specific contacts between the protein surfaces differ significantly from a previous model and other SAM:SAM complexes. Molecular dynamics and docking simulations indicate fluctuations in the complex toward alternate, higher energy conformations. The interface suggests that EphA family members bind to SHIP2 SAM, whereas EphB members may not; correspondingly, we demonstrate binding of EphA1, but not of EphB2, to SHIP2. A variant of EphB2 SAM was designed that binds SHIP2. Functional characterization of a mutant EphA2 compromised in SHIP2 binding reveals two previously unrecognized functions of SHIP2 in suppressing ligand-induced activation of EphA2 and in promoting receptor coordinated chemotactic cell migration.
Collapse
Affiliation(s)
- Hyeong J Lee
- Department of Physiology and Biophysics, MetroHealth, Cleveland, OH 44109, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Mercurio FA, Marasco D, Pirone L, Pedone EM, Pellecchia M, Leone M. Solution structure of the first Sam domain of Odin and binding studies with the EphA2 receptor. Biochemistry 2012; 51:2136-45. [PMID: 22332920 DOI: 10.1021/bi300141h] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The EphA2 receptor plays key roles in many physiological and pathological events, including cancer. The process of receptor endocytosis and the consequent degradation have attracted attention as possible means of overcoming the negative outcomes of EphA2 in cancer cells and decreasing tumor malignancy. A recent study indicates that Sam (sterile alpha motif) domains of Odin, a member of the ANKS (ankyrin repeat and sterile alpha motif domain-containing) family of proteins, are important for the regulation of EphA2 endocytosis. Odin contains two tandem Sam domains (Odin-Sam1 and -Sam2). Herein, we report on the nuclear magnetic resonance (NMR) solution structure of Odin-Sam1; through a variety of assays (employing NMR, surface plasmon resonance, and isothermal titration calorimetry techniques), we clearly demonstrate that Odin-Sam1 binds to the Sam domain of EphA2 in the low micromolar range. NMR chemical shift perturbation experiments and molecular modeling studies point out that the two Sam domains interact with a head-to-tail topology characteristic of several Sam-Sam complexes. This binding mode is similar to that we have previously proposed for the association between the Sam domains of the lipid phosphatase Ship2 and EphA2. This work further validates structural elements relevant for the heterotypic Sam-Sam interactions of EphA2 and provides novel insights for the design of potential therapeutic compounds that can modulate receptor endocytosis.
Collapse
Affiliation(s)
- Flavia Anna Mercurio
- Department of Biological Sciences, University of Naples Federico II, Naples, Italy
| | | | | | | | | | | |
Collapse
|
46
|
Eph/ephrin signaling in epidermal differentiation and disease. Semin Cell Dev Biol 2011; 23:92-101. [PMID: 22040910 DOI: 10.1016/j.semcdb.2011.10.017] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Accepted: 10/17/2011] [Indexed: 01/09/2023]
Abstract
Eph receptor tyrosine kinases mediate cell-cell communication by interacting with ephrin ligands residing on adjacent cell surfaces. In doing so, these juxtamembrane signaling complexes provide important contextual information about the cellular microenvironment that helps orchestrate tissue morphogenesis and maintain homeostasis. Eph/ephrin signaling has been implicated in various aspects of mammalian skin physiology, with several members of this large family of receptor tyrosine kinases and their ligands present in the epidermis, hair follicles, sebaceous glands, and underlying dermis. This review focuses on the emerging role of Eph receptors and ephrins in epidermal keratinocytes where they can modulate proliferation, migration, differentiation, and death. The activation of Eph receptors by ephrins at sites of cell-cell contact also appears to play a key role in the maturation of intercellular junctional complexes as keratinocytes move out of the basal layer and differentiate in the suprabasal layers of this stratified, squamous epithelium. Furthermore, alterations in the epidermal Eph/ephrin axis have been associated with cutaneous malignancy, wound healing defects and inflammatory skin conditions. These collective observations suggest that the Eph/ephrin cell-cell communication pathway may be amenable to therapeutic intervention for the purpose of restoring epidermal tissue homeostasis and integrity in dermatological disorders.
Collapse
|
47
|
Knight MJ, Leettola C, Gingery M, Li H, Bowie JU. A human sterile alpha motif domain polymerizome. Protein Sci 2011; 20:1697-706. [PMID: 21805519 DOI: 10.1002/pro.703] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Revised: 07/11/2011] [Accepted: 07/12/2011] [Indexed: 11/11/2022]
Abstract
The sterile alpha motif (SAM) domain is one of the most common protein modules found in eukaryotic genomes. Many SAM domains have been shown to form helical polymer structures suggesting that SAM modules can be used to create large protein complexes in the cell. Because many polymeric SAM domains form heterogenous and insoluble aggregates that are experimentally intractable when isolated, it is likely that many polymeric SAM domains have gone uncharacterized. We, therefore, developed a method to maintain polymeric SAM domains in a soluble form that allowed rapid screening for potential SAM polymers. SAM domains were expressed as fusions to a super-negatively charged green fluorescent protein (negGFP). The negGFP imparts three useful properties to the SAM domains: (1) the charge helps to maintain solubility; (2) the charge leads to reliable migration toward the cathode on native gels; and (3) the fluorescence emission allows visualization in crude extracts. Using the negGFP-SAM fusions, we screened a large library of human SAM domains for polymerization using a native gel screen. A selected set of hSAM domains were then purified and examined for true polymer formation by electron microscopy. In this manner, we identified a set of new potential SAM polymers: ANKS3, Atherin, BicaudalC1, Caskin1, Caskin2, Kazrin, L3MBTL3, L3MBTL4, LBP, LiprinB1, LiprinB2, SAMD8, SAMD9, and STIM2. While further characterization will be necessary to verify that the SAM domains identified here truly form polymers, our results provide a much stronger working hypothesis for a large number of proteins that was possible from sequence analysis alone.
