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1.
Cell Metab ; 35(2): 332-344.e7, 2023 02 07.
Artigo em Inglês | MEDLINE | ID: mdl-36634673

RESUMO

Hyperinsulinemia often precedes type 2 diabetes. Palmitoylation, implicated in exocytosis, is reversed by acyl-protein thioesterase 1 (APT1). APT1 biology was altered in pancreatic islets from humans with type 2 diabetes, and APT1 knockdown in nondiabetic islets caused insulin hypersecretion. APT1 knockout mice had islet autonomous increased glucose-stimulated insulin secretion that was associated with prolonged insulin granule fusion. Using palmitoylation proteomics, we identified Scamp1 as an APT1 substrate that localized to insulin secretory granules. Scamp1 knockdown caused insulin hypersecretion. Expression of a mutated Scamp1 incapable of being palmitoylated in APT1-deficient cells rescued insulin hypersecretion and nutrient-induced apoptosis. High-fat-fed islet-specific APT1-knockout mice and global APT1-deficient db/db mice showed increased ß cell failure. These findings suggest that APT1 is regulated in human islets and that APT1 deficiency causes insulin hypersecretion leading to ß cell failure, modeling the evolution of some forms of human type 2 diabetes.


Assuntos
Diabetes Mellitus Tipo 2 , Células Secretoras de Insulina , Ilhotas Pancreáticas , Camundongos , Animais , Humanos , Insulina/metabolismo , Diabetes Mellitus Tipo 2/metabolismo , Lipoilação , Células Secretoras de Insulina/metabolismo , Ilhotas Pancreáticas/metabolismo , Glucose/metabolismo , Camundongos Knockout , Proteínas de Transporte Vesicular/metabolismo
2.
Pathogens ; 11(11)2022 Oct 27.
Artigo em Inglês | MEDLINE | ID: mdl-36364996

RESUMO

Dynamic post-translational modifications allow the rapid, specific, and tunable regulation of protein functions in eukaryotic cells. S-acylation is the only reversible lipid modification of proteins, in which a fatty acid, usually palmitate, is covalently attached to a cysteine residue of a protein by a zDHHC palmitoyl acyltransferase enzyme. Depalmitoylation is required for acylation homeostasis and is catalyzed by an enzyme from the alpha/beta hydrolase family of proteins usually acyl-protein thioesterase (APT1). The enzyme responsible for depalmitoylation in Trypanosoma brucei parasites is currently unknown. We demonstrate depalmitoylation activity in live bloodstream and procyclic form trypanosomes sensitive to dose-dependent inhibition with the depalmitoylation inhibitor, palmostatin B. We identified a homologue of human APT1 in Trypanosoma brucei which we named TbAPT-like (TbAPT-L). Epitope-tagging of TbAPT-L at N- and C- termini indicated a cytoplasmic localization. Knockdown or over-expression of TbAPT-L in bloodstream forms led to robust changes in TbAPT-L mRNA and protein expression but had no effect on parasite growth in vitro, or cellular depalmitoylation activity. Esterase activity in cell lysates was also unchanged when TbAPT-L was modulated. Unexpectedly, recombinant TbAPT-L possesses esterase activity with specificity for short- and medium-chain fatty acid substrates, leading to the conclusion, TbAPT-L is a lipase, not a depalmitoylase.

3.
Sci Adv ; 8(15): eabj8633, 2022 04 15.
Artigo em Inglês | MEDLINE | ID: mdl-35427157

RESUMO

Genetic CLN5 variants are associated with childhood neurodegeneration and Alzheimer's disease; however, the molecular function of ceroid lipofuscinosis neuronal protein 5 (Cln5) is unknown. We solved the Cln5 crystal structure and identified a region homologous to the catalytic domain of members of the N1pC/P60 superfamily of papain-like enzymes. However, we observed no protease activity for Cln5; and instead, we discovered that Cln5 and structurally related PPPDE1 and PPPDE2 have efficient cysteine palmitoyl thioesterase (S-depalmitoylation) activity using fluorescent substrates. Mutational analysis revealed that the predicted catalytic residues histidine-166 and cysteine-280 are critical for Cln5 thioesterase activity, uncovering a new cysteine-based catalytic mechanism for S-depalmitoylation enzymes. Last, we found that Cln5-deficient neuronal progenitor cells showed reduced thioesterase activity, confirming live cell function of Cln5 in setting S-depalmitoylation levels. Our results provide new insight into the function of Cln5, emphasize the importance of S-depalmitoylation in neuronal homeostasis, and disclose a new, unexpected enzymatic function for the N1pC/P60 superfamily of proteins.


