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1.
J Biol Chem ; 298(10): 102376, 2022 10.
Article in English | MEDLINE | ID: mdl-35970395

ABSTRACT

T cell signaling starts with assembling several tyrosine kinases and adapter proteins to the T cell receptor (TCR), following the antigen binding to the TCR. The stability of the TCR-antigen complex and the delay between the recruitment and activation of each kinase determines the T cell response. Integration of such delays constitutes a kinetic proofreading mechanism to regulate T cell response to the antigen binding. However, the mechanism of these delays is not fully understood. Combining biochemical experiments and kinetic modeling, here we report a thermodynamic brake in the regulatory module of the tyrosine kinase ZAP-70, which determines the ligand selectivity, and may delay the ZAP-70 activation upon antigen binding to TCR. The regulatory module of ZAP-70 comprises of a tandem SH2 domain that binds to its ligand, doubly-phosphorylated ITAM peptide (ITAM-Y2P), in two kinetic steps: a fast step and a slow step. We show the initial encounter complex formation between the ITAM-Y2P and tandem SH2 domain follows a fast-kinetic step, whereas the conformational transition to the holo-state follows a slow-kinetic step. We further observed a thermodynamic penalty imposed during the second phosphate-binding event reduces the rate of structural transition to the holo-state. Phylogenetic analysis revealed the evolution of the thermodynamic brake coincides with the divergence of the adaptive immune system to the cell-mediated and humoral responses. In addition, the paralogous kinase Syk expressed in B cells does not possess such a functional thermodynamic brake, which may explain the higher basal activation and lack of ligand selectivity in Syk.


Subject(s)
Evolution, Molecular , Receptors, Antigen, T-Cell , T-Lymphocytes , ZAP-70 Protein-Tyrosine Kinase , Ligands , Phosphorylation , Phylogeny , Receptors, Antigen, T-Cell/genetics , Receptors, Antigen, T-Cell/metabolism , T-Lymphocytes/enzymology , Thermodynamics , Animals , ZAP-70 Protein-Tyrosine Kinase/chemistry , src Homology Domains
2.
Protein Sci ; 30(12): 2373-2384, 2021 12.
Article in English | MEDLINE | ID: mdl-34601763

ABSTRACT

The catalytic activity of Syk-family tyrosine kinases is regulated by a tandem Src homology 2 module (tSH2 module). In the autoinhibited state, this module adopts a conformation that stabilizes an inactive conformation of the kinase domain. The binding of the tSH2 module to phosphorylated immunoreceptor tyrosine-based activation motifs necessitates a conformational change, thereby relieving kinase inhibition and promoting activation. We determined the crystal structure of the isolated tSH2 module of Syk and find, in contrast to ZAP-70, that its conformation more closely resembles that of the peptide-bound state, rather than the autoinhibited state. Hydrogen-deuterium exchange by mass spectrometry, as well as molecular dynamics simulations, reveal that the dynamics of the tSH2 modules of Syk and ZAP-70 differ, with most of these differences occurring in the C-terminal SH2 domain. Our data suggest that the conformational landscapes of the tSH2 modules in Syk and ZAP-70 have been tuned differently, such that the autoinhibited conformation of the Syk tSH2 module is less stable. This feature of Syk likely contributes to its ability to more readily escape autoinhibition when compared to ZAP-70, consistent with tighter control of downstream signaling pathways in T cells.


Subject(s)
Molecular Dynamics Simulation , Syk Kinase/chemistry , ZAP-70 Protein-Tyrosine Kinase/chemistry , Adaptive Immunity , Animals , B-Lymphocytes/immunology , B-Lymphocytes/metabolism , Binding Sites , Biological Evolution , Cloning, Molecular , Crystallography, X-Ray , Deuterium Exchange Measurement , Escherichia coli/genetics , Escherichia coli/metabolism , Gene Expression , Genetic Vectors/chemistry , Genetic Vectors/metabolism , Humans , Protein Binding , Protein Conformation, alpha-Helical , Protein Conformation, beta-Strand , Protein Interaction Domains and Motifs , Recombinant Proteins , Signal Transduction , Syk Kinase/genetics , Syk Kinase/immunology , T-Lymphocytes/immunology , T-Lymphocytes/metabolism , ZAP-70 Protein-Tyrosine Kinase/genetics , ZAP-70 Protein-Tyrosine Kinase/immunology
3.
Dev Comp Immunol ; 124: 104177, 2021 11.
Article in English | MEDLINE | ID: mdl-34153283

