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Yang W, Feng R, Peng G, Wang Z, Cen M, Jing Y, Feng W, Long T, Liu Y, Li Z, Huang K, Chang G. Glycoursodeoxycholic Acid Alleviates Arterial Thrombosis via Suppressing Diacylglycerol Kinases Activity in Platelet. Arterioscler Thromb Vasc Biol 2024; 44:1283-1301. [PMID: 38572646 DOI: 10.1161/atvbaha.124.320728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/19/2024] [Indexed: 04/05/2024]
Abstract
BACKGROUND Glycoursodeoxycholic acid (GUDCA) has been acknowledged for its ability to regulate lipid homeostasis and provide benefits for various metabolic disorders. However, the impact of GUDCA on arterial thrombotic events remains unexplored. The objective of this study is to examine the effects of GUDCA on thrombogenesis and elucidate its underlying mechanisms. METHODS Plasma samples from patients with arterial thrombotic events and diet-induced obese mice were collected to determine the GUDCA concentrations using mass spectrometry. Multiple in vivo murine thrombosis models and in vitro platelet functional assays were conducted to comprehensively evaluate the antithrombotic effects of GUDCA. Moreover, lipidomic analysis was performed to identify the alterations of intraplatelet lipid components following GUDCA treatment. RESULTS Plasma GUDCA level was significantly decreased in patients with arterial thrombotic events and negatively correlated with thrombotic propensity in diet-induced obese mice. GUDCA exhibited prominent suppressing effects on platelet reactivity as evidenced by the attenuation of platelet activation, secretion, aggregation, spreading, and retraction (P<0.05). In vivo, GUDCA administration robustly alleviated thrombogenesis (P<0.05) without affecting hemostasis. Mechanistically, GUDCA inhibited DGK (diacylglycerol kinase) activity, leading to the downregulation of the phosphatidic acid-mediated signaling pathway. Conversely, phosphatidic acid supplementation was sufficient to abolish the antithrombotic effects of GUDCA. More importantly, long-term oral administration of GUDCA normalized the enhanced DGK activity, thereby remarkably alleviating the platelet hyperreactivity as well as the heightened thrombotic tendency in diet-induced obese mice (P<0.05). CONCLUSIONS Our study implicated that GUDCA reduces platelet hyperreactivity and improves thrombotic propensity by inhibiting DGKs activity, which is a potentially effective prophylactic approach and promising therapeutic agent for arterial thrombotic events.
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Affiliation(s)
- Wenchao Yang
- Division of Vascular Surgery, National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Diseases, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China (W.Y., R.F., G.P., Z.W., Y.J., W.F., T.L., Y.L., Z.L, K.H., G.C.)
| | - Ruijia Feng
- Division of Vascular Surgery, National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Diseases, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China (W.Y., R.F., G.P., Z.W., Y.J., W.F., T.L., Y.L., Z.L, K.H., G.C.)
| | - Guiyan Peng
- Division of Vascular Surgery, National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Diseases, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China (W.Y., R.F., G.P., Z.W., Y.J., W.F., T.L., Y.L., Z.L, K.H., G.C.)
| | - Zhecun Wang
- Division of Vascular Surgery, National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Diseases, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China (W.Y., R.F., G.P., Z.W., Y.J., W.F., T.L., Y.L., Z.L, K.H., G.C.)
| | - Meifeng Cen
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, China (M.C.)
| | - Yexiang Jing
- Division of Vascular Surgery, National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Diseases, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China (W.Y., R.F., G.P., Z.W., Y.J., W.F., T.L., Y.L., Z.L, K.H., G.C.)
| | - Weiqi Feng
- Division of Vascular Surgery, National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Diseases, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China (W.Y., R.F., G.P., Z.W., Y.J., W.F., T.L., Y.L., Z.L, K.H., G.C.)
| | - Ting Long
- Division of Vascular Surgery, National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Diseases, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China (W.Y., R.F., G.P., Z.W., Y.J., W.F., T.L., Y.L., Z.L, K.H., G.C.)
| | - Yunchong Liu
- Division of Vascular Surgery, National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Diseases, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China (W.Y., R.F., G.P., Z.W., Y.J., W.F., T.L., Y.L., Z.L, K.H., G.C.)
| | - Zilun Li
- Division of Vascular Surgery, National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Diseases, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China (W.Y., R.F., G.P., Z.W., Y.J., W.F., T.L., Y.L., Z.L, K.H., G.C.)
| | - Kan Huang
- Division of Vascular Surgery, National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Diseases, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China (W.Y., R.F., G.P., Z.W., Y.J., W.F., T.L., Y.L., Z.L, K.H., G.C.)
| | - Guangqi Chang
- Division of Vascular Surgery, National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Diseases, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China (W.Y., R.F., G.P., Z.W., Y.J., W.F., T.L., Y.L., Z.L, K.H., G.C.)
