12 research outputs found
Integrative annotation and knowledge discovery of kinase post-translational modifications and cancer-associated mutations through federated protein ontologies and resources.
Many bioinformatics resources with unique perspectives on the protein landscape are currently available. However, generating new knowledge from these resources requires interoperable workflows that support cross-resource queries. In this study, we employ federated queries linking information from the Protein Kinase Ontology, iPTMnet, Protein Ontology, neXtProt, and the Mouse Genome Informatics to identify key knowledge gaps in the functional coverage of the human kinome and prioritize understudied kinases, cancer variants and post-translational modifications (PTMs) for functional studies. We identify 32 functional domains enriched in cancer variants and PTMs and generate mechanistic hypotheses on overlapping variant and PTM sites by aggregating information at the residue, protein, pathway and species level from these resources. We experimentally test the hypothesis that S768 phosphorylation in the C-helix of EGFR is inhibitory by showing that oncogenic variants altering S768 phosphorylation increase basal EGFR activity. In contrast, oncogenic variants altering conserved phosphorylation sites in the \u27hydrophobic motif\u27 of PKCĪ²II (S660F and S660C) are loss-of-function in that they reduce kinase activity and enhance membrane translocation. Our studies provide a framework for integrative, consistent, and reproducible annotation of the cancer kinomes. Sci Rep 2018 Apr 25; 8(1):6518
mTORC2 controls the activity of PKC and Akt by phosphorylating a conserved TOR interaction motif
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The Molecular Basis of Protein Kinase C Regulatory Mechanisms in Cancer and Neurodegenerative Disease
Protein kinase C (PKC) isozymes transduce the myriad of signals downstream of phospholipid hydrolysis that potentiate an array of cellular processes including proliferation, differentiation, migration, and memory. PKC function is dysregulated in a variety of pathological states, including cancer and neurodegenerative disease. To maintain signaling fidelity, PKCs rely upon precise regulatory mechanisms that orchestrate the phosphorylations and conformational transitions that specify their signaling output. This thesis describes the molecular mechanisms by which PKC phosphorylation and autoinhibition depends upon the kinases PDK1 and mTORC2, and is opposed by PHLPP phosphatases, to produce a primed enzyme that is appropriately tuned to respond to activating signals. Specifically, we uncover the molecular basis for the controversial role of mTORC2 in AGC kinase activation by identifying a novel and conserved mTOR phosphorylation site in the C-terminal tail. Phosphorylation of this, which we term the TOR-Interaction Motif (TIM), promotes PDK1 phosphorylation of the activation loop and intramolecular autophosphorylation of the hydrophobic motif to control activation of PKC and related AGC kianse Akt. Examination of the interrelated processes of phosphorylation and autoinhibition unveils a critical role for the pseudosubstrate in protecting PKC from dephosphorylation by phosphatase PHLPP1, which selectively promotes the dephosphorylation and degradation of aberrantly active PKCs to provide a PKC quality control mechanism. High-throughput protein-level analysis from patient samples reveals that PKC quality control is a critical signaling node that sets PKC expression levels and serves as a prominent loss-of-function mechanism to impair PKC tumor-suppressive function in cancer. Critically, diseases driven by PKC dysregulation rely upon impaired PKC quality control. LOF PKC mutations in chordoid glioma act in a dominant-negative fashion to globally suppress PKC output; whereas, GOF PKC mutations in spinocerebellar ataxia drive phosphoproteome-wide changes in the cerebellum. Taken together, this thesis expands upon biochemical mechanisms of PKC maturation to identify the structural and molecular determinants of PKC phosphorylation and implicates PHLPP1 as the master regulator of PKC signaling fidelity through PKC quality control. This work is not only relevant to the pathology of disease-associated mutations in cancer and neurodegenerative disease, but also to the development of therapeutics that attempt to modulate PKC activity by targeting these regulatory mechanisms
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The Molecular Basis of Protein Kinase C Regulatory Mechanisms in Cancer and Neurodegenerative Disease
Protein kinase C (PKC) isozymes transduce the myriad of signals downstream of phospholipid hydrolysis that potentiate an array of cellular processes including proliferation, differentiation, migration, and memory. PKC function is dysregulated in a variety of pathological states, including cancer and neurodegenerative disease. To maintain signaling fidelity, PKCs rely upon precise regulatory mechanisms that orchestrate the phosphorylations and conformational transitions that specify their signaling output. This thesis describes the molecular mechanisms by which PKC phosphorylation and autoinhibition depends upon the kinases PDK1 and mTORC2, and is opposed by PHLPP phosphatases, to produce a primed enzyme that is appropriately tuned to respond to activating signals. Specifically, we uncover the molecular basis for the controversial role of mTORC2 in AGC kinase activation by identifying a novel and conserved mTOR phosphorylation site in the C-terminal tail. Phosphorylation of this, which we term the TOR-Interaction Motif (TIM), promotes PDK1 phosphorylation of the activation loop and intramolecular autophosphorylation of the hydrophobic motif to control activation of PKC and related AGC kianse Akt. Examination of the interrelated processes of phosphorylation and autoinhibition unveils a critical role for the pseudosubstrate in protecting PKC from dephosphorylation by phosphatase PHLPP1, which selectively promotes the dephosphorylation and degradation of aberrantly active PKCs to provide a PKC quality control mechanism. High-throughput protein-level analysis from patient samples reveals that PKC quality control is a critical signaling node that sets PKC expression levels and serves as a prominent loss-of-function mechanism to impair PKC tumor-suppressive function in cancer. Critically, diseases driven by PKC dysregulation rely upon impaired PKC quality control. LOF PKC mutations in chordoid glioma act in a dominant-negative fashion to globally suppress PKC output; whereas, GOF PKC mutations in spinocerebellar ataxia drive phosphoproteome-wide changes in the cerebellum. Taken together, this thesis expands upon biochemical mechanisms of PKC maturation to identify the structural and molecular determinants of PKC phosphorylation and implicates PHLPP1 as the master regulator of PKC signaling fidelity through PKC quality control. This work is not only relevant to the pathology of disease-associated mutations in cancer and neurodegenerative disease, but also to the development of therapeutics that attempt to modulate PKC activity by targeting these regulatory mechanisms
Protein Kinase C Quality Control by Phosphatase PHLPP1 Unveils Loss-of-Function Mechanism in Cancer.
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Protein Kinase C Quality Control by Phosphatase PHLPP1 Unveils Loss-of-Function Mechanism in Cancer
Protein kinase C (PKC) isozymes function as tumor suppressors in increasing contexts. In contrast to oncogenic kinases, whose function is acutely regulated by transient phosphorylation, PKC is constitutively phosphorylated following biosynthesis to yield a stable, autoinhibited enzyme that is reversibly activated by second messengers. Here, we report that the phosphatase PHLPP1 opposes PKC phosphorylation during maturation, leading to the degradation of aberrantly active species that do not become autoinhibited. Cancer-associated hotspot mutations in the pseudosubstrate of PKCĪ² that impair autoinhibition result in dephosphorylated and unstable enzymes. Protein-level analysis reveals that PKCĪ± is fully phosphorylated at the PHLPP site in over 5,000 patient tumors, with higher PKC levels correlating (1) inversely with PHLPP1 levels and (2) positively with improved survival in pancreatic adenocarcinoma. Thus, PHLPP1 provides a proofreading step that maintains the fidelity of PKC autoinhibition and reveals a prominent loss-of-function mechanism in cancer by suppressing the steady-state levels of PKC
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Mutations in protein kinase CĪ³ promote spinocerebellar ataxia type 14 by impairing kinase autoinhibition
Spinocerebellar ataxia type 14 (SCA14) is a neurodegenerative disease caused by germline variants in the diacylglycerol (DAG)/Ca2+-regulated protein kinase CĪ³ (PKCĪ³), leading to Purkinje cell degeneration and progressive cerebellar dysfunction. Most of the identified mutations cluster in the DAG-sensing C1 domains. Here, we found with a FRET-based activity reporter that SCA14-associated PKCĪ³ mutations, including a previously undescribed variant, D115Y, enhanced the basal activity of the kinase by compromising its autoinhibition. Unlike other mutations in PKC that impair its autoinhibition but lead to its degradation, the C1 domain mutations protected PKCĪ³ from such down-regulation. This enhanced basal signaling rewired the brain phosphoproteome, as revealed by phosphoproteomic analysis of cerebella from mice expressing a human SCA14-associated H101Y mutant PKCĪ³ transgene. Mutations that induced a high basal activity in vitro were associated with earlier average age of onset in patients. Furthermore, the extent of disrupted autoinhibition, but not agonist-stimulated activity, correlated with disease severity. Molecular modeling indicated that almost all SCA14 variants not within the C1 domain were located at interfaces with the C1B domain, suggesting that mutations in and proximal to the C1B domain are a susceptibility for SCA14 because they uniquely enhance PKCĪ³ basal activity while protecting the enzyme from down-regulation. These results provide insight into how PKCĪ³ activation is modulated and how deregulation of the cerebellar phosphoproteome by SCA14-associated mutations affects disease progression
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mTORC2 controls the activity of PKC and Akt by phosphorylating a conserved TOR interaction motif.
The complex mTORC2 is accepted to be the kinase that controls the phosphorylation of the hydrophobic motif, a key regulatory switch for AGC kinases, although whether mTOR directly phosphorylates this motif remains controversial. Here, we identified an mTOR-mediated phosphorylation site that we termed the TOR interaction motif (TIM; F-x3-F-pT), which controls the phosphorylation of the hydrophobic motif of PKC and Akt and the activity of these kinases. The TIM is invariant in mTORC2-dependent AGC kinases, is evolutionarily conserved, and coevolved with mTORC2 components. Mutation of this motif in Akt1 and PKCĪ²II abolished cellular kinase activity by impairing activation loop and hydrophobic motif phosphorylation. mTORC2 directly phosphorylated the PKC TIM in vitro, and this phosphorylation event was detected in mouse brain. Overexpression of PDK1 in mTORC2-deficient cells rescued hydrophobic motif phosphorylation of PKC and Akt by a mechanism dependent on their intrinsic catalytic activity, revealing that mTORC2 facilitates the PDK1 phosphorylation step, which, in turn, enables autophosphorylation. Structural analysis revealed that PKC homodimerization is driven by a TIM-containing helix, and biophysical proximity assays showed that newly synthesized, unphosphorylated PKC dimerizes in cells. Furthermore, disruption of the dimer interface by stapled peptides promoted hydrophobic motif phosphorylation. Our data support a model in which mTORC2 relieves nascent PKC dimerization through TIM phosphorylation, recruiting PDK1 to phosphorylate the activation loop and triggering intramolecular hydrophobic motif autophosphorylation. Identification of TIM phosphorylation and its role in the regulation of PKC provides the basis for AGC kinase regulation by mTORC2