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1.
FASEB J ; 35(8): e21815, 2021 08.
Article in English | MEDLINE | ID: mdl-34314064

ABSTRACT

The Src homology 2 containing inositol 5-phosphatase 2 (SHIP2) is a large multidomain enzyme that catalyzes the dephosphorylation of the phospholipid phosphatidylinositol 3,4,5-triphosphate (PI(3,4,5)P3 ) to form PI(3,4)P2 . PI(3,4,5)P3 is a key lipid second messenger controlling the recruitment of signaling proteins to the plasma membrane, thereby regulating a plethora of cellular events, including proliferation, growth, apoptosis, and cytoskeletal rearrangements. SHIP2, alongside PI3K and PTEN, regulates PI(3,4,5)P3 levels at the plasma membrane and has been heavily implicated in serious diseases such as cancer and type 2 diabetes; however, many aspects of its regulation mechanism remain elusive. We recently reported an activating effect of the SHIP2 C2 domain and here we describe an additional layer of regulation via the pleckstrin homology-related (PHR) domain. We show a phosphoinositide-induced transition to a high activity state of the enzyme that increases phosphatase activity up to 10-15 fold. We further show that PI(3,4)P2 directly interacts with the PHR domain to trigger this allosteric activation. Modeling of the PHR-phosphatase-C2 region of SHIP2 on the membrane suggests no major inter-domain interactions with the PHR domain, but close contacts between the two linkers offer a possible path of allosteric communication. Together, our data show that the PHR domain acts as an allosteric module regulating the catalytic activity of SHIP2 in response to specific phosphoinositide levels in the cell membrane.


Subject(s)
Cell Membrane/metabolism , Phosphatidylinositol Phosphates/metabolism , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases , Pleckstrin Homology Domains , Allosteric Regulation , Biocatalysis , Humans , Models, Molecular , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/chemistry , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/metabolism
2.
Structure ; 29(10): 1200-1213.e2, 2021 10 07.
Article in English | MEDLINE | ID: mdl-34081910

ABSTRACT

C2 domains facilitate protein interactions with lipid bilayers in either a Ca2+-dependent or -independent manner. We used molecular dynamics (MD) simulations to explore six Ca2+-independent C2 domains, from KIBRA, PI3KC2α, RIM2, PTEN, SHIP2, and Smurf2. In coarse-grained MD simulations these C2 domains formed transient interactions with zwitterionic bilayers, compared with longer-lived interactions with anionic bilayers containing phosphatidylinositol bisphosphate (PIP2). Type I C2 domains bound non-canonically via the front, back, or side of the ß sandwich, whereas type II C2 domains bound canonically, via the top loops. C2 domains interacted strongly with membranes containing PIP2, causing bound anionic lipids to cluster around the protein. Binding modes were refined via atomistic simulations. For PTEN and SHIP2, CG simulations of their phosphatase plus C2 domains with PIP2-containing bilayers were also performed, and the roles of the two domains in membrane localization compared. These studies establish a simulation protocol for membrane-recognition proteins.


Subject(s)
Lipid Bilayers/chemistry , Molecular Docking Simulation/methods , Molecular Dynamics Simulation , Binding Sites , Calcium/metabolism , Humans , Intracellular Signaling Peptides and Proteins/chemistry , Intracellular Signaling Peptides and Proteins/metabolism , Lipid Bilayers/metabolism , PTEN Phosphohydrolase/chemistry , PTEN Phosphohydrolase/metabolism , Phosphatidylinositol 4,5-Diphosphate/chemistry , Phosphatidylinositol 4,5-Diphosphate/metabolism , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/chemistry , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/metabolism , Protein Binding , Ubiquitin-Protein Ligases/chemistry , Ubiquitin-Protein Ligases/metabolism , rab3 GTP-Binding Proteins/chemistry , rab3 GTP-Binding Proteins/metabolism
3.
Front Immunol ; 12: 607044, 2021.
Article in English | MEDLINE | ID: mdl-33717088