ABSTRACT

ZAP70 is essential for initiating the early events of T-cell antigen receptor (TCR) signaling cascade to ensure proper T cell activation and function. However, whether this molecule takes part in the T cell immune response of early vertebrates remains unclear. In the present study, using a teleost model Nile tilapia (Oreochromis niloticus), we investigated the potential involvement of ZAP70 in the T cell activation and adaptive immunity of fish species. Both primary and tertiary structures of O. niloticus ZAP70 (On-ZAP70) are highly conserved with those from other vertebrates. On-ZAP70 protein was widely expressed in lymphoid tissues, and with the highest level in thymus. Once Nile tilapia was infected by Aeromonas hydrophila, mRNA of On-ZAP70 in spleen lymphocytes was induced on day 5 and 8 after infection; meanwhile, phosphorylation of On-ZAP70 was also enhanced, suggesting that On-ZAP70 potentially participated in primary adaptive immune response of Nile tilapia. Furthermore, the frequency of ZAP70 positive lymphocytes was increased during the anti-bacterial adaptive immune response. More importantly, when spleen lymphocytes were activated by T cell specific mitogen PHA, a dramatical augment of On-ZAP70 could be observed at transcription, phosphorylation and cellular level, indicating the involvement of this molecule in T cells activation of Nile tilapia. Altogether, our results demonstrated that ZAP70 activation is an early event of T cell immunity that involved in the anti-bacterial adaptive immune response of Nile tilapia, and thus provided a new evidence to understand the evolution of the lymphocyte-mediated adaptive immunity.


Subject(s)
Adaptive Immunity , Cichlids/immunology , T-Lymphocytes/immunology , ZAP-70 Protein-Tyrosine Kinase/immunology , Amino Acid Sequence , Animals , Bacterial Infections/immunology , Bacterial Infections/veterinary , Fish Diseases/immunology , Fish Proteins/chemistry , Fish Proteins/genetics , Fish Proteins/immunology , Fish Proteins/metabolism , Gene Expression , Lymphocyte Activation , Phylogeny , Protein Structure, Tertiary , Synteny , Tissue Distribution , ZAP-70 Protein-Tyrosine Kinase/chemistry , ZAP-70 Protein-Tyrosine Kinase/genetics , ZAP-70 Protein-Tyrosine Kinase/metabolism
4.
J Biol Chem ; 296: 100311, 2021.
Article in English | MEDLINE | ID: mdl-33482200

ABSTRACT

ZAP-70 is a tyrosine kinase essential for T cell immune responses. Upon engagement of the T cell receptor (TCR), ZAP-70 is recruited to the specialized plasma membrane domains, becomes activated, and is released to phosphorylate its laterally segregated targets. A shift in ZAP-70 distribution at the plasma membrane is recognized as a critical step in TCR signal transduction and amplification. However, the molecular mechanism supporting stimulation-dependent plasma membrane compartmentalization of ZAP-70 remains poorly understood. In this study, we identified previously uncharacterized lipidation (S-acylation) of ZAP-70 using Acyl-Biotin Exchange assay, a technique that selectively captures S-acylated proteins. We found that this posttranslational modification of ZAP-70 is dispensable for its enzymatic activity. However, the lipidation-deficient mutant of ZAP-70 failed to propagate the TCR pathway suggesting that S-acylation is essential for ZAP-70 interaction with its protein substrates. The kinetics of ZAP-70 S-acylation were consistent with TCR signaling events indicating that agonist-induced S-acylation is a part of the signaling mechanism controlling T cell activation and function. Taken together, our results suggest that TCR-induced S-acylation of ZAP-70 can serve as a critical regulator of T cell-mediated immunity.


Subject(s)
Immunity, Cellular/genetics , Receptors, Antigen, T-Cell/genetics , T-Lymphocytes/immunology , ZAP-70 Protein-Tyrosine Kinase/genetics , Acylation/genetics , Acyltransferases/chemistry , Acyltransferases/genetics , Cell Membrane/chemistry , Cell Membrane/genetics , Gene Expression Regulation, Enzymologic/genetics , Humans , Immunity, Cellular/immunology , Lipoylation/genetics , Mutation/genetics , Protein Processing, Post-Translational/genetics , Receptors, Antigen, T-Cell/immunology , Signal Transduction/genetics , Substrate Specificity/genetics , T-Lymphocytes/chemistry , ZAP-70 Protein-Tyrosine Kinase/chemistry
5.
Biochem J ; 477(7): 1287-1308, 2020 04 17.
Article in English | MEDLINE | ID: mdl-32203568

ABSTRACT

T-cell receptor (TCR) signaling is initiated by recruiting ZAP-70 to the cytosolic part of TCR. ZAP-70, a non-receptor tyrosine kinase, is composed of an N-terminal tandem SH2 (tSH2) domain connected to the C-terminal kinase domain. The ZAP-70 is recruited to the membrane through binding of tSH2 domain and the doubly phosphorylated ITAM motifs of CD3 chains in the TCR complex. Our results show that the tSH2 domain undergoes a biphasic structural transition while binding to the doubly phosphorylated ITAM-ζ1 peptide. The C-terminal SH2 domain binds first to the phosphotyrosine residue of ITAM peptide to form an encounter complex leading to subsequent binding of second phosphotyrosine residue to the N-SH2 domain. We decipher a network of noncovalent interactions that allosterically couple the two SH2 domains during binding to doubly phosphorylated ITAMs. Mutation in the allosteric network residues, for example, W165C, uncouples the formation of encounter complex to the subsequent ITAM binding thus explaining the altered recruitment of ZAP-70 to the plasma membrane causing autoimmune arthritis in mice. The proposed mechanism of allosteric coupling is unique to ZAP-70, which is fundamentally different from Syk, a close homolog of ZAP-70 expressed in B-cells.