Assuntos
Cisteína , Lipofuscinoses Ceroides Neuronais , Criança , Humanos , Proteínas de Membrana Lisossomal/genética , Proteínas de Membrana Lisossomal/metabolismo , Proteínas de Membrana/metabolismo , Lipofuscinoses Ceroides Neuronais/genética , Lipofuscinoses Ceroides Neuronais/metabolismo
4.
Bioorg Med Chem ; 47: 116393, 2021 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-34509862

RESUMO

The continued toll of COVID-19 has halted the smooth functioning of civilization on a global scale. With a limited understanding of all the essential components of viral machinery and the lack of structural information of this new virus, initial drug discovery efforts had limited success. The availability of high-resolution crystal structures of functionally essential SARS-CoV-2 proteins, including 3CLpro, supports the development of target-specific therapeutics. 3CLpro, the main protease responsible for the processing of viral polypeptide, plays a vital role in SARS-CoV-2 viral replication and translation and is an important target in other coronaviruses. Additionally, 3CLpro is the target of repurposed drugs, such as lopinavir and ritonavir. In this study, target proteins were retrieved from the protein data bank (PDB IDs: 6 M03, 6LU7, 2GZ7, 6 W63, 6SQS, 6YB7, and 6YVF) representing different open states of the main protease to accommodate macromolecular substrate. A hydroxyethylamine (HEA) library was constructed from harvested chemical structures from all the series being used in our laboratories for screening against malaria and Leishmania parasites. The database consisted of ∼1000 structure entries, of which 70% were new to ChemSpider at the time of screening. This in-house library was subjected to high throughput virtual screening (HTVS), followed by standard precision (SP) and then extra precision (XP) docking (Schrodinger LLC 2021). The ligand strain and complex energy of top hits were calculated by Molecular Mechanics Generalized Born Surface Area (MM/GBSA) method. Promising hit compounds (n = 40) specifically binding to 3CLpro with high energy and average MM/GBSA scores were then subjected to (100-ns) MD simulations. Using this sequential selection followed by an in-silico validation approach, we found a promising HEA-based compound (N,N'-((3S,3'S)-piperazine-1,4-diylbis(3-hydroxy-1-phenylbutane-4,2-diyl))bis(2-(5-methyl-1,3-dioxoisoindolin-2-yl)-3-phenylpropanamide)), which showed high in vitro antiviral activity against SARS-CoV-2. Further to reduce the size of the otherwise larger ligand, a pharmacophore-based predicted library of âˆ¼42 derivatives was constructed, which were added to the previous compound library and rescreened virtually. Out of several hits from the predicted library, two compounds were synthesized, tested against SARS-CoV-2 culture, and found to have markedly improved antiviral activity.


Assuntos
Antivirais/química , Proteases 3C de Coronavírus/antagonistas & inibidores , Etilaminas/química , Inibidores de Proteases/química , SARS-CoV-2/enzimologia , Animais , Antivirais/metabolismo , Antivirais/farmacologia , Sítios de Ligação , COVID-19/patologia , COVID-19/virologia , Domínio Catalítico , Sobrevivência Celular/efeitos dos fármacos , Chlorocebus aethiops , Proteases 3C de Coronavírus/metabolismo , Etilaminas/metabolismo , Etilaminas/farmacologia , Humanos , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Inibidores de Proteases/metabolismo , Inibidores de Proteases/farmacologia , SARS-CoV-2/isolamento & purificação , Termodinâmica , Células Vero
5.
ACS Chem Biol ; 16(8): 1546-1556, 2021 08 20.
Artigo em Inglês | MEDLINE | ID: mdl-34309372