ABSTRACT

Suppressive mechanisms operating within T cells are linked to immune dysfunction in the tumor microenvironment. We have previously reported using adoptive T cell immunotherapy models that tumor-bearing mice treated with a regimen of proteasome inhibitor, bortezomib - a dipeptidyl boronate, show increased antitumor lymphocyte effector function and survival. Here, we identify a mechanism for the improved antitumor CD8+ T cell function following bortezomib treatment. Intravenous administration of bortezomib at a low dose (1 mg/kg body weight) in wild-type or tumor-bearing mice altered the expression of a number of miRNAs in CD8+ T cells. Specifically, the effect of bortezomib was prominent on miR-155 - a key cellular miRNA involved in T cell function. Importantly, bortezomib-induced upregulation of miR-155 was associated with the downregulation of its targets, the suppressor of cytokine signaling 1 (SOCS1) and inositol polyphosphate-5-phosphatase (SHIP1). Genetic and biochemical analysis confirmed a functional link between miR-155 and these targets. Moreover, activated CD8+ T cells treated with bortezomib exhibited a significant reduction in programmed cell death-1 (PD-1) expressing SHIP1+ phenotype. These data underscore a mechanism of action by which bortezomib induces miR-155-dependent downregulation of SOCS1 and SHIP1 negative regulatory proteins, leading to a suppressed PD-1-mediated T cell exhaustion. Collectively, data provide novel molecular insights into bortezomib-mediated lymphocyte-stimulatory effects that could overcome immunosuppressive actions of tumor on antitumor T cell functions. The findings support the approach that bortezomib combined with other immunotherapies would lead to improved therapeutic outcomes by overcoming T cell exhaustion in the tumor microenvironment.


Subject(s)
Antineoplastic Agents/pharmacology , Bortezomib/pharmacology , Gene Expression Regulation, Neoplastic/drug effects , MicroRNAs/genetics , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/genetics , Proteasome Inhibitors/pharmacology , Suppressor of Cytokine Signaling 1 Protein/genetics , Animals , CD8-Positive T-Lymphocytes/drug effects , CD8-Positive T-Lymphocytes/immunology , CD8-Positive T-Lymphocytes/metabolism , Cell Line, Tumor , Cytokines/metabolism , Disease Models, Animal , Humans , Lymphocyte Count , Mice , MicroRNAs/chemistry , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/chemistry , RNA Folding , RNA Interference , Signal Transduction , Suppressor of Cytokine Signaling 1 Protein/chemistry
4.
J Med Chem ; 64(7): 3813-3826, 2021 04 08.
Article in English | MEDLINE | ID: mdl-33724834

ABSTRACT

Src homology 2 domain-containing inositol phosphate phosphatase 2 (SHIP2) is one of the 10 human inositol phosphate 5-phosphatases. One of its physiological functions is dephosphorylation of phosphatidylinositol 3,4,5-trisphosphate, PtdIns(3,4,5)P3. It is therefore a therapeutic target for pathophysiologies dependent on PtdIns(3,4,5)P3 and PtdIns(3,4)P2. Therapeutic interventions are limited by the dearth of crystallographic data describing ligand/inhibitor binding. An active site-directed fluorescent probe facilitated screening of compound libraries for SHIP2 ligands. With two additional orthogonal assays, several ligands including galloflavin were identified as low micromolar Ki inhibitors. One ligand, an oxo-linked ethylene-bridged dimer of benzene 1,2,4-trisphosphate, was shown to be an uncompetitive inhibitor that binds to a regulatory site on the catalytic domain. We posit that binding of ligands to this site restrains L4 loop motions that are key to interdomain communications that accompany high catalytic activity with phosphoinositide substrate. This site may, therefore, be a future druggable target for medicinal chemistry.


Subject(s)
Fluoresceins/metabolism , Fluorescent Dyes/metabolism , Inositol Phosphates/metabolism , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/antagonists & inhibitors , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/metabolism , Allosteric Site , Amino Acid Sequence , Animals , Catalytic Domain , Cell Line, Tumor , Crystallography, X-Ray , Enzyme Inhibitors/metabolism , Enzyme Inhibitors/pharmacology , Humans , Ligands , Mice , Molecular Docking Simulation , NIH 3T3 Cells , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/chemistry , Protein Binding
5.
Protein Expr Purif ; 180: 105821, 2021 04.
Article in English | MEDLINE | ID: mdl-33421554

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.