Subject(s)
Allosteric Site , Receptors, Antigen, T-Cell/metabolism , T-Lymphocytes/metabolism , ZAP-70 Protein-Tyrosine Kinase/chemistry , ZAP-70 Protein-Tyrosine Kinase/metabolism , Allosteric Regulation , Animals , Arthritis, Rheumatoid/genetics , Arthritis, Rheumatoid/metabolism , Disease Models, Animal , Escherichia coli/genetics , Immunoreceptor Tyrosine-Based Activation Motif , Mice , Molecular Dynamics Simulation , Phosphorylation , Point Mutation , Signal Transduction , Syk Kinase/genetics , Syk Kinase/metabolism , ZAP-70 Protein-Tyrosine Kinase/genetics , src Homology Domains/genetics
6.
Elife ; 72018 03 16.
Article in English | MEDLINE | ID: mdl-29547119

ABSTRACT

The specificity of tyrosine kinases is attributed predominantly to localization effects dictated by non-catalytic domains. We developed a method to profile the specificities of tyrosine kinases by combining bacterial surface-display of peptide libraries with next-generation sequencing. Using this, we showed that the tyrosine kinase ZAP-70, which is critical for T cell signaling, discriminates substrates through an electrostatic selection mechanism encoded within its catalytic domain (Shah et al., 2016). Here, we expand this high-throughput platform to analyze the intrinsic specificity of any tyrosine kinase domain against thousands of peptides derived from human tyrosine phosphorylation sites. Using this approach, we find a difference in the electrostatic recognition of substrates between the closely related Src-family kinases Lck and c-Src. This divergence likely reflects the specialization of Lck to act in concert with ZAP-70 in T cell signaling. These results point to the importance of direct recognition at the kinase active site in fine-tuning specificity.


Subject(s)
High-Throughput Screening Assays/methods , Lymphocyte Specific Protein Tyrosine Kinase p56(lck)/metabolism , Peptides/metabolism , ZAP-70 Protein-Tyrosine Kinase/metabolism , src-Family Kinases/metabolism , Amino Acid Sequence , CSK Tyrosine-Protein Kinase , Humans , Lymphocyte Specific Protein Tyrosine Kinase p56(lck)/chemistry , Lymphocyte Specific Protein Tyrosine Kinase p56(lck)/genetics , Models, Molecular , Peptide Library , Peptides/chemistry , Phosphorylation , Phylogeny , Sequence Homology, Amino Acid , Substrate Specificity , ZAP-70 Protein-Tyrosine Kinase/chemistry , ZAP-70 Protein-Tyrosine Kinase/genetics , src Homology Domains , src-Family Kinases/chemistry , src-Family Kinases/genetics
7.
Annu Rev Immunol ; 36: 127-156, 2018 04 26.
Article in English | MEDLINE | ID: mdl-29237129

ABSTRACT

T cells possess an array of functional capabilities important for host defense against pathogens and tumors. T cell effector functions require the T cell antigen receptor (TCR). The TCR has no intrinsic enzymatic activity, and thus signal transduction from the receptor relies on additional signaling molecules. One such molecule is the cytoplasmic tyrosine kinase ZAP-70, which associates with the TCR complex and is required for initiating the canonical biochemical signal pathways downstream of the TCR. In this article, we describe recent structure-based insights into the regulation and substrate specificity of ZAP-70, and then we review novel methods for determining the role of ZAP-70 catalytic activity-dependent and -independent signals in developing and mature T cells. Lastly, we discuss the disease states in mouse models and humans, which range from immunodeficiency to autoimmunity, that are caused by mutations in ZAP-70.


Subject(s)
Disease Susceptibility , Signal Transduction , T-Lymphocytes/metabolism , ZAP-70 Protein-Tyrosine Kinase/metabolism , Animals , Autoimmunity , Biomarkers , Catalysis , Cell Differentiation/genetics , Cell Differentiation/immunology , Gene Expression Regulation , Humans , Immunity , Lymphocyte Activation/genetics , Lymphocyte Activation/immunology , Phosphorylation , Protein Transport , Structure-Activity Relationship , Substrate Specificity , T-Lymphocytes/immunology , ZAP-70 Protein-Tyrosine Kinase/antagonists & inhibitors , ZAP-70 Protein-Tyrosine Kinase/chemistry , ZAP-70 Protein-Tyrosine Kinase/genetics
8.
Bioconjug Chem ; 28(9): 2384-2392, 2017 09 20.
Article in English | MEDLINE | ID: mdl-28767218