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2
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Traczyk G, Hromada-Judycka A, Świątkowska A, Wiśniewska J, Ciesielska A, Kwiatkowska K. Diacylglycerol kinase-ε is S-palmitoylated on cysteine in the cytoplasmic end of its N-terminal transmembrane fragment. J Lipid Res 2024; 65:100480. [PMID: 38008259 PMCID: PMC10759177 DOI: 10.1016/j.jlr.2023.100480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 11/17/2023] [Accepted: 11/18/2023] [Indexed: 11/28/2023] Open
Abstract
Diacylglycerol kinase-ε (DGKε) catalyzes phosphorylation of diacylglycerol to phosphatidic acid with a unique specificity toward 1-stearoyl-2-arachidonoyl-sn-glycerol, which is a backbone of phosphatidylinositol (PI). Owing to this specificity, DGKε is involved in the PI cycle maintaining the cellular level of phosphorylated PI derivatives of signaling activity and was also found crucial for lipid metabolism. DGKε dysfunction is linked with the development of atypical hemolytic uremic syndrome (aHUS) and possibly other human diseases. Despite the DGKε significance, data on its regulation by cotranslational and/or post-translational modifications are scarce. Here, we report that DGKε is S-palmitoylated at Cys38/40 (mouse/human DGKε) located in the cytoplasmic end of its N-terminal putative transmembrane fragment. The S-palmitoylation of DGKε was revealed by metabolic labeling of cells with a palmitic acid analogue followed by click chemistry and with acyl-biotin and acyl-polyethylene glycol exchange assays. The S-acyltransferases zDHHC7 (zinc finger DHHC domain containing) and zDHHC17 and the zDHHC6/16 tandem were found to catalyze DGKε S-palmitoylation, which also increased the DGKε abundance. Mouse DGKε-Myc ectopically expressed in human embryonic kidney 293 cells localized to the endoplasmic reticulum where zDHHC6/16 reside and in small amounts also to the Golgi apparatus where zDHHC7 and zDHHC17 are present. The Cys38Ala substitution upregulated, whereas hyperpalmitoylation of wild-type DGKε reduced the kinase activity, indicating an inhibitory effect of the Cys38 S-palmitoylation. In addition, the substitution of neighboring Pro31 with Ala also diminished the activity of DGKε. Taken together, our data indicate that S-palmitoylation can fine-tune DGKε activity in distinct cellular compartments, possibly by affecting the distance between the kinase and its substrate in a membrane.
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Affiliation(s)
- Gabriela Traczyk
- Laboratory of Molecular Membrane Biology, Nencki Institute of Experimental Biology PAS, Warsaw, Poland
| | - Aneta Hromada-Judycka
- Laboratory of Molecular Membrane Biology, Nencki Institute of Experimental Biology PAS, Warsaw, Poland
| | - Anna Świątkowska
- Laboratory of Molecular Membrane Biology, Nencki Institute of Experimental Biology PAS, Warsaw, Poland
| | - Julia Wiśniewska
- Laboratory of Molecular Membrane Biology, Nencki Institute of Experimental Biology PAS, Warsaw, Poland
| | - Anna Ciesielska
- Laboratory of Molecular Membrane Biology, Nencki Institute of Experimental Biology PAS, Warsaw, Poland
| | - Katarzyna Kwiatkowska
- Laboratory of Molecular Membrane Biology, Nencki Institute of Experimental Biology PAS, Warsaw, Poland.