Subject(s)
Escherichia coli , Gene Expression , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases , Escherichia coli/genetics , Escherichia coli/metabolism , Humans , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/biosynthesis , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/chemistry , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/genetics , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/isolation & purification , Protein Domains , Recombinant Proteins/biosynthesis , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/isolation & purification , rhoA GTP-Binding Protein
6.
Cancer Sci ; 111(5): 1596-1606, 2020 May.
Article in English | MEDLINE | ID: mdl-32198795

ABSTRACT

Chronic infection with Helicobacter pylori cagA-positive strains is causally associated with the development of gastric diseases, most notably gastric cancer. The cagA-encoded CagA protein, which is injected into gastric epithelial cells by bacterial type IV secretion, undergoes tyrosine phosphorylation at the Glu-Pro-Ile-Tyr-Ala (EPIYA) segments (EPIYA-A, EPIYA-B, EPIYA-C, and EPIYA-D), which are present in various numbers and combinations in its C-terminal polymorphic region, thereby enabling CagA to promiscuously interact with SH2 domain-containing host cell proteins, including the prooncogenic SH2 domain-containing protein tyrosine phosphatase 2 (SHP2). Perturbation of host protein functions by aberrant complex formation with CagA has been considered to contribute to the development of gastric cancer. Here we show that SHIP2, an SH2 domain-containing phosphatidylinositol 5'-phosphatase, is a hitherto undiscovered CagA-binding host protein. Similar to SHP2, SHIP2 binds to the Western CagA-specific EPIYA-C segment or East Asian CagA-specific EPIYA-D segment through the SH2 domain in a tyrosine phosphorylation-dependent manner. In contrast to the case of SHP2, however, SHIP2 binds more strongly to EPIYA-C than to EPIYA-D. Interaction with CagA tethers SHIP2 to the plasma membrane, where it mediates production of phosphatidylinositol 3,4-diphosphate [PI(3,4)P2 ]. The CagA-SHIP2 interaction also potentiates the morphogenetic activity of CagA, which is caused by CagA-deregulated SHP2. This study indicates that initially delivered CagA interacts with SHIP2 and thereby strengthens H. pylori-host cell attachment by altering membrane phosphatidylinositol compositions, which potentiates subsequent delivery of CagA that binds to and thereby deregulates the prooncogenic phosphatase SHP2.


Subject(s)
Antigens, Bacterial/metabolism , Bacterial Proteins/metabolism , Epithelial Cells/metabolism , Gastric Mucosa/metabolism , Helicobacter Infections/metabolism , Helicobacter pylori/metabolism , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/metabolism , Amino Acid Motifs , Animals , Antigens, Bacterial/chemistry , Antigens, Bacterial/genetics , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Cell Line , Cell Membrane/metabolism , Epithelial Cells/microbiology , Epithelial Cells/pathology , Epithelial-Mesenchymal Transition , Gastric Mucosa/microbiology , Gastric Mucosa/pathology , Helicobacter Infections/microbiology , Helicobacter pylori/genetics , Humans , Phosphatidylinositol Phosphates/metabolism , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/chemistry , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/genetics , Phosphorylation , Protein Binding , Protein Transport , Protein Tyrosine Phosphatase, Non-Receptor Type 11/chemistry , Protein Tyrosine Phosphatase, Non-Receptor Type 11/metabolism , src Homology Domains
7.
Int J Mol Sci ; 21(6)2020 Mar 13.
Article in English | MEDLINE | ID: mdl-32183047

ABSTRACT

Previous studies have shown reduced expression of Src homology 2-containing inositol 5-phosphatase 2 (SHIP2) and its tumor-suppressive role in gastric cancer (GC). However, the precise role of SHIP2 in the migration and invasion of GC cells remains unclear. Here, an IQ motif containing the GTPase-activating protein 2 (IQGAP2) as a SHIP2 binding partner, was screened and identified by co-immunoprecipitation and mass spectrometry studies. While IQGAP2 ubiquitously expressed in GC cells, IQGAP2 and SHIP2 co-localized in the cytoplasm of GC cells, and this physical association was confirmed by the binding of IQGAP2 to PRD and SAM domains of SHIP2. The knockdown of either SHIP2 or IQGAP2 promoted cell migration and invasion by inhibiting SHIP2 phosphatase activity, activating Akt and subsequently increasing epithelial-mesenchymal transition (EMT). Furthermore, knockdown of IQGAP2 in SHIP2-overexpressing GC cells reversed the inhibition of cell migration and invasion by SHIP2 induction, which was associated with the suppression of elevated SHIP2 phosphatase activity. Moreover, the deletion of PRD and SAM domains of SHIP2 abrogated the interaction and restored cell migration and invasion. Collectively, these results indicate that IQGAP2 interacts with SHIP2, leading to the increment of SHIP2 phosphatase activity, and thereby inhibiting the migration and invasion of GC cells via the inactivation of Akt and reduction in EMT.