RESUMO

Protein S-acylation is a dynamic lipid post-translational modification that can modulate the localization and activity of target proteins. In humans, the installation of the lipid onto target proteins is catalyzed by a family of 23 Asp-His-His-Cys domain-containing protein acyltransferases (DHHC-PATs). DHHCs are increasingly recognized as critical players in cellular signaling events and in human disease. However, progress elucidating the functions and mechanisms of DHHC "writers" has been hampered by a lack of chemical tools to perturb their activity in live cells. Herein, we report the synthesis and characterization of cyano-myracrylamide (CMA), a broad-spectrum DHHC family inhibitor with similar potency to 2-bromopalmitate (2BP), the most commonly used DHHC inhibitor in the field. Possessing an acrylamide warhead instead of 2BP's α-halo fatty acid, CMA inhibits DHHC family proteins in cellulo while demonstrating decreased toxicity and avoiding inhibition of the S-acylation eraser enzymes, two of the major weaknesses of 2BP. Our studies show that CMA engages with DHHC family proteins in cells, inhibits protein S-acylation, and disrupts DHHC-regulated cellular events. CMA represents an improved chemical scaffold for untangling the complexities of DHHC-mediated cell signaling by protein S-acylation.


Assuntos
Acrilamidas/farmacologia , Aciltransferases/antagonistas & inibidores , Antígenos CD36/metabolismo , Inibidores Enzimáticos/farmacologia , Acrilamidas/síntese química , Acrilamidas/toxicidade , Acilação/efeitos dos fármacos , Animais , Linhagem Celular Tumoral , Inibidores Enzimáticos/síntese química , Inibidores Enzimáticos/toxicidade , Receptores ErbB/metabolismo , Humanos , Lipoilação/efeitos dos fármacos , Camundongos , Processamento de Proteína Pós-Traducional/efeitos dos fármacos
6.
Science ; 373(6557): 931-936, 2021 08 20.
Artigo em Inglês | MEDLINE | ID: mdl-34285133

RESUMO

There is an urgent need for antiviral agents that treat severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. We screened a library of 1900 clinically safe drugs against OC43, a human beta coronavirus that causes the common cold, and evaluated the top hits against SARS-CoV-2. Twenty drugs significantly inhibited replication of both viruses in cultured human cells. Eight of these drugs inhibited the activity of the SARS-CoV-2 main protease, 3CLpro, with the most potent being masitinib, an orally bioavailable tyrosine kinase inhibitor. X-ray crystallography and biochemistry show that masitinib acts as a competitive inhibitor of 3CLpro. Mice infected with SARS-CoV-2 and then treated with masitinib showed >200-fold reduction in viral titers in the lungs and nose, as well as reduced lung inflammation. Masitinib was also effective in vitro against all tested variants of concern (B.1.1.7, B.1.351, and P.1).


Assuntos
Antivirais/farmacologia , Tratamento Farmacológico da COVID-19 , Proteases 3C de Coronavírus/antagonistas & inibidores , Coronavirus Humano OC43/efeitos dos fármacos , Inibidores de Cisteína Proteinase/farmacologia , SARS-CoV-2/efeitos dos fármacos , Tiazóis/farmacologia , Células A549 , Animais , Antivirais/química , Antivirais/metabolismo , Antivirais/uso terapêutico , Benzamidas , COVID-19/virologia , Domínio Catalítico , Proteases 3C de Coronavírus/química , Proteases 3C de Coronavírus/metabolismo , Coronavirus Humano OC43/fisiologia , Inibidores de Cisteína Proteinase/química , Inibidores de Cisteína Proteinase/metabolismo , Células HEK293 , Humanos , Concentração Inibidora 50 , Camundongos , Camundongos Transgênicos , Testes de Sensibilidade Microbiana , Piperidinas , Piridinas , SARS-CoV-2/enzimologia , SARS-CoV-2/fisiologia , Tiazóis/química , Tiazóis/metabolismo , Tiazóis/uso terapêutico , Carga Viral/efeitos dos fármacos , Replicação Viral/efeitos dos fármacos
7.
Nat Commun ; 12(1): 743, 2021 02 02.
Artigo em Inglês | MEDLINE | ID: mdl-33531496

RESUMO

The pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) continues to expand. Papain-like protease (PLpro) is one of two SARS-CoV-2 proteases potentially targetable with antivirals. PLpro is an attractive target because it plays an essential role in cleavage and maturation of viral polyproteins, assembly of the replicase-transcriptase complex, and disruption of host responses. We report a substantive body of structural, biochemical, and virus replication studies that identify several inhibitors of the SARS-CoV-2 enzyme. We determined the high resolution structure of wild-type PLpro, the active site C111S mutant, and their complexes with inhibitors. This collection of structures details inhibitors recognition and interactions providing fundamental molecular and mechanistic insight into PLpro. All compounds inhibit the peptidase activity of PLpro in vitro, some block SARS-CoV-2 replication in cell culture assays. These findings will accelerate structure-based drug design efforts targeting PLpro to identify high-affinity inhibitors of clinical value.