Collapse
Affiliation(s)
- Mary Jane Knight
- Department of Chemistry and Biochemistry, UCLA-DOE Institute of Genomics and Proteomics, Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California 90095, USA
| | | | | | | | | |
Collapse
|
48
|
Sathyamurthy A, Freund SMV, Johnson CM, Allen MD, Bycroft M. Structural basis of p63α SAM domain mutants involved in AEC syndrome. FEBS J 2011; 278:2680-8. [DOI: 10.1111/j.1742-4658.2011.08194.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
49
|
Balasubramaniam D, Paul LN, Homan KT, Hall MC, Stauffacher CV. Specificity of HCPTP variants toward EphA2 tyrosines by quantitative selected reaction monitoring. Protein Sci 2011; 20:1172-81. [PMID: 21538645 DOI: 10.1002/pro.646] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2011] [Revised: 04/09/2011] [Accepted: 04/20/2011] [Indexed: 11/08/2022]
Abstract
EphA2 receptor tyrosine kinase and the human cytoplasmic protein tyrosine phosphatase (HCPTP) are overexpressed in a number of epithelial cancers. Overexpressed EphA2 in these cancers shows a significant decrease in phosphotyrosine content which results in suppression of receptor signaling and endocytosis and an increase in metastatic potential. The decreased phosphotyrosine content of EphA2 has been associated with decreased contact with its ligand, ephrin A1 and dephosphorylation by HCPTP. Potential specificity of the two HCPTP variants for tyrosines on EphA2 has not been investigated. We have used a mass spectrometry assay to measure relative rates of dephosphorylation for the two HCPTP variants at phosphotyrosine sites associated with control of the EphA2 kinase activity or interaction with downstream targets. Our results suggest that although both variants dephosphorylate the EphA2 receptor, the rate and specificity of dephosphorylation for specific tyrosines are different for HCPTP-A and HCPTP-B. The SAM domain tyrosine Y960 which has been implicated in downstream PI3K signaling is dephosphorylated exclusively by HCPTP-B. The activation loop tyrosine (Y772) which directly controls kinase activity is dephosphorylated about six times faster by HCPTP-A. In contrast, the juxtamembrane tyrosines (Y575, Y588 and Y594) which are implicated in both control of kinase activity and downstream signaling are dephosphorylated by both variants with similar rates. This difference in preference for dephosphorylation sites on EphA2 not only illuminates the different roles of the two variants of the phosphatase in EphA2 signaling, but also explains why both HCPTP variants are highly conserved in most mammals.
Collapse
Affiliation(s)
- Deepa Balasubramaniam
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
| | | | | | | | | |
Collapse
|
50
|
Abstract
IMPORTANCE OF THE FIELD Inositol polyphosphate 5-phosphatase (SHIP2) is an important negative regulator of intracellular phosphatidylinositol phosphate, a key second messenger of various intracellular signaling pathways. The functional upregulation of SHIP2 results in signaling blockade, leading to related disorders. AREAS COVERED IN THIS REVIEW We first summarize the role of SHIP2 in the regulation of insulin signaling and type 2 diabetes, including remarkable advances in pharmacological approaches. In addition, this review highlights new findings regarding the involvement of SHIP2 in a number of diseases, including cancer, neurodegenerative diseases, and atherosclerosis. WHAT THE READER WILL GAIN Recently identified small-molecule inhibitors of SHIP2 phosphatase activity emphasize the potential therapeutic value of SHIP2. In addition, currently available evidence demonstrates the importance of the scaffolding-type protein function of SHIP2. Understanding this interesting function will help clarify the complicated involvement of SHIP2 in various disorders. TAKE HOME MESSAGE Recent studies have demonstrated that SHIP2 is a promising therapeutic target for not only type 2 diabetes, but also cancer, neurodegenerative diseases, and atherosclerosis. Targeting SHIP2 through specific small-molecule inhibitors will have beneficial effects on these diseases.
Collapse
Affiliation(s)
- Akira Suwa
- Astellas Pharma, Inc., Pharmacology Research Labs, Drug Discovery Research, 21, Miyukigaoka, Tsukuba-shi, Ibaraki 305-8585, Japan.
| | | | | |
Collapse
|