Subject(s)
Cell Movement , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/metabolism , Stomach Neoplasms/metabolism , ras GTPase-Activating Proteins/metabolism , Binding Sites , Cell Line, Tumor , Epithelial-Mesenchymal Transition , Gastric Mucosa/metabolism , Gastric Mucosa/pathology , HEK293 Cells , Humans , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/chemistry , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/genetics , Protein Binding , ras GTPase-Activating Proteins/genetics
8.
Biochem Soc Trans ; 48(1): 291-300, 2020 02 28.
Article in English | MEDLINE | ID: mdl-32049315

ABSTRACT

Modulating the activity of the Src Homology 2 (SH2) - containing Inositol 5'-Phosphatase (SHIP) enzyme family with small molecule inhibitors provides a useful and unconventional method of influencing cell signaling in the PI3K pathway. The development of small molecules that selectively target one of the SHIP paralogs (SHIP1 or SHIP2) as well as inhibitors that simultaneously target both enzymes have provided promising data linking the phosphatase activity of the SHIP enzymes to disorders and disease states that are in dire need of new therapeutic targets. These include cancer, immunotherapy, diabetes, obesity, and Alzheimer's disease. In this mini-review, we will provide a brief overview of research in these areas that support targeting SHIP1, SHIP2 or both enzymes for therapeutic purposes.


Subject(s)
Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/antagonists & inhibitors , Small Molecule Libraries/pharmacology , Alzheimer Disease/drug therapy , Alzheimer Disease/metabolism , Animals , Diabetes Mellitus/drug therapy , Diabetes Mellitus/metabolism , Drug Discovery , Humans , Neoplasms/drug therapy , Neoplasms/metabolism , Obesity/drug therapy , Obesity/metabolism , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/chemistry , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/metabolism
9.
Cell Signal ; 63: 109380, 2019 11.
Article in English | MEDLINE | ID: mdl-31377397

ABSTRACT

Binding of proteins with SH2 domains to tyrosine-phosphorylated signaling proteins is a key mechanism for transmission of biological signals within the cell. Characterization of dysregulated proteins in cell signaling pathways is important for the development of therapeutic approaches. The AKT pathway is a frequently upregulated pathway in most cancer cells and the SH2-containing inositol 5-phosphatase SHIP1 is a negative regulator of the AKT pathway. In this study we investigated different mutations of the conserved FLVR motif of the SH2 domain and putative phosphorylation sites of SHIP1 which are located in close proximity to its FLVR motif. We demonstrate that patient-derived SHIP1-FLVR motif mutations e.g. F28L, and L29F possess reduced protein expression and increased phospho-AKT-S473 levels in comparison to SHIP1 wildtype. The estimated half-life of SHIP1-F28L protein was reduced from 23.2 h to 0.89 h in TF-1 cells and from 4.7 h to 0.6 h in Jurkat cells. These data indicate that the phenylalanine residue at position 28 of SHIP1 is important for its stability. Replacement of F28 with other aromatic residues like tyrosine and tryptophan preserves protein stability while replacement with non-aromatic amino acids like leucine, isoleucine, valine or alanine severely affects the stability of SHIP1. In consequence, a SHIP1-mutant with an aromatic amino acid at position 28 i.e. F28W can rescue the inhibitory function of wild type SHIP1, whereas SHIP1-mutants with non-aromatic amino acids i.e. F28V do not inhibit cell growth anymore. A detailed structural analysis revealed that F28 forms hydrophobic surface contacts in particular with W5, I83, L97 and P100 which can be maintained by tyrosine and tryptophan residues, but not by non-aromatic residues at position 28. In line with this model of mutation-induced instability of SHIP1-F28L, treatment of cells with proteasomal inhibitor MG132 was able to rescue expression of SHIP1-F28L. In addition, mutation of putative phosphorylation sites S27 and S33 adjacent to the FLVR motif of SHIP1 have an influence on its protein stability. These results further support a functional role of SHIP1 as tumor suppressor protein and indicate a regulation of protein expression of SH2 domain containing proteins via the FLVR motif.