ABSTRACT

Members of the Syk family of tyrosine kinases arrange Src homology 2 (SH2) domains in tandem to allow the firm binding of immunoreceptor tyrosine-based interaction motifs (ITAMs). While the advantages provided by the bivalency enhanced interactions are evident, the impact on binding specificity is less-clear. For example, the spleen tyrosine kinase (Syk) and the ζ-chain-associated protein kinase (ZAP-70) recognize the consensus sequence pYXXI/L(X)6-8 pYXXI/L with near-identical nanomolar affinity. The nondiscriminatory recognition, on the one hand, poses a specificity challenge for the design of subtype selective protein binders and, on the other hand, raises the question as to how differential activation of Syk and ZAP-70 is ensured when both kinases are co-expressed. Herein, we identified the criteria for the design of binders that specifically address either the Syk or the Zap-70 tSH2 domain. Our approach is based on DNA-programmed spatial screening. Tyrosine-phosphorylated peptides containing the pYXXI/L motif were attached to oligonucleotides and aligned in tandem on a DNA template by means of nucleic acid hybridization. The distance between the pYXXI/L motifs and the orientation of strands were varied. The exploration exposed remarkably different recognition characteristics. While Syk tSH2 has a rather broad substrate scope, ZAP-70 tSH2 required a proximal arrangement of the phosphotyrosine ligands in defined strand orientation. The spatial screen led to the design of mutually selective, DNA-free binders, which discriminate Zap-70 and Syk tSH2 by 1 order of magnitude in affinity.


Subject(s)
Peptides/metabolism , Phosphotyrosine/metabolism , Syk Kinase/metabolism , ZAP-70 Protein-Tyrosine Kinase/metabolism , Amino Acid Sequence , Binding Sites , DNA/chemistry , DNA/metabolism , Humans , Models, Molecular , Peptides/chemistry , Phosphotyrosine/chemistry , Protein Binding , Substrate Specificity , Syk Kinase/chemistry , ZAP-70 Protein-Tyrosine Kinase/chemistry , src Homology Domains
9.
Biochem Biophys Res Commun ; 488(3): 541-546, 2017 07 01.
Article in English | MEDLINE | ID: mdl-28526413

ABSTRACT

T cell antigen receptor (TCR) binding of a peptide antigen presented by antigen-presenting cells (APCs) in the context of surface MHC molecules initiates signaling events that regulate T cell activation, proliferation and differentiation. A key event in the activation process is the phosphorylation of the conserved tyrosine residues within the CD3 chain immunoreceptor tyrosine-based activation motifs (ITAMs), which operate as docking sites for SH2 domain-containing effector proteins. Phosphorylation of the CD3ζ ITAMs renders the CD3 chain capable of binding the ζ-chain associated protein 70 kDa (ZAP70), a protein tyrosine kinase that is essential for T cell activation. We found that TCR/CD3 crosslinking in Jurkat T cells promotes the association of Crk adaptor proteins with the transiently phosphorylated CD3ζ chain. Pull down assays using bead-immobilized GST fusion proteins revealed that the Crk-SH2 domain mediates binding of phospho-CD3ζ. Phospho-CD3ζ binding is selective and is mediated by the three types of Crk, including CrkI, CrkII, and CrkL, but not by other SH2 domain-containing adaptor proteins, such as Grb2, GRAP and Nck. Crk interaction with phospho-CD3ζ is rapid and transient, peaking 1 min post TCR/CD3 crosslinking. The results suggest the involvement of Crk adaptor proteins in the early stages of T cell activation in which Crk might help recruiting effector proteins to the vicinity of the phospho-CD3ζ and contribute to the fine-tuning of the TCR/CD3-coupled signal transduction pathways.


Subject(s)
Proto-Oncogene Proteins c-crk/metabolism , Receptors, Antigen, T-Cell/metabolism , ZAP-70 Protein-Tyrosine Kinase/chemistry , ZAP-70 Protein-Tyrosine Kinase/metabolism , Binding Sites , Humans , Phosphotyrosine/metabolism , Protein Binding , Tumor Cells, Cultured
10.
Oncotarget ; 8(19): 30805-30816, 2017 May 09.
Article in English | MEDLINE | ID: mdl-28415650

ABSTRACT

ζ-associated protein of 70 kDa (Zap70) is crucial for T-cell receptor (TCR) signaling. Loss of Zap70 in both humans and mice results in severe immunodeficiency. On the other hand, the expression of Zap70 in B-cell malignancies correlates with the severity of the disease. Because of its role in immune-related disorders, Zap70 has become a therapeutic target for the treatment of human diseases. It is well-established that the activity/expression of Zap70 is regulated by post-translational modifications of crucial amino acids including the phosphorylation of tyrosines and the ubiquitination of lysines. Here, we have investigated whether also oxidation of cysteine residues regulates Zap70 functions. We have identified C575 as a major sulfenylation site of Zap70. A C575A substitution results in protein instability, reduced activity, and increased dependency on the Hsp90/Cdc37 chaperone system. Indeed, Cdc37 overexpression reconstituted partially the expression but fully the function of Zap70C575A. C575 lies within a Mx(2)CWx(6)R motif which is highly conserved among almost all human tyrosine kinases. Mutation of any of the conserved amino acids, but not of a non-conserved residue preceding the cysteine, also results in Zap70 instability. Collectively, we have identified a new redox-active motif which is crucial for the regulation of Zap70 stability/activity. We believe that this motif has the potential to become a novel target for the development of therapeutic tools to modulate the expression/activity of kinases.