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3
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Martin-Salgado M, Ochoa-Echeverría A, Mérida I. Diacylglycerol kinases: A look into the future of immunotherapy. Adv Biol Regul 2024; 91:100999. [PMID: 37949728 DOI: 10.1016/j.jbior.2023.100999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 11/01/2023] [Indexed: 11/12/2023]
Abstract
Cancer still represents the second leading cause of death right after cardiovascular diseases. According to the World Health Organization (WHO), cancer provoked around 10 million deaths in 2020, with lung and colon tumors accounting for the deadliest forms of cancer. As tumor cells become resistant to traditional therapeutic approaches, immunotherapy has emerged as a novel strategy for tumor control. T lymphocytes are key players in immune responses against tumors. Immunosurveillance allows identification, targeting and later killing of cancerous cells. Nevertheless, tumors evolve through different strategies to evade the immune response and spread in a process called metastasis. The ineffectiveness of traditional strategies to control tumor growth and expansion has led to novel approaches considering modulation of T cell activation and effector functions. Program death receptor 1 (PD-1) and cytotoxic T-lymphocyte antigen 4 (CTLA-4) showed promising results in the early 90s and nowadays are still being exploited together with other drugs for several cancer types. Other negative regulators of T cell activation are diacylglycerol kinases (DGKs) a family of enzymes that catalyze the conversion of diacylglycerol (DAG) into phosphatidic acid (PA). In T cells, DGKα and DGKζ limit the PLCγ/Ras/ERK axis thus attenuating DAG mediated signaling and T cell effector functions. Upregulation of either of both isoforms results in impaired Ras activation and anergy induction, whereas germline knockdown mice showed enhanced antitumor properties and more effective immune responses against pathogens. Here we review the mechanisms used by DGKs to ameliorate T cell activation and how inhibition could be used to reinvigorate T cell functions in cancer context. A better knowledge of the molecular mechanisms involved upon T cell activation will help to improve current therapies with DAG promoting agents.
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Affiliation(s)
- Miguel Martin-Salgado
- Department of Immunology and Oncology. National Centre for Biotechnology. Spanish Research Council (CNB-CSIC), Spain
| | - Ane Ochoa-Echeverría
- Department of Immunology and Oncology. National Centre for Biotechnology. Spanish Research Council (CNB-CSIC), Spain
| | - Isabel Mérida
- Department of Immunology and Oncology. National Centre for Biotechnology. Spanish Research Council (CNB-CSIC), Spain.
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4
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Gonzales DT, Schuhmacher M, Lennartz HM, Iglesias-Artola JM, Kuhn SM, Barahtjan P, Zechner C, Nadler A. Quantifying single-cell diacylglycerol signaling kinetics after uncaging. Biophys J 2023; 122:4699-4709. [PMID: 37978803 PMCID: PMC10754688 DOI: 10.1016/j.bpj.2023.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 07/07/2023] [Accepted: 11/15/2023] [Indexed: 11/19/2023] Open
Abstract
Studying the role of molecularly distinct lipid species in cell signaling remains challenging due to a scarcity of methods for performing quantitative lipid biochemistry in living cells. We have recently used lipid uncaging to quantify lipid-protein affinities and rates of lipid trans-bilayer movement and turnover in the diacylglycerol signaling pathway. This approach is based on acquiring live-cell dose-response curves requiring light dose titrations and experimental determination of uncaging photoreaction efficiency. We here aimed to develop a methodological approach that allows us to retrieve quantitative kinetic data from uncaging experiments that 1) require only typically available datasets without the need for specialized additional constraints and 2) should in principle be applicable to other types of photoactivation experiments. Our new analysis framework allows us to identify model parameters such as diacylglycerol-protein affinities and trans-bilayer movement rates, together with initial uncaged diacylglycerol levels, using noisy single-cell data for a broad variety of structurally different diacylglycerol species. We find that lipid unsaturation degree and side-chain length generally correlate with faster lipid trans-bilayer movement and turnover and also affect lipid-protein affinities. In summary, our work demonstrates how rate parameters and lipid-protein affinities can be quantified from single-cell signaling trajectories with sufficient sensitivity to resolve the subtle kinetic differences caused by the chemical diversity of cellular signaling lipid pools.