Subject(s)
Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/chemistry , Enzyme Stability , HEK293 Cells , Humans , Jurkat Cells , Mutation , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/genetics , src Homology Domains/genetics
10.
J Chem Theory Comput ; 15(8): 4318-4331, 2019 Aug 13.
Article in English | MEDLINE | ID: mdl-31241940

ABSTRACT

The relative prevalence of native protein-protein interactions (PPIs) are the cornerstone for understanding the structure, dynamics and mechanisms of function of protein complexes. In this study, we develop a scheme for scaling the protein-water interaction in the CHARMM36 force field, in order to better fit the solvation free energy of amino acids side-chain analogues. We find that the molecular dynamics simulation with the scaled force field, CHARMM36s, as well as a recently released version, CHARMM36m, effectively improve on the overly sticky association of proteins, such as ubiquitin. We investigate the formation of a heterodimer protein complex between the SAM domains of the EphA2 receptor and the SHIP2 enzyme by performing a combined total of 48 µs simulations with the different potential functions. While the native SAM heterodimer is only predicted at a low rate of 6.7% with the original CHARMM36 force field, the yield is increased to 16.7% with CHARMM36s, and to 18.3% with CHARMM36m. By analyzing the 25 native SAM complexes formed in the simulations, we find that their formation involves a preorientation guided by Coulomb interactions, consistent with an electrostatic steering mechanism. In 12 cases, the complex could directly transform to the native protein interaction surfaces with only small adjustments in domain orientation. In the other 13 cases, orientational and/or translational adjustments are needed to reach the native complex. Although the tendency for non-native complexes to dissociate has nearly doubled with the modified potential functions, a dissociation followed by a reassociation to the correct complex structure is still rare. Instead, the remaining non-native complexes undergo configurational changes/surface searching, which, however, rarely leads to native structures on a time scale of 250 ns. These observations provide a rich picture of the mechanisms of protein-protein complex formation and suggest that computational predictions of native complex PPIs could be improved further.


Subject(s)
Protein Interaction Maps , Proteins/metabolism , Humans , Molecular Dynamics Simulation , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/chemistry , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/metabolism , Protein Binding , Protein Conformation , Protein Multimerization , Proteins/chemistry , Receptor, EphA2/chemistry , Receptor, EphA2/metabolism , Static Electricity , Thermodynamics , Ubiquitin/chemistry , Ubiquitin/metabolism , Water/metabolism
11.
Arch Biochem Biophys ; 656: 31-37, 2018 10 15.
Article in English | MEDLINE | ID: mdl-30165040

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.


Subject(s)
Peptide Fragments/metabolism , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/chemistry , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/metabolism , Phosphotyrosine/metabolism , Proto-Oncogene Proteins c-met/metabolism , src Homology Domains , Amino Acid Sequence , Binding Sites , Humans , Magnetic Resonance Spectroscopy , Mutation , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/genetics , Protein Binding , Sequence Alignment , src Homology Domains/genetics
12.
Bioorg Chem ; 80: 602-610, 2018 10.
Article in English | MEDLINE | ID: mdl-30036816

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.


Subject(s)
Peptides/chemistry , Peptides/pharmacology , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/metabolism , Protein Interaction Maps/drug effects , Receptor, EphA2/metabolism , Amino Acid Sequence , Drug Discovery , Humans , Models, Molecular , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/chemistry , Protein Binding/drug effects , Receptor, EphA2/chemistry , Sterile Alpha Motif/drug effects
13.
Elife ; 72018 05 11.
Article in English | MEDLINE | ID: mdl-29749928