Subject(s)
Amino Acid Motifs/genetics , Conserved Sequence , Protein Interaction Domains and Motifs/genetics , ZAP-70 Protein-Tyrosine Kinase/genetics , ZAP-70 Protein-Tyrosine Kinase/metabolism , Amino Acid Sequence , Cell Line , Humans , Mutation , Oxidation-Reduction , Protein Binding , Protein Stability , Receptors, Antigen, T-Cell/metabolism , Signal Transduction , ZAP-70 Protein-Tyrosine Kinase/chemistry
11.
J Exp Med ; 214(3): 833-849, 2017 03 06.
Article in English | MEDLINE | ID: mdl-28159798

ABSTRACT

Zap70 plays a critical role in normal T cell development and T cell function. However, little is known about how perturbation of allosteric autoinhibitory mechanisms in Zap70 impacts T cell biology. Here, we analyze mice with a hypermorphic Zap70 mutation, W131A, which destabilizes the autoinhibitory conformation of Zap70, rendering the kinase in a semiactive state. W131A mutant mice with wild-type T cell receptor (TCR) repertoires exhibited relatively normal T cell development. However, crossing the W131A mutant mice to OTII TCR transgenic mice resulted in increased negative selection of OTII+ thymocytes and in increased thymic and peripheral T regulatory cells. Strikingly, increased basal TCR signaling was associated with a marked increase in inhibitory receptor expression and with T cells that were relatively refractory to TCR stimulation. PD-1 inhibitory receptor blockade partially reversed T cell unresponsiveness. Collectively, disruption of normal Zap70 autoinhibition engaged negative feedback mechanisms by which negative selection and inhibitory receptors restrain TCR signaling to enforce both central and peripheral tolerance.


Subject(s)
Receptors, Antigen, T-Cell/physiology , T-Lymphocytes/physiology , ZAP-70 Protein-Tyrosine Kinase/physiology , Animals , Apoptosis , Interleukin-2/biosynthesis , Mice , Mice, Inbred C57BL , Programmed Cell Death 1 Receptor/analysis , Programmed Cell Death 1 Receptor/physiology , Protein Conformation , Protein Stability , Signal Transduction/physiology , T-Lymphocytes, Regulatory/physiology , Up-Regulation , ZAP-70 Protein-Tyrosine Kinase/chemistry
12.
Elife ; 52016 10 04.
Article in English | MEDLINE | ID: mdl-27700984

ABSTRACT

The sequence of events that initiates T cell signaling is dictated by the specificities and order of activation of the tyrosine kinases that signal downstream of the T cell receptor. Using a platform that combines exhaustive point-mutagenesis of peptide substrates, bacterial surface-display, cell sorting, and deep sequencing, we have defined the specificities of the first two kinases in this pathway, Lck and ZAP-70, for the T cell receptor ζ chain and the scaffold proteins LAT and SLP-76. We find that ZAP-70 selects its substrates by utilizing an electrostatic mechanism that excludes substrates with positively-charged residues and favors LAT and SLP-76 phosphosites that are surrounded by negatively-charged residues. This mechanism prevents ZAP-70 from phosphorylating its own activation loop, thereby enforcing its strict dependence on Lck for activation. The sequence features in ZAP-70, LAT, and SLP-76 that underlie electrostatic selectivity likely contribute to the specific response of T cells to foreign antigens.


Subject(s)
Lymphocyte Specific Protein Tyrosine Kinase p56(lck)/chemistry , Lymphocyte Specific Protein Tyrosine Kinase p56(lck)/metabolism , Receptors, Antigen, T-Cell/metabolism , Signal Transduction , Static Electricity , ZAP-70 Protein-Tyrosine Kinase/chemistry , ZAP-70 Protein-Tyrosine Kinase/metabolism , HEK293 Cells , Humans , Substrate Specificity
13.
Mol Cell Biol ; 36(18): 2396-402, 2016 09 15.
Article in English | MEDLINE | ID: mdl-27354065

ABSTRACT

The initiation of signaling in T lymphocytes in response to the binding of the T cell receptor (TCR) to cognate ligands is a key step in the emergence of adaptive immune responses. Conventional models posit that TCR signaling is initiated by the phosphorylation of receptor-associated immune receptor activation motifs (ITAMs). The cytoplasmic tyrosine kinase Zap70 binds to phosphorylated ITAMs, is subsequently activated, and then propagates downstream signaling. While evidence for such models is provided by experiments with cell lines, in vivo, Zap70 is bound to phosphorylated ITAMs in resting T cells. However, Zap70 is activated only upon TCR binding to cognate ligand. We report the results of computational studies of a new model for the initiation of TCR signaling that incorporates these in vivo observations. Importantly, the new model is shown to allow better and faster TCR discrimination between self-ligands and foreign ligands. The new model is consistent with many past experimental observations, and experiments that could further test the model are proposed.