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Affiliation(s)
- David T Gonzales
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany; Center for Systems Biology Dresden, Dresden, Germany
| | - Milena Schuhmacher
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany; École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - H Mathilda Lennartz
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Sascha M Kuhn
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Pavel Barahtjan
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Christoph Zechner
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany; Center for Systems Biology Dresden, Dresden, Germany.
| | - André Nadler
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
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5
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Wichroski M, Benci J, Liu SQ, Chupak L, Fang J, Cao C, Wang C, Onorato J, Qiu H, Shan Y, Banas D, Powles R, Locke G, Witt A, Stromko C, Qi H, Zheng X, Martin S, Ding M, Gentles R, Meanwell N, Velaparthi U, Olson R, Wee S, Tenney D, Parker CG, Cravatt BF, Lawrence M, Borzilleri R, Lees E. DGKα/ζ inhibitors combine with PD-1 checkpoint therapy to promote T cell-mediated antitumor immunity. Sci Transl Med 2023; 15:eadh1892. [PMID: 37878674 DOI: 10.1126/scitranslmed.adh1892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 10/04/2023] [Indexed: 10/27/2023]
Abstract
Programmed cell death protein 1 (PD-1) immune checkpoint blockade therapy has revolutionized cancer treatment. Although PD-1 blockade is effective in a subset of patients with cancer, many fail to respond because of either primary or acquired resistance. Thus, next-generation strategies are needed to expand the depth and breadth of clinical responses. Toward this end, we designed a human primary T cell phenotypic high-throughput screening strategy to identify small molecules with distinct and complementary mechanisms of action to PD-1 checkpoint blockade. Through these efforts, we selected and optimized a chemical series that showed robust potentiation of T cell activation and combinatorial activity with αPD-1 blockade. Target identification was facilitated by chemical proteomic profiling with a lipid-based photoaffinity probe, which displayed enhanced binding to diacylglycerol kinase α (DGKα) in the presence of the active compound, a phenomenon that correlated with the translocation of DGKα to the plasma membrane. We further found that optimized leads within this chemical series were potent and selective inhibitors of both DGKα and DGKζ, lipid kinases that constitute an intracellular T cell checkpoint that blunts T cell signaling through diacylglycerol metabolism. We show that dual DGKα/ζ inhibition amplified suboptimal T cell receptor signaling mediated by low-affinity antigen presentation and low major histocompatibility complex class I expression on tumor cells, both hallmarks of resistance to PD-1 blockade. In addition, DGKα/ζ inhibitors combined with αPD-1 therapy to elicit robust tumor regression in syngeneic mouse tumor models. Together, these findings support targeting DGKα/ζ as a next-generation T cell immune checkpoint strategy.
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Affiliation(s)
- Michael Wichroski
- Research and Development, Bristol Myers Squibb Company, Cambridge, MA 02142, USA
| | - Joseph Benci
- Research and Development, Bristol Myers Squibb Company, Lawrenceville, NJ 08648, USA
| | - Si-Qi Liu
- Research and Development, Bristol Myers Squibb Company, Cambridge, MA 02142, USA
| | - Louis Chupak
- Research and Development, Bristol Myers Squibb Company, Cambridge, MA 02142, USA
| | - Jie Fang
- Research and Development, Bristol Myers Squibb Company, Lawrenceville, NJ 08648, USA
| | - Carolyn Cao
- Research and Development, Bristol Myers Squibb Company, Lawrenceville, NJ 08648, USA
| | - Cindy Wang
- Research and Development, Bristol Myers Squibb Company, Lawrenceville, NJ 08648, USA
| | - Joelle Onorato
- Research and Development, Bristol Myers Squibb Company, Lawrenceville, NJ 08648, USA
| | - Hongchen Qiu
- Research and Development, Bristol Myers Squibb Company, Cambridge, MA 02142, USA
| | - Yongli Shan
- Research and Development, Bristol Myers Squibb Company, Cambridge, MA 02142, USA
| | - Dana Banas
- Research and Development, Bristol Myers Squibb Company, Lawrenceville, NJ 08648, USA
| | - Ryan Powles
- Research and Development, Bristol Myers Squibb Company, Cambridge, MA 02142, USA
| | - Gregory Locke
- Research and Development, Bristol Myers Squibb Company, Lawrenceville, NJ 08648, USA
| | - Abigail Witt
- Research and Development, Bristol Myers Squibb Company, Cambridge, MA 02142, USA
| | - Caitlyn Stromko
- Research and Development, Bristol Myers Squibb Company, Lawrenceville, NJ 08648, USA
| | - Huilin Qi
- Research and Development, Bristol Myers Squibb Company, Cambridge, MA 02142, USA
| | - Xiaofan Zheng
- Research and Development, Bristol Myers Squibb Company, Cambridge, MA 02142, USA
| | - Scott Martin
- Research and Development, Bristol Myers Squibb Company, Cambridge, MA 02142, USA
| | - Min Ding
- Research and Development, Bristol Myers Squibb Company, Cambridge, MA 02142, USA
| | - Robert Gentles
- Research and Development, Bristol Myers Squibb Company, Cambridge, MA 02142, USA
| | - Nicholas Meanwell
- Research and Development, Bristol Myers Squibb Company, Lawrenceville, NJ 08648, USA
| | - Upender Velaparthi
- Research and Development, Bristol Myers Squibb Company, Lawrenceville, NJ 08648, USA
| | - Richard Olson
- Research and Development, Bristol Myers Squibb Company, Cambridge, MA 02142, USA
| | - Susan Wee
- Research and Development, Bristol Myers Squibb Company, Lawrenceville, NJ 08648, USA
| | - Daniel Tenney
- Research and Development, Bristol Myers Squibb Company, Lawrenceville, NJ 08648, USA
| | | | - Benjamin F Cravatt
- Department of Chemistry, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael Lawrence
- Research and Development, Bristol Myers Squibb Company, Lawrenceville, NJ 08648, USA
| | - Robert Borzilleri
- Research and Development, Bristol Myers Squibb Company, Lawrenceville, NJ 08648, USA
| | - Emma Lees
- Research and Development, Bristol Myers Squibb Company, Cambridge, MA 02142, USA
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6
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Chupak L, Wichroski M, Zheng X, Ding M, Martin S, Allard C, Shi J, Gentles R, Meanwell NA, Fang J, Tenney D, Tokarski J, Cao C, Wee S. Discovery of Potent, Dual-Inhibitors of Diacylglycerol Kinases Alpha and Zeta Guided by Phenotypic Optimization. ACS Med Chem Lett 2023; 14:929-935. [PMID: 37465293 PMCID: PMC10351048 DOI: 10.1021/acsmedchemlett.3c00063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 06/01/2023] [Indexed: 07/20/2023] Open
Abstract
We describe a phenotypic screening and optimization strategy to discover compounds that block intracellular checkpoint signaling in T-cells. We identified dual DGKα and ζ inhibitors notwithstanding the modest similarity between α and ζ relative to other DGK isoforms. Optimized compounds produced cytokine release and T-cell proliferation consistent with DGK inhibition and potentiated an immune response in human and mouse T-cells. Additionally, lead inhibitor BMS-502 demonstrated dose-dependent immune stimulation in the mouse OT-1 model, setting the stage for a drug discovery program.
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Affiliation(s)
- Louis Chupak
- Bristol
Myers Squibb Research and Early Development, 100 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Michael Wichroski
- Bristol
Myers Squibb Research and Early Development, 100 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Xiaofan Zheng
- Bristol
Myers Squibb Research and Early Development, 100 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Min Ding
- Bristol
Myers Squibb Research and Early Development, 100 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Scott Martin
- Bristol
Myers Squibb Research and Early Development, 100 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Christopher Allard
- Bristol
Myers Squibb Research and Early Development, 100 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Jianliang Shi
- Bristol
Myers Squibb Research and Early Development, PO Box 4000, Princeton, New Jersey 08543-4000, United
States
| | - Robert Gentles
- Bristol
Myers Squibb Research and Early Development, 100 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Nicholas A. Meanwell
- Bristol
Myers Squibb Research and Early Development, PO Box 4000, Princeton, New Jersey 08543-4000, United
States
| | - Jie Fang
- Bristol
Myers Squibb Research and Early Development, PO Box 4000, Princeton, New Jersey 08543-4000, United
States
| | - Daniel Tenney
- Bristol
Myers Squibb Research and Early Development, PO Box 4000, Princeton, New Jersey 08543-4000, United
States
| | - John Tokarski
- Bristol
Myers Squibb Research and Early Development, PO Box 4000, Princeton, New Jersey 08543-4000, United
States
| | - Carolyn Cao
- Bristol
Myers Squibb Research and Early Development, PO Box 4000, Princeton, New Jersey 08543-4000, United
States
| | - Susan Wee
- Bristol
Myers Squibb Research and Early Development, PO Box 4000, Princeton, New Jersey 08543-4000, United
States
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7
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Mendez R, Shaikh M, Lemke MC, Yuan K, Libby AH, Bai DL, Ross MM, Harris TE, Hsu KL. Predicting small molecule binding pockets on diacylglycerol kinases using chemoproteomics and AlphaFold. RSC Chem Biol 2023; 4:422-430. [PMID: 37292058 PMCID: PMC10246554 DOI: 10.1039/d3cb00057e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 05/13/2023] [Indexed: 06/10/2023] Open
Abstract
Diacylglycerol kinases (DGKs) are metabolic kinases involved in regulating cellular levels of diacylglycerol and phosphatidic lipid messengers. The development of selective inhibitors for individual DGKs would benefit from discovery of protein pockets available for inhibitor binding in cellular environments. Here we utilized a sulfonyl-triazole probe (TH211) bearing a DGK fragment ligand for covalent binding to tyrosine and lysine sites on DGKs in cells that map to predicted small molecule binding pockets in AlphaFold structures. We apply this chemoproteomics-AlphaFold approach to evaluate probe binding of DGK chimera proteins engineered to exchange regulatory C1 domains between DGK subtypes (DGKα and DGKζ). Specifically, we discovered loss of TH211 binding to a predicted pocket in the catalytic domain when C1 domains on DGKα were exchanged that correlated with impaired biochemical activity as measured by a DAG phosphorylation assay. Collectively, we provide a family-wide assessment of accessible sites for covalent targeting that combined with AlphaFold revealed predicted small molecule binding pockets for guiding future inhibitor development of the DGK superfamily.
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Affiliation(s)
- Roberto Mendez
- Department of Chemistry, University of Virginia Charlottesville Virginia 22904 USA +1 434-297-4864
| | - Minhaj Shaikh
- Department of Chemistry, University of Virginia Charlottesville Virginia 22904 USA +1 434-297-4864
| | - Michael C Lemke
- Department of Pharmacology, University of Virginia School of Medicine Charlottesville Virginia 22908 USA
| | - Kun Yuan
- Department of Chemistry, University of Virginia Charlottesville Virginia 22904 USA +1 434-297-4864
| | - Adam H Libby
- Department of Chemistry, University of Virginia Charlottesville Virginia 22904 USA +1 434-297-4864
- University of Virginia Cancer Center, University of Virginia Charlottesville VA 22903 USA
| | - Dina L Bai
- Department of Chemistry, University of Virginia Charlottesville Virginia 22904 USA +1 434-297-4864
| | - Mark M Ross
- Department of Chemistry, University of Virginia Charlottesville Virginia 22904 USA +1 434-297-4864
| | - Thurl E Harris
- Department of Pharmacology, University of Virginia School of Medicine Charlottesville Virginia 22908 USA
| | - Ku-Lung Hsu
- Department of Chemistry, University of Virginia Charlottesville Virginia 22904 USA +1 434-297-4864
- Department of Pharmacology, University of Virginia School of Medicine Charlottesville Virginia 22908 USA
- Department of Molecular Physiology and Biological Physics, University of Virginia Charlottesville Virginia 22908 USA
- University of Virginia Cancer Center, University of Virginia Charlottesville VA 22903 USA
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8
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Overduin M, Kervin TA, Klarenbach Z, Adra TRC, Bhat RK. Comprehensive classification of proteins based on structures that engage lipids by COMPOSEL. Biophys Chem 2023; 295:106971. [PMID: 36801589 DOI: 10.1016/j.bpc.2023.106971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 02/05/2023] [Indexed: 02/11/2023]
Abstract
Structures can now be predicted for any protein using programs like AlphaFold and Rosetta, which rely on a foundation of experimentally determined structures of architecturally diverse proteins. The accuracy of such artificial intelligence and machine learning (AI/ML) approaches benefits from the specification of restraints which assist in navigating the universe of folds to converge on models most representative of a given protein's physiological structure. This is especially pertinent for membrane proteins, with structures and functions that depend on their presence in lipid bilayers. Structures of proteins in their membrane environments could conceivably be predicted from AI/ML approaches with user-specificized parameters that describe each element of the architecture of a membrane protein accompanied by its lipid environment. We propose the Classification Of Membrane Proteins based On Structures Engaging Lipids (COMPOSEL), which builds on existing nomenclature types for monotopic, bitopic, polytopic and peripheral membrane proteins as well as lipids. Functional and regulatory elements are also defined in the scripts, as shown with membrane fusing synaptotagmins, multidomain PDZD8 and Protrudin proteins that recognize phosphoinositide (PI) lipids, the intrinsically disordered MARCKS protein, caveolins, the β barrel assembly machine (BAM), an adhesion G-protein coupled receptor (aGPCR) and two lipid modifying enzymes - diacylglycerol kinase DGKε and fatty aldehyde dehydrogenase FALDH. This demonstrates how COMPOSEL communicates lipid interactivity as well as signaling mechanisms and binding of metabolites, drug molecules, polypeptides or nucleic acids to describe the operations of any protein. Moreover COMPOSEL can be scaled to express how genomes encode membrane structures and how our organs are infiltrated by pathogens such as SARS-CoV-2.
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Affiliation(s)
- Michael Overduin
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada.
| | - Troy A Kervin
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | | | - Trixie Rae C Adra
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Rakesh K Bhat
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
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9
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Overduin M, Tran A, Eekels DM, Overduin F, Kervin TA. Transmembrane Membrane Readers form a Novel Class of Proteins That Include Peripheral Phosphoinositide Recognition Domains and Viral Spikes. MEMBRANES 2022; 12:1161. [PMID: 36422153 PMCID: PMC9692390 DOI: 10.3390/membranes12111161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/11/2022] [Accepted: 11/15/2022] [Indexed: 06/16/2023]
Abstract
Membrane proteins are broadly classified as transmembrane (TM) or peripheral, with functions that pertain to only a single bilayer at a given time. Here, we explicate a class of proteins that contain both transmembrane and peripheral domains, which we dub transmembrane membrane readers (TMMRs). Their transmembrane and peripheral elements anchor them to one bilayer and reversibly attach them to another section of bilayer, respectively, positioning them to tether and fuse membranes while recognizing signals such as phosphoinositides (PIs) and modifying lipid chemistries in proximity to their transmembrane domains. Here, we analyze full-length models from AlphaFold2 and Rosetta, as well as structures from nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography, using the Membrane Optimal Docking Area (MODA) program to map their membrane-binding surfaces. Eukaryotic TMMRs include phospholipid-binding C1, C2, CRAL-TRIO, FYVE, GRAM, GTPase, MATH, PDZ, PH, PX, SMP, StART and WD domains within proteins including protrudin, sorting nexins and synaptotagmins. The spike proteins of SARS-CoV-2 as well as other viruses are also TMMRs, seeing as they are anchored into the viral membrane while mediating fusion with host cell membranes. As such, TMMRs have key roles in cell biology and membrane trafficking, and include drug targets for diseases such as COVID-19.
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Affiliation(s)
- Michael Overduin
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Anh Tran
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | | | - Finn Overduin
- Institute of Nutritional Science, University of Potsdam, 14476 Potsdam, Germany
| | - Troy A. Kervin
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
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10
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Traczyk G, Świątkowska A, Hromada-Judycka A, Janikiewicz J, Kwiatkowska K. An intact zinc finger motif of the C1B domain is critical for stability and activity of diacylglycerol kinase-ε. Int J Biochem Cell Biol 2022; 152:106295. [PMID: 36113832 DOI: 10.1016/j.biocel.2022.106295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/08/2022] [Accepted: 09/08/2022] [Indexed: 10/31/2022]
Abstract
Diacylglycerol kinase-ε (DGKε) phosphorylates DAG to phosphatidic acid with unique specificity toward 18:0/20:4 DAG (SAG). SAG is a typical backbone of phosphatidylinositol and its derivatives, therefore DGKε activity is crucial for the turnover of these signaling lipids. Malfunction of DGKε contributes to several pathophysiological conditions, including atypical hemolytic uremic syndrome (aHUS) linked with DGKE mutations. In the present study we analyzed the role of a zinc finger motif of the C1B domain of DGKε, as some aHUS-linked mutations affect this ill-defined part of the kinase. For this, we introduce a novel fluorescent assay for determination of DGKε activity which relies on the use of NBD-SAG in mixed micelles as a substrate, followed by TLC separation of NBD-phosphatidic acid formed. The assay reliably determines the activity of purified human GST-DGKε, also endogenous DGKε or overexpressed mouse DGKε-Myc in cell lysates, homogenates, and kinase immunoprecipitates. Using the above assay we found that four amino acids, Cys135, Cys138, His161 and Cys164, forming the zinc finger motif in the C1B domain are required for the DGKε-Myc activity and stability. Substitution of any of these amino acids with Ala or Trp in DGKε-Myc abolished its activity and led to its proteasomal degradation, possibly assisted by Hsp70/90/40 chaperones. Inhibition of the 26S proteasome prevented the degradation but the mutated proteins were inactive. The present data on the deleterious effect of the zinc finger motif disruption contribute to the understanding of the DGKε-linked aHUS, as the Cys164Trp substitution in mouse DGKε corresponds to the Cys167Trp one in human DGKε found in some aHUS patients.
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Affiliation(s)
- Gabriela Traczyk
- Laboratory of Molecular Membrane Biology, Nencki Institute of Experimental Biology PAS, 3 Pasteur St., 02-093 Warsaw, Poland.
| | - Anna Świątkowska
- Laboratory of Molecular Membrane Biology, Nencki Institute of Experimental Biology PAS, 3 Pasteur St., 02-093 Warsaw, Poland.
| | - Aneta Hromada-Judycka
- Laboratory of Molecular Membrane Biology, Nencki Institute of Experimental Biology PAS, 3 Pasteur St., 02-093 Warsaw, Poland.
| | - Justyna Janikiewicz
- Laboratory of Cell Signaling and Metabolic Disorders, Nencki Institute of Experimental Biology PAS, 3 Pasteur St., 02-093 Warsaw, Poland.
| | - Katarzyna Kwiatkowska
- Laboratory of Molecular Membrane Biology, Nencki Institute of Experimental Biology PAS, 3 Pasteur St., 02-093 Warsaw, Poland.
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11
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Bozelli JC, Yune J, Aulakh SS, Cao Z, Fernandes A, Seitova A, Tong Y, Schreier S, Epand RM. Human Diacylglycerol Kinase ε N-Terminal Segment Regulates the Phosphatidylinositol Cycle, Controlling the Rate but Not the Acyl Chain Composition of Its Lipid Intermediates. ACS Chem Biol 2022; 17:2495-2506. [PMID: 35767833 DOI: 10.1021/acschembio.2c00387] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Diacylglycerol kinase ε (DGKε), an enzyme of the phosphatidylinositol (PI) cycle, bears a highly conserved hydrophobic N-terminal segment, which was proposed to anchor the enzyme into the membrane. However, the importance of this segment to the DGKε function remains to be determined. To address this question, it is here reported an in silico and in vitro combined research strategy. Capitalizing on the AlphaFold 2.0 predicted structure of human DGKε, it is shown that its hydrophobic N-terminal segment anchors it into the membrane via a transmembrane α-helix. Coarse-grained based elastic network model studies showed that a conformational change in the hydrophobic N-terminal segment determines the proximity between the active site of DGKε and the membrane-water interface, likely regulating its kinase activity. In vitro studies with a purified DGKε construct lacking the hydrophobic N-terminal segment (His-SUMO*-Δ50-DGKε) corroborated the role of the N-terminus in regulating DGKε enzymatic properties. The comparison between the enzymatic properties of DGKε and His-SUMO*-Δ50-DGKε showed that the conserved N-terminal segment markedly inhibits the enzyme activity and its sensitivity to membrane intrinsic negative curvature, while also playing a role in the modulation of the enzyme by phosphatidylserine. On the other hand, this segment did not strongly affect its diacylglycerol acyl chain specificity, the modulation of the enzyme by membrane morphological changes, or the activation by phosphatidic acid-rich lipid domains. Hence, these results suggest that the conservation of the hydrophobic N-terminal segment of DGKε throughout evolution guaranteed not only membrane anchorage but also an efficient and elegant manner to regulate the rate of the PI cycle.
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Affiliation(s)
- José Carlos Bozelli