ABSTRACT

The Eph receptor tyrosine kinase (RTK) family is the largest subfamily of RTKs playing critical roles in many developmental processes such as tissue patterning, neurogenesis and neuronal circuit formation, angiogenesis, etc. How the 14 Eph proteins, via their highly similar cytoplasmic domains, can transmit diverse and sometimes opposite cellular signals upon engaging ephrins is a major unresolved question. Here, we systematically investigated the bindings of each SAM domain of Eph receptors to the SAM domains from SHIP2 and Odin, and uncover a highly specific SAM-SAM interaction-mediated cytoplasmic Eph-effector binding pattern. Comparative X-ray crystallographic studies of several SAM-SAM heterodimer complexes, together with biochemical and cell biology experiments, not only revealed the exquisite specificity code governing Eph/effector interactions but also allowed us to identify SAMD5 as a new Eph binding partner. Finally, these Eph/effector SAM heterodimer structures can explain many Eph SAM mutations identified in patients suffering from cancers and other diseases.


Subject(s)
Carrier Proteins/metabolism , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/metabolism , Receptor, EphA2/metabolism , Signal Transduction , Adaptor Proteins, Signal Transducing , Animals , Carrier Proteins/chemistry , Crystallography, X-Ray , Mice , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/chemistry , Protein Binding , Protein Conformation , Protein Multimerization , Receptor, EphA2/chemistry , Sterile Alpha Motif
14.
Growth Factors ; 36(5-6): 213-231, 2018 12.
Article in English | MEDLINE | ID: mdl-30764683

ABSTRACT

SHIP-1 is a hematopoietic-specific inositol phosphatase activated downstream of a multitude of receptors including those for growth factors, cytokines, antigen, immunoglobulin and toll-like receptor agonists where it exerts inhibitory control. While it is constitutively expressed in all immune cells, SHIP-1 expression is negatively regulated by the inflammatory and oncogenic micro-RNA miR-155. Knockout mouse studies have shown the importance of SHIP-1 in various immune cell subsets and have revealed a range of immune-mediated pathologies that are engendered due to loss of SHIP-1's regulatory activity, impelling investigations into the role of SHIP-1 in human disease. In this review, we provide an overview of the literature relating to the role of SHIP-1 in hematopoietic cell signaling and function, we summarize recent reports that highlight the dysregulation of the SHIP-1 pathway in cancers, autoimmune disorders and inflammatory diseases, and lastly we discuss the importance of SHIP-1 in restraining myeloid growth factor signaling.


Subject(s)
Granulocyte Colony-Stimulating Factor/metabolism , Hematopoietic Stem Cells/metabolism , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/metabolism , Signal Transduction , Animals , Humans , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/chemistry
15.
Sci Rep ; 7(1): 17474, 2017 12 12.
Article in English | MEDLINE | ID: mdl-29234063

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.


Subject(s)
Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/antagonists & inhibitors , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/metabolism , Receptor, EphA2/antagonists & inhibitors , Receptor, EphA2/metabolism , Sterile Alpha Motif , Antineoplastic Agents/pharmacology , Binding Sites , Cell Line, Tumor , Drug Design , Escherichia coli , Fibroblasts/drug effects , Fibroblasts/metabolism , Humans , Male , Membrane Proteins , Models, Molecular , Necrosis/chemically induced , Necrosis/metabolism , Nuclear Magnetic Resonance, Biomolecular , Peptides/chemistry , Peptides/pharmacology , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/chemistry , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/genetics , Preliminary Data , Prostatic Neoplasms/drug therapy , Prostatic Neoplasms/metabolism , Protein Binding , Receptor, EphA2/chemistry , Receptor, EphA2/genetics , Saccharomyces cerevisiae Proteins , Sterile Alpha Motif/drug effects
16.
Elife ; 62017 08 09.
Article in English | MEDLINE | ID: mdl-28792888

ABSTRACT

SH2-containing-inositol-5-phosphatases (SHIPs) dephosphorylate the 5-phosphate of phosphatidylinositol-3,4,5-trisphosphate (PI(3,4,5)P3) and play important roles in regulating the PI3K/Akt pathway in physiology and disease. Aiming to uncover interdomain regulatory mechanisms in SHIP2, we determined crystal structures containing the 5-phosphatase and a proximal region adopting a C2 fold. This reveals an extensive interface between the two domains, which results in significant structural changes in the phosphatase domain. Both the phosphatase and C2 domains bind phosphatidylserine lipids, which likely helps to position the active site towards its substrate. Although located distant to the active site, the C2 domain greatly enhances catalytic turnover. Employing molecular dynamics, mutagenesis and cell biology, we identify two distinct allosteric signaling pathways, emanating from hydrophobic or polar interdomain interactions, differentially affecting lipid chain or headgroup moieties of PI(3,4,5)P3. Together, this study reveals details of multilayered C2-mediated effects important for SHIP2 activity and points towards interesting new possibilities for therapeutic interventions.