Subject(s)
Lymphocyte Specific Protein Tyrosine Kinase p56(lck)/metabolism , Receptors, Antigen, T-Cell/metabolism , Tyrosine/metabolism , ZAP-70 Protein-Tyrosine Kinase/metabolism , Binding Sites , Computer Simulation , Models, Molecular , Phosphorylation , Protein Binding , Signal Transduction , ZAP-70 Protein-Tyrosine Kinase/chemistry
14.
Mol Cell ; 62(1): 7-20, 2016 Apr 07.
Article in English | MEDLINE | ID: mdl-27052731

ABSTRACT

The Src-homology 2 (SH2) domain is a protein interaction domain that directs myriad phosphotyrosine (pY)-signaling pathways. Genome-wide screening of human SH2 domains reveals that ∼90% of SH2 domains bind plasma membrane lipids and many have high phosphoinositide specificity. They bind lipids using surface cationic patches separate from pY-binding pockets, thus binding lipids and the pY motif independently. The patches form grooves for specific lipid headgroup recognition or flat surfaces for non-specific membrane binding and both types of interaction are important for cellular function and regulation of SH2 domain-containing proteins. Cellular studies with ZAP70 showed that multiple lipids bind its C-terminal SH2 domain in a spatiotemporally specific manner and thereby exert exquisite spatiotemporal control over its protein binding and signaling activities in T cells. Collectively, this study reveals how lipids control SH2 domain-mediated cellular protein-protein interaction networks and suggest a new strategy for therapeutic modulation of pY-signaling pathways.


Subject(s)
Lipid Metabolism , T-Lymphocytes/metabolism , ZAP-70 Protein-Tyrosine Kinase/chemistry , ZAP-70 Protein-Tyrosine Kinase/metabolism , src Homology Domains , Binding Sites , Cells, Cultured , Humans , Jurkat Cells , Models, Molecular , Molecular Docking Simulation , Phosphotyrosine/drug effects , Phosphotyrosine/metabolism , Protein Binding , Protein Structure, Tertiary , Signal Transduction
15.
J Exp Med ; 213(2): 155-65, 2016 Feb 08.
Article in English | MEDLINE | ID: mdl-26783323

ABSTRACT

A brother and sister developed a previously undescribed constellation of autoimmune manifestations within their first year of life, with uncontrollable bullous pemphigoid, colitis, and proteinuria. The boy had hemophilia due to a factor VIII autoantibody and nephrotic syndrome. Both children required allogeneic hematopoietic cell transplantation (HCT), which resolved their autoimmunity. The early onset, severity, and distinctive findings suggested a single gene disorder underlying the phenotype. Whole-exome sequencing performed on five family members revealed the affected siblings to be compound heterozygous for two unique missense mutations in the 70-kD T cell receptor ζ-chain associated protein (ZAP-70). Healthy relatives were heterozygous mutation carriers. Although pre-HCT patient T cells were not available, mutation effects were determined using transfected cell lines and peripheral blood from carriers and controls. Mutation R192W in the C-SH2 domain exhibited reduced binding to phosphorylated ζ-chain, whereas mutation R360P in the N lobe of the catalytic domain disrupted an autoinhibitory mechanism, producing a weakly hyperactive ZAP-70 protein. Although human ZAP-70 deficiency can have dysregulated T cells, and autoreactive mouse thymocytes with weak Zap-70 signaling can escape tolerance, our patients' combination of hypomorphic and activating mutations suggested a new disease mechanism and produced previously undescribed human ZAP-70-associated autoimmune disease.


Subject(s)
Autoimmune Diseases/enzymology , Autoimmune Diseases/genetics , Mutant Proteins/genetics , Mutation, Missense , ZAP-70 Protein-Tyrosine Kinase/genetics , Amino Acid Sequence , Animals , Autoimmune Diseases/immunology , Base Sequence , Cell Line , Child, Preschool , Female , Hematopoietic Stem Cell Transplantation , Hemophilia A/enzymology , Hemophilia A/genetics , Hemophilia A/immunology , Heterozygote , Humans , Infant , Male , Mice , Models, Molecular , Molecular Sequence Data , Mutant Proteins/chemistry , Mutant Proteins/metabolism , Pedigree , Pemphigoid, Bullous/enzymology , Pemphigoid, Bullous/genetics , Pemphigoid, Bullous/pathology , Phenotype , Protein Conformation , Receptors, Antigen, T-Cell/metabolism , Severe Combined Immunodeficiency/enzymology , Severe Combined Immunodeficiency/genetics , Severe Combined Immunodeficiency/immunology , Siblings , Syndrome , T-Lymphocytes/enzymology , T-Lymphocytes/immunology , Transplantation, Homologous , ZAP-70 Protein-Tyrosine Kinase/chemistry , ZAP-70 Protein-Tyrosine Kinase/deficiency , ZAP-70 Protein-Tyrosine Kinase/immunology , ZAP-70 Protein-Tyrosine Kinase/metabolism
16.
PLoS Comput Biol ; 11(10): e1004560, 2015 Oct.
Article in English | MEDLINE | ID: mdl-26473606