Assuntos
Papaína/metabolismo , Peptídeo Hidrolases/metabolismo , SARS-CoV-2/efeitos dos fármacos , SARS-CoV-2/enzimologia , Antivirais/farmacologia , Humanos , Mutação , Poliproteínas/metabolismo , Especificidade por Substrato , Replicação Viral/efeitos dos fármacos
8.
Methods ; 195: 57-71, 2021 11.
Artigo em Inglês | MEDLINE | ID: mdl-33453392

RESUMO

SARS-CoV-2, the virus that causes COVID-19 consists of several enzymes with essential functions within its proteome. Here, we focused on repurposing approved and investigational drugs/compounds. We targeted seven proteins with enzymatic activities known to be essential at different stages of the viral cycle including PLpro, 3CLpro, RdRP, Helicase, ExoN, NendoU, and 2'-O-MT. For virtual screening, energy minimization of a crystal structure of the modeled protein was carried out using the Protein Preparation Wizard (Schrodinger LLC 2020-1). Following active site selection based on data mining and COACH predictions, we performed a high-throughput virtual screen of drugs and investigational molecules (n = 5903). The screening was performed against viral targets using three sequential docking modes (i.e., HTVS, SP, and XP). Virtual screening identified ∼290 potential inhibitors based on the criteria of energy, docking parameters, ligand, and binding site strain and score. Drugs specific to each target protein were further analyzed for binding free energy perturbation by molecular mechanics (prime MM-GBSA) and pruning the hits to the top 32 candidates. The top lead from each target pool was further subjected to molecular dynamics simulation using the Desmond module. The resulting top eight hits were tested for their SARS-CoV-2 anti-viral activity in-vitro. Among these, a known inhibitor of protein kinase C isoforms, Bisindolylmaleimide IX (BIM IX), was found to be a potent inhibitor of SARS-CoV-2. Further, target validation through enzymatic assays confirmed 3CLpro to be the target. This is the first study that has showcased BIM IX as a COVID-19 inhibitor thereby validating our pipeline.


Assuntos
Antivirais/administração & dosagem , Proteases 3C de Coronavírus/antagonistas & inibidores , Sistemas de Liberação de Medicamentos/normas , Indóis/administração & dosagem , Maleimidas/administração & dosagem , SARS-CoV-2/efeitos dos fármacos , SARS-CoV-2/enzimologia , Antivirais/metabolismo , Proteases 3C de Coronavírus/química , Proteases 3C de Coronavírus/metabolismo , Relação Dose-Resposta a Droga , Sistemas de Liberação de Medicamentos/métodos , Avaliação Pré-Clínica de Medicamentos/métodos , Reposicionamento de Medicamentos/métodos , Reposicionamento de Medicamentos/normas , Ensaios de Triagem em Larga Escala/métodos , Ensaios de Triagem em Larga Escala/normas , Humanos , Indóis/química , Indóis/metabolismo , Maleimidas/química , Maleimidas/metabolismo , Simulação de Acoplamento Molecular/métodos , Simulação de Acoplamento Molecular/normas , Estrutura Secundária de Proteína , Reprodutibilidade dos Testes , SARS-CoV-2/química
9.
bioRxiv ; 2020 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-32908976

RESUMO

There is an urgent need for anti-viral agents that treat SARS-CoV-2 infection. The shortest path to clinical use is repurposing of drugs that have an established safety profile in humans. Here, we first screened a library of 1,900 clinically safe drugs for inhibiting replication of OC43, a human beta-coronavirus that causes the common-cold and is a relative of SARS-CoV-2, and identified 108 effective drugs. We further evaluated the top 26 hits and determined their ability to inhibit SARS-CoV-2, as well as other pathogenic RNA viruses. 20 of the 26 drugs significantly inhibited SARS-CoV-2 replication in human lung cells (A549 epithelial cell line), with EC50 values ranging from 0.1 to 8 micromolar. We investigated the mechanism of action for these and found that masitinib, a drug originally developed as a tyrosine-kinase inhibitor for cancer treatment, strongly inhibited the activity of the SARS-CoV-2 main protease 3CLpro. X-ray crystallography revealed that masitinib directly binds to the active site of 3CLpro, thereby blocking its enzymatic activity. Mastinib also inhibited the related viral protease of picornaviruses and blocked picornaviruses replication. Thus, our results show that masitinib has broad anti-viral activity against two distinct beta-coronaviruses and multiple picornaviruses that cause human disease and is a strong candidate for clinical trials to treat SARS-CoV-2 infection.