Subject(s)
Phosphatidylinositol Phosphates/metabolism , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/chemistry , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/metabolism , Catalytic Domain , Crystallography, X-Ray , DNA Mutational Analysis , Humans , Models, Molecular , Molecular Dynamics Simulation , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/genetics , Phosphatidylserines/metabolism , Protein Binding , Protein Conformation , Protein Domains
17.
Biochim Biophys Acta Proteins Proteom ; 1865(9): 1095-1104, 2017 Sep.
Article in English | MEDLINE | ID: mdl-28602916

ABSTRACT

Ephrin A2 receptor (EphA2) plays a key role in cancer, it is up-regulated in several types of tumors and the process of ligand-induced receptor endocytosis, followed by degradation, is considered as a potential path to diminish tumor malignancy. Protein modulators of this mechanism are recruited at the cytosolic Sterile alpha motif (Sam) domain of EphA2 (EphA2-Sam) through heterotypic Sam-Sam associations. These interactions engage the C-terminal helix of EphA2 and close loop regions (the so called End Helix side). In addition, several studies report on destabilizing mutations in EphA2 related to cataract formation and located in/or close to the Sam domain. Herein, we analyzed from a structural point of view, one of these mutants characterized by the insertion of a novel 39 residue long polypeptide at the C-terminus of EphA2-Sam. A 3D structural model was built by computational methods and revealed partial disorder in the acquired C-terminal tail and a few residues participating in an α-helix and two short ß-strands. We investigated by CD and NMR studies the conformational properties in solution of two peptides encompassing the whole C-terminal tail and its predicted helical region, respectively. NMR binding experiments demonstrated that these peptides do not interact relevantly with either EphA2-Sam or its interactor Ship2-Sam. Molecular dynamics (MD) simulations further indicated that the EphA2 mutant could be represented only through a conformational ensemble and that the C-terminal tail should not largely wrap the EphA2-Sam End-Helix interface and affect binding to other Sam domains.


Subject(s)
Receptor, EphA2/chemistry , Amino Acid Motifs , Amino Acid Sequence , Cataract/genetics , Circular Dichroism , Humans , Mass Spectrometry , Models, Molecular , Molecular Dynamics Simulation , Mutagenesis, Insertional , Neoplasm Proteins/chemistry , Neoplasm Proteins/genetics , Neoplasm Proteins/metabolism , Nuclear Magnetic Resonance, Biomolecular , Peptide Fragments/chemical synthesis , Peptide Fragments/chemistry , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/chemistry , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/metabolism , Protein Binding , Protein Interaction Mapping , Protein Structure, Secondary , Receptor, EphA2/genetics , Receptor, EphA2/metabolism , Recombinant Fusion Proteins/chemistry , Structure-Activity Relationship
18.
Eur J Immunol ; 47(6): 932-945, 2017 06.
Article in English | MEDLINE | ID: mdl-28480512

ABSTRACT

The phosphoinositide phosphatase SHIP is a critical regulator of immune cell activation. Despite considerable study, the mechanisms controlling SHIP activity to ensure balanced cell activation remain incompletely understood. SHIP dampens BCR signaling in part through its association with the inhibitory coreceptor Fc gamma receptor IIB, and serves as an effector for other inhibitory receptors in various immune cell types. The established paradigm emphasizes SHIP's inhibitory receptor-dependent function in regulating phosphoinositide 3-kinase signaling by dephosphorylating the phosphoinositide PI(3,4,5)P3 ; however, substantial evidence indicates that SHIP can be activated independently of inhibitory receptors and can function as an intrinsic brake on activation signaling. Here, we integrate historical and recent reports addressing the regulation and function of SHIP in immune cells, which together indicate that SHIP acts as a multifunctional protein controlled by multiple regulatory inputs, and influences downstream signaling via both phosphatase-dependent and -independent means. We further summarize accumulated evidence regarding the functions of SHIP in B cells, T cells, NK cells, dendritic cells, mast cells, and macrophages, and data suggesting defective expression or activity of SHIP in autoimmune and malignant disorders. Lastly, we discuss the biological activities, therapeutic promise, and limitations of small molecule modulators of SHIP enzymatic activity.


Subject(s)
Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/genetics , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/metabolism , Signal Transduction , Animals , B-Lymphocytes/enzymology , B-Lymphocytes/immunology , Dendritic Cells/enzymology , Dendritic Cells/immunology , Gene Expression Regulation , Homeostasis , Humans , Killer Cells, Natural/enzymology , Killer Cells, Natural/immunology , Macrophages/enzymology , Macrophages/immunology , Mast Cells/enzymology , Mast Cells/immunology , Mice , Phosphatidylinositol 3-Kinases/metabolism , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/chemistry , Phosphorylation , Proteins/metabolism , Signal Transduction/genetics , T-Lymphocytes/enzymology , T-Lymphocytes/immunology
19.
Chembiochem ; 18(3): 233-247, 2017 02 01.
Article in English | MEDLINE | ID: mdl-27907247

ABSTRACT

SHIP2 is a phosphatase that acts at the 5-position of phosphatidylinositol 3,4,5-trisphosphate. It is one of several enzymes that catalyse dephosphorylation at the 5-position of phosphoinositides or inositol phosphates. SHIP2 has a confirmed role in opsismodysplasia, a disease of bone development, but also interacts with proteins involved in insulin signalling, cytoskeletal function (thus having an impact on endocytosis, adhesion, proliferation and apoptosis) and immune system function. The structure of three domains (constituting about 38 % of the protein) is known. Inhibitors of SHIP2 activity have been designed to interact with the catalytic domain with sub-micromolar IC50 values: these come from a range of structural classes and have been shown to have in vivo effects consistent with SHIP2 inhibition. Much remains unknown about the roles of SHIP2, and possible future directions for research are indicated.


Subject(s)
Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/metabolism , Binding Sites , Catalytic Domain , Humans , Immune System/metabolism , Insulin/metabolism , Ligands , Osteochondrodysplasias/metabolism , Osteochondrodysplasias/pathology , Phosphatidylinositol Phosphates/metabolism , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/antagonists & inhibitors , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/chemistry , Signal Transduction
20.
Protein J ; 35(3): 225-30, 2016 06.
Article in English | MEDLINE | ID: mdl-27170292

ABSTRACT

The Src homology 2 containing inositol 5-phosphatase 2 (SHIP2) catalyses the dephosphorylation of the phospholipid phosphatidylinositol 3,4,5-triphosphate (PI(3,4,5)P3) to form PI(3,4)P2. PI(3,4,5)P3 is a key lipid second messenger, which can recruit signalling proteins to the plasma membrane and subsequently initiate numerous downstream signalling pathways responsible for the regulation of a plethora of cellular events such as proliferation, growth, apoptosis and cytoskeletal rearrangements. SHIP2 has been heavily implicated with several serious diseases such as cancer and type 2 diabetes but its regulation remains poorly understood. In order to gain insight into the mechanisms of SHIP2 regulation, a fragment of human SHIP2 containing the phosphatase domain and a region proposed to resemble a C2 domain was crystallized. Currently, no structural information is available on the putative C2-related domain or its relative position with respect to the phosphatase domain. Initial crystals were polycrystalline, but were optimized to obtain diffraction data to a resolution of 2.1 Å. Diffraction data analysis revealed a P212121 space group with unit cell parameters a = 136.04 Å, b = 175.84 Å, c = 176.89 Å. The Matthews coefficient is 2.54 Å(3) Da(-1) corresponding to 8 molecules in the asymmetric unit with a solvent content of 51.7 %.


Subject(s)
Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/chemistry , Cloning, Molecular , Crystallography, X-Ray , Escherichia coli/genetics , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/genetics , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/isolation & purification , Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatases/metabolism , Protein Domains , Signal Transduction
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