ABSTRACT

ZAP-70 (Zeta-chain-associated protein kinase 70) is a tyrosine kinase that interacts directly with the activated T-cell receptor to transduce downstream signals, and is hence a major player in the regulation of the adaptive immune response. Dysfunction of ZAP-70 causes selective T cell deficiency that in turn results in persistent infections. ZAP-70 is activated by a variety of signals including phosphorylation of the kinase domain (KD), and binding of its regulatory tandem Src homology 2 (SH2) domains to the T cell receptor. The present study investigates molecular mechanisms of activation and inhibition of ZAP-70 via atomically detailed molecular dynamics simulation approaches. We report microsecond timescale simulations of five distinct states of the ZAP-70 KD, comprising apo, inhibited and three phosphorylated variants. Extensive analysis of local flexibility and correlated motions reveal crucial transitions between the states, thus elucidating crucial steps in the activation mechanism of the ZAP-70 KD. Furthermore, we rationalize previously observed staurosporine-bound crystal structures, suggesting that whilst the KD superficially resembles an "active-like" conformation, the inhibitor modulates the underlying protein dynamics and restricts it in a compact, rigid state inaccessible to ligands or cofactors. Finally, our analysis reveals a novel, potentially druggable pocket in close proximity to the activation loop of the kinase, and we subsequently use its structure in fragment-based virtual screening to develop a pharmacophore model. The pocket is distinct from classical type I or type II kinase pockets, and its discovery offers promise in future design of specific kinase inhibitors, whilst mutations in residues associated with this pocket are implicated in immunodeficiency in humans.


Subject(s)
Models, Chemical , Molecular Dynamics Simulation , Phosphotransferases/chemistry , Phosphotransferases/ultrastructure , ZAP-70 Protein-Tyrosine Kinase/chemistry , ZAP-70 Protein-Tyrosine Kinase/ultrastructure , Binding Sites , Enzyme Activation , Enzyme Stability , Protein Binding , Protein Conformation , Protein Structure, Tertiary , Structure-Activity Relationship , Substrate Specificity
17.
Biochem J ; 465(1): 149-61, 2015 Jan 01.
Article in English | MEDLINE | ID: mdl-25287889

ABSTRACT

Zeta-chain associated protein of 70 kDa (ZAP-70) and spleen tyrosine kinase (Syk) are non-receptor tyrosine kinases that are essential for T-cell and B-cell antigen receptor signalling respectively. They are recruited, via their tandem-SH2 (Src-homology domain 2) domains, to doubly phosphorylated immunoreceptor tyrosine-based activation motifs (ITAMs) on invariant chains of immune antigen receptors. Because of their critical roles in immune signalling, ZAP-70 and Syk are targets for the development of drugs for autoimmune diseases. We show that three thiol-reactive small molecules can prevent the tandem-SH2 domains of ZAP-70 and Syk from binding to phosphorylated ITAMs. We identify a specific cysteine residue in the phosphotyrosine-binding pocket of each protein (Cys39 in ZAP-70, Cys206 in Syk) that is necessary for inhibition by two of these compounds. We also find that ITAM binding to ZAP-70 and Syk is sensitive to the presence of H2O2 and these two cysteine residues are also necessary for inhibition by H2O2. Our findings suggest a mechanism by which the reactive oxygen species generated during responses to antigen could attenuate signalling through these kinases and may also inform the development of ZAP-70 and Syk inhibitors that bind covalently to their SH2 domains.


Subject(s)
Cysteine/metabolism , Intracellular Signaling Peptides and Proteins/chemistry , Intracellular Signaling Peptides and Proteins/metabolism , Phosphopeptides/metabolism , Protein-Tyrosine Kinases/chemistry , Protein-Tyrosine Kinases/metabolism , ZAP-70 Protein-Tyrosine Kinase/chemistry , ZAP-70 Protein-Tyrosine Kinase/metabolism , src Homology Domains , Amino Acid Motifs , Binding Sites , Humans , Hydrogen Peroxide/pharmacology , Models, Molecular , Oxidation-Reduction/drug effects , Phosphorylation/drug effects , Phosphotyrosine/metabolism , Protein Binding/drug effects , Small Molecule Libraries/chemistry , Small Molecule Libraries/pharmacology , Sulfhydryl Compounds/metabolism , Syk Kinase , ZAP-70 Protein-Tyrosine Kinase/antagonists & inhibitors
18.
Mol Cell Biol ; 33(11): 2188-201, 2013 Jun.
Article in English | MEDLINE | ID: mdl-23530057

ABSTRACT

Serial activation of the tyrosine kinases Lck and ZAP-70 initiates signaling downstream of the T cell receptor. We previously reported the structure of an autoinhibited ZAP-70 variant in which two regulatory tyrosine residues (315 and 319) in the SH2-kinase linker were replaced by phenylalanine. We now present a crystal structure of ZAP-70 in which Tyr 315 and Tyr 319 are not mutated, leading to the recognition of a five-residue sequence register error in the SH2-kinase linker of the original crystallographic model. The revised model identifies distinct roles for these two tyrosines. As seen in a recently reported structure of the related tyrosine kinase Syk, Tyr 315 of ZAP-70 is part of a hydrophobic interface between the regulatory apparatus and the kinase domain, and the integrity of this interface would be lost upon engagement of doubly phosphorylated peptides by the SH2 domains. Tyr 319 is not necessarily dislodged by SH2 engagement, which activates ZAP-70 only ∼5-fold in vitro. In contrast, phosphorylation by Lck activates ZAP-70 ∼100-fold. This difference is due to the ability of Tyr 319 to suppress ZAP-70 activity even when the SH2 domains are dislodged from the kinase domain, providing stringent control of ZAP-70 activity downstream of Lck.


Subject(s)
ZAP-70 Protein-Tyrosine Kinase/chemistry , ZAP-70 Protein-Tyrosine Kinase/metabolism , Adaptor Proteins, Signal Transducing/genetics , Adaptor Proteins, Signal Transducing/metabolism , Crystallography, X-Ray , Fluorescence Resonance Energy Transfer , GRB2 Adaptor Protein/genetics , GRB2 Adaptor Protein/metabolism , Humans , Hydrogen Bonding , Hydrophobic and Hydrophilic Interactions , Intracellular Signaling Peptides and Proteins/chemistry , Intracellular Signaling Peptides and Proteins/metabolism , Lymphocyte Specific Protein Tyrosine Kinase p56(lck)/genetics , Lymphocyte Specific Protein Tyrosine Kinase p56(lck)/metabolism , Membrane Proteins/genetics , Membrane Proteins/metabolism , Models, Molecular , Phosphorylation , Protein Conformation , Protein Structure, Tertiary , Protein-Tyrosine Kinases/chemistry , Protein-Tyrosine Kinases/metabolism , Syk Kinase , Tyrosine/chemistry , Tyrosine/metabolism , ZAP-70 Protein-Tyrosine Kinase/genetics , src Homology Domains , src-Family Kinases/chemistry , src-Family Kinases/metabolism
19.
J Mol Graph Model ; 39: 165-75, 2013 Feb.
Article in English | MEDLINE | ID: mdl-23280414

ABSTRACT

In the present study, diverse inhibitor molecules of two protein tyrosine kinases i.e. Syk and ZAP-70 were considered for the pharmacophore and docking analyses to design new multi-targeted agents for these enzymes. These enzymes are non-receptor protein tyrosine kinases and both are expressed mainly in B and T-lymphocytes where they play a crucial role in immune signaling. The role of these two enzymes in inflammatory and autoimmune diseases makes them potential therapeutic targets for the designing of new multi-targeted agents to combat disease conditions associated with them. The pharmacophore models were developed for Syk and ZAP-70 inhibitors using PHASE module of Schrödinger software. The generated pharmacophore models for both enzymes were clustered and top five models for each target were selected on the basis of survival minus inactive score that were subsequently used for the 3D-QSAR analysis. The best model for Syk (ADHR.45-5) and ZAP-70 (AADRR.265-3) were selected corresponding to highest value of Q(2). Both models were employed for the screening of a PHASE database of approximately 1.5 million compounds, subsequently the retrieved hits were screened employing docking simulations with Syk and ZAP-70 proteins. Finally, the screened compounds having structural features of both pharmacophore models and displaying essential interactions with both proteins were investigated for ADME properties. Thus, the new leads obtained in this way would show inhibitory activity against Syk and ZAP-70, and may serve as novel therapeutic agents for the treatment of inflammatory disorders.


Subject(s)
Computer Simulation , Drug Design , Intracellular Signaling Peptides and Proteins/chemistry , Protein Kinase Inhibitors/chemistry , Protein-Tyrosine Kinases/chemistry , Quantitative Structure-Activity Relationship , ZAP-70 Protein-Tyrosine Kinase/chemistry , Humans , Models, Molecular , Molecular Docking Simulation , Reproducibility of Results , Syk Kinase
20.
J Biol Chem ; 288(7): 5127-35, 2013 Feb 15.
Article in English | MEDLINE | ID: mdl-23264619

ABSTRACT

CLEC-2 is a member of new family of C-type lectin receptors characterized by a cytosolic YXXL downstream of three acidic amino acids in a sequence known as a hemITAM (hemi-immunoreceptor tyrosine-based activation motif). Dimerization of two phosphorylated CLEC-2 molecules leads to recruitment of the tyrosine kinase Syk via its tandem SH2 domains and initiation of a downstream signaling cascade. Using Syk-deficient and Zap-70-deficient cell lines we show that hemITAM signaling is restricted to Syk and that the upstream triacidic amino acid sequence is required for signaling. Using surface plasmon resonance and phosphorylation studies, we demonstrate that the triacidic amino acids are required for phosphorylation of the YXXL. These results further emphasize the distinct nature of the proximal events in signaling by hemITAM relative to ITAM receptors.


Subject(s)
Blood Platelets/metabolism , Tyrosine/chemistry , Amino Acid Sequence , Amino Acids/chemistry , Cytosol/metabolism , Humans , Intracellular Signaling Peptides and Proteins/metabolism , Kinetics , Lectins, C-Type/chemistry , Lectins, C-Type/metabolism , Membrane Glycoproteins/metabolism , Models, Biological , Molecular Sequence Data , Phosphorylation , Protein-Tyrosine Kinases/metabolism , Sequence Homology, Amino Acid , Signal Transduction , Surface Plasmon Resonance , Syk Kinase , Viper Venoms/chemistry , ZAP-70 Protein-Tyrosine Kinase/chemistry
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