10.
Circ Res ; 127(2): 249-265, 2020 07 03.
Artigo em Inglês | MEDLINE | ID: mdl-32233916

RESUMO

RATIONALE: Peripheral artery disease, common in metabolic syndrome and diabetes mellitus, responds poorly to medical interventions and is characterized by chronic vessel immaturity leading to lower extremity amputations. OBJECTIVE: To define the role of reversible palmitoylation at the endothelium in the maintenance of vascular maturity. METHODS AND RESULTS: Endothelial knockout of the depalmitoylation enzyme APT-1 (acyl-protein thioesterase 1) in mice impaired recovery from chronic hindlimb ischemia, a model of peripheral artery disease. Endothelial APT-1 deficiency decreased fibronectin processing, disrupted adherens junctions, and inhibited in vitro lumen formation. In an unbiased palmitoylation proteomic screen of endothelial cells from genetically modified mice, R-Ras, known to promote vessel maturation, was preferentially affected by APT-1 deficiency. R-Ras was validated as an APT-1 substrate, and click chemistry analyses demonstrated increased R-Ras palmitoylation in cells with APT-1 deficiency. APT-1 enzyme activity was decreased in endothelial cells from db/db mice. Hyperglycemia decreased APT-1 activity in human umbilical vein endothelial cells, due, in part, to altered acetylation of the APT-1 protein. Click chemistry analyses demonstrated increased R-Ras palmitoylation in the setting of hyperglycemia. Altered R-Ras trafficking, increased R-Ras palmitoylation, and fibronectin retention were found in diabetes mellitus models. Loss of R-Ras depalmitoylation caused by APT-1 deficiency constrained R-Ras membrane trafficking, as shown by total internal reflection fluorescence imaging. To rescue cellular phenotypes, we generated an R-Ras molecule with an inserted hydrophilic domain to circumvent membrane rigidity caused by defective palmitoylation turnover. This modification corrected R-Ras membrane trafficking, restored fibronectin processing, increased adherens junctions, and rescued defective lumen formation induced by APT-1 deficiency. CONCLUSIONS: These results suggest that endothelial depalmitoylation is regulated by the metabolic milieu and controls plasma membrane partitioning to maintain vascular homeostasis.


Assuntos
Doença Arterial Periférica/metabolismo , Tioléster Hidrolases/metabolismo , Remodelação Vascular , Proteínas ras/metabolismo , Animais , Células Endoteliais da Veia Umbilical Humana/metabolismo , Humanos , Lipoilação , Camundongos , Doença Arterial Periférica/patologia , Transporte Proteico , Tioléster Hidrolases/genética , Proteínas ras/genética
11.
Nat Chem Biol ; 15(12): 1232-1240, 2019 12.
Artigo em Inglês | MEDLINE | ID: mdl-31740833

RESUMO

S-Palmitoylation is a reversible lipid post-translational modification that has been observed on mitochondrial proteins, but both the regulation and functional consequences of mitochondrial S-palmitoylation are poorly understood. Here, we show that perturbing the 'erasers' of S-palmitoylation, acyl protein thioesterases (APTs), with either pan-active inhibitors or a mitochondrial-targeted APT inhibitor, diminishes the antioxidant buffering capacity of mitochondria. Surprisingly, this effect was not mediated by the only known mitochondrial APT, but rather by a resident mitochondrial protein with no known endogenous function, ABHD10. We show that ABHD10 is a member of the APT family of regulatory proteins and identify peroxiredoxin-5 (PRDX5), a key antioxidant protein, as a target of ABHD10 S-depalmitoylase activity. We then find that ABHD10 regulates the S-palmitoylation status of the nucleophilic active site residue of PRDX5, providing a direct mechanistic connection between ABHD10-mediated S-depalmitoylation of PRDX5 and its antioxidant capacity.


Assuntos
Esterases/fisiologia , Homeostase , Peroxirredoxinas/metabolismo , Células HEK293 , Humanos , Mitocôndrias/metabolismo , Oxirredução
12.
Acc Chem Res ; 52(11): 3029-3038, 2019 11 19.
Artigo em Inglês | MEDLINE | ID: mdl-31577124

RESUMO

While lipids were first appreciated as a critical hydrophobic barrier, our understanding of their roles at the cellular and organismal levels continues to grow. Not only are they important independent operators, providing a platform for both static and dynamic organization and communication within the cell, they also exert significant effects via the chemical modification of proteins. Addition of a lipid post-translational modification (PTM) alters protein hydrophobicity and behavior, with distinct consequences for subcellular trafficking, localization, intra- and intermolecular interactions, and stability. One of the most abundant and widespread protein lipidation events is S-acylation, installation of a long-chain lipid to the thiol of a cysteine side chain through a thioester linkage. S-Acylation is often referred to as S-palmitoylation, due to the prevalence of palmitate as the lipid modification. Unlike many lipid PTMs, S-acylation is enzymatically reversible, enabling the cell to tune proteome-wide properties through dynamic alterations in protein lipidation status. While much has been uncovered about the molecular effects of S-acylation and its implications for physiology, current biochemical and chemical methods only assess substrate lipidation levels or steady-state levels of enzyme activity. Yet, the writer protein acyl transferases (PATs) and eraser acyl protein thioesterases (APTs) are dynamically active, responsible for sometimes-rapid changes in S-palmitoylation status of target proteins. Thus, to understand the full scope, significance, and subtlety of S-deacylation and its regulation in the cell, it is necessary to observe the timing and cellular geography of regulatory enzyme activities. In this Account, we review the chemical tools developed by our group to selectively visualize and perturb the activity of APTs in live cells, highlighting the biological insights gained from their application. To visualize APT activity, we masked fluorogenic molecules with thioacylated, peptide-based APT substrate mimetics; APT activity and thus thiol deprotection releases a fluorescent product in the turn-on depalmitoylation probes (DPPs), while in ratiometric depalmitoylation probes (RDPs) the emission of the parent fluorophore is altered. Application of these probes in live cells reveals that APT activity is sensitive to cell signaling events and metabolic disturbances. Additionally, as indicated above, the location of regulatory enzymes is critical in lipid signaling, and one organelle of particular interest, due to its role in maintaining cellular homeostasis and its legion of lipidated proteins, is the mitochondria. Therefore, we developed a class of spatially constrained mitoDPPs to visualize mitochondrial APT activity as well as a selective inhibitor of mitochondrial deacylation activity, mitoFP. With these tools, we identify two mitochondrial S-depalmitoylases and connect mitochondrial S-depalmitoylation to redox buffering capacity. Moreover, some of the changes in activity observed are specific to the mitochondria, confirming spatial as well as temporal regulation of eraser protein activity. Overall, this chemical toolkit for S-depalmitoylase activity, imaging reagents and a targeted inhibitor, will continue to illuminate the regulatory mechanisms and roles of S-depalmitoylation within the complex homeostatic networks of the cell.


Assuntos
Esterases , Esterases/química , Esterases/metabolismo , Humanos , Lipídeos/química , Modelos Moleculares , Processamento de Proteína Pós-Traducional
13.
Cell Commun Signal ; 17(1): 90, 2019 08 05.
Artigo em Inglês | MEDLINE | ID: mdl-31382980

RESUMO

BACKGROUND: Binding of tumor necrosis factor (TNF) to TNF-receptor 1 (TNF-R1) can induce either cell survival or cell death. The selection between these diametrically opposed effects depends on the subcellular location of TNF-R1: plasma membrane retention leads to survival, while endocytosis leads to cell death. How the respective TNF-R1 associated signaling complexes are recruited to the distinct subcellular location is not known. Here, we identify palmitoylation of TNF-R1 as a molecular mechanism to achieve signal diversification. METHODS: Human monocytic U937 cells were analyzed. Palmitoylated proteins were enriched by acyl resin assisted capture (AcylRAC) and analyzed by western blot and mass spectrometry. Palmitoylation of TNF-R1 was validated by metabolic labeling. TNF induced depalmitoylation and involvement of APT2 was analyzed by enzyme activity assays, pharmacological inhibition and shRNA mediated knock-down. TNF-R1 palmitoylation site analysis was done by mutated TNF-R1 expression in TNF-R1 knock-out cells. Apoptosis (nuclear DNA fragmentation, caspase 3 assays), NF-κB activation and TNF-R1 internalization were used as biological readouts. RESULTS: We identify dynamic S-palmitoylation as a new mechanism that controls selective TNF signaling. TNF-R1 itself is constitutively palmitoylated and depalmitoylated upon ligand binding. We identified the palmitoyl thioesterase APT2 to be involved in TNF-R1 depalmitoylation and TNF induced NF-κB activation. Mutation of the putative palmitoylation site C248 interferes with TNF-R1 localization to the plasma membrane and thus, proper signal transduction. CONCLUSIONS: Our results introduce palmitoylation as a new layer of dynamic regulation of TNF-R1 induced signal transduction at a very early step of the TNF induced signaling cascade. Understanding the underlying mechanism may allow novel therapeutic options for disease treatment in future.


Assuntos
Lipoilação , Receptores Tipo I de Fatores de Necrose Tumoral/metabolismo , Transdução de Sinais , Linhagem Celular , Regulação da Expressão Gênica , Humanos , NF-kappa B/metabolismo , Transporte Proteico , Tioléster Hidrolases/metabolismo
14.
Methods Mol Biol ; 2009: 99-109, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31152398

RESUMO

S-palmitoylation is a reversible lipid posttranslational modification (PTM) that can mediate protein localization, trafficking, interaction with membranes, and a host of other biophysical characteristics. Over the past decade, a suite of chemoproteomic strategies have uncovered the breadth of S-palmitoylation, revealing widespread susceptibility to modification by this PTM throughout the human proteome. A focal point of research toward understanding the role of S-palmitoylation in varied cellular processes has focused on understanding how "writer" and "eraser" proteins function together to control the levels of S-palmitoylation of target proteins. The spatial and temporal regulation of S-palmitoylation by its "erasers"-acyl protein thioesterases (APTs)-is not fully understood. Tools which enable monitoring of the activity levels of the APTs in real-time in live cells illuminate how spatial control of these enzymes redecorate the lipidation state of the local proteome. To this end, we have developed fluorescence-based depalmitoylation probes (DPPs), which report S-depalmitoylase activity in live cells. Using DPPs, we have demonstrated that S-depalmitoylase activity changes in response to growth factor stimulation, unveiling potential regulation of cell growth and metabolism by APTs. Additionally, we recently discovered APTs in mitochondria using targeted DPPs, indicating new roles for S-depalmitoylation in this critical cellular compartment. Here, we present detailed protocols on how to carry out in vitro S-depalmitoylase activity assays and live cell fluorescence imaging employing the growing DPP toolbox.


Assuntos
Corantes Fluorescentes/química , Lipoilação , Mitocôndrias/metabolismo , Proteínas Mitocondriais/metabolismo , Processamento de Proteína Pós-Traducional , Coloração e Rotulagem/métodos , Células HeLa , Humanos , Microscopia de Fluorescência
16.
Nat Commun ; 9(1): 334, 2018 01 23.
Artigo em Inglês | MEDLINE | ID: mdl-29362370

RESUMO

The reversible modification of cysteine residues by thioester formation with palmitate (S-palmitoylation) is an abundant lipid post-translational modification (PTM) in mammalian systems. S-palmitoylation has been observed on mitochondrial proteins, providing an intriguing potential connection between metabolic lipids and mitochondrial regulation. However, it is unknown whether and/or how mitochondrial S-palmitoylation is regulated. Here we report the development of mitoDPPs, targeted fluorescent probes that measure the activity levels of "erasers" of S-palmitoylation, acyl-protein thioesterases (APTs), within mitochondria of live cells. Using mitoDPPs, we discover active S-depalmitoylation in mitochondria, in part mediated by APT1, an S-depalmitoylase previously thought to reside in the cytosol and on the Golgi apparatus. We also find that perturbation of long-chain acyl-CoA cytoplasm and mitochondrial regulatory proteins, respectively, results in selective responses from cytosolic and mitochondrial S-depalmitoylases. Altogether, this work reveals that mitochondrial S-palmitoylation is actively regulated by "eraser" enzymes that respond to alterations in mitochondrial lipid homeostasis.


Assuntos
Corantes Fluorescentes/metabolismo , Mitocôndrias/metabolismo , Dinâmica Mitocondrial , Tioléster Hidrolases/metabolismo , Células A549 , Acil Coenzima A/metabolismo , Células HEK293 , Células HeLa , Humanos , Cinética , Lipoilação , Células MCF-7 , Microscopia Confocal , Interferência de RNA , Tioléster Hidrolases/genética
17.
Biochemistry ; 57(2): 221-225, 2018 01 16.
Artigo em Inglês | MEDLINE | ID: mdl-29023093

RESUMO

S-Palmitoylation is an abundant lipid post-translational modification that is dynamically installed on and removed from target proteins to regulate their activity and cellular localization. A dearth of tools for studying the activities and regulation of protein S-depalmitoylases, thioesterase "erasers" of protein cysteine S-palmitoylation, has contributed to an incomplete understanding of the role of dynamic S-palmitoylation in regulating proteome lipidation. Recently, we developed "depalmitoylation probes" (DPPs), small molecule probes that become fluorescent upon S-depalmitoylase enzymatic activity. To be suitable for application in live cells, the first-generation DPPs relied on a shorter lipid substrate (C8 vs naturally occurring C16), which enhanced solubility and cell permeability. However, the use of an unnatural lipid substrate on the probes potentially limits the utility of the approach. Herein, we present a new member of the DPP family, DPP-5, which features an anionic carboxylate functional group that increases the probe water solubility. The enhanced water solubility of DPP-5 permits the use of a natural, palmitoylated substrate (C16), rather than a surrogate lipid. We show that DPP-5 is capable of monitoring endogenous S-depalmitoylases in live mammalian cells and that it can reveal changes in S-depalmitoylation levels due to lipid stress. DPP-5 should prove to be a useful new tool for probing the regulation of proteome lipidation through dynamic S-depalmitoylation.


Assuntos
Carbamatos/análise , Corantes Fluorescentes/análise , Microscopia Intravital/métodos , Piperazinas/análise , Processamento de Proteína Pós-Traducional , Ativação Metabólica , Animais , Carbamatos/química , Cisteína/metabolismo , Corantes Fluorescentes/química , Células HEK293 , Humanos , Lipoilação , Mamíferos/metabolismo , Microscopia de Fluorescência , Palmitatos/metabolismo , Piperazinas/química , Propiolactona/análogos & derivados , Propiolactona/farmacologia , Solubilidade , Relação Estrutura-Atividade , Tioléster Hidrolases/antagonistas & inibidores , Tioléster Hidrolases/metabolismo , Água , Xantonas/química
18.
Nat Chem Biol ; 13(2): 150-152, 2017 02.
Artigo em Inglês | MEDLINE | ID: mdl-27992880

RESUMO

Hundreds of human proteins are modified by reversible palmitoylation of cysteine residues (S-palmitoylation), but the regulation of depalmitoylation is poorly understood. Here, we develop 'depalmitoylation probes' (DPPs), small-molecule fluorophores, to monitor the endogenous activity levels of 'erasers' of S-palmitoylation, acylprotein thioesterases (APTs). Live-cell analysis with DPPs reveals rapid growth-factor-mediated inhibition of the depalmitoylation activity of APTs, exposing a novel regulatory mechanism of dynamic lipid signaling.


Assuntos
Cisteína/química , Cisteína/metabolismo , Corantes Fluorescentes/análise , Transdução de Sinais , Tioléster Hidrolases/metabolismo , Sobrevivência Celular , Corantes Fluorescentes/síntese química , Corantes Fluorescentes/química , Humanos , Estrutura Molecular , Células Tumorais Cultivadas
19.
Chem Sci ; 8(11): 7588-7592, 2017 Nov 01.
Artigo em Inglês | MEDLINE | ID: mdl-29568422

RESUMO

The reversible modification of cysteine residues through thioester formation with palmitate (protein S-palmitoylation) is a prevalent chemical modification that regulates the function, localization, and stability of many proteins. Current methods for monitoring the "erasers" of S-palmitoylation, acyl-protein thioesterases (APTs), rely on destructive proteomic methods or "turn-on" probes, precluding deployment in heterogeneous samples such as primary tissues. To address these challenges, we present the design, synthesis, and biological evaluation of Ratiometric Depalmitoylation Probes (RDPs). RDPs respond to APTs with a robust ratiometric change in fluorescent signal both in vitro and in live cells. Moreover, RDPs can monitor endogenous APT activities in heterogeneous primary human tissues such as colon organoids, presaging the utility of these molecules in uncovering novel roles for APTs in metabolic regulation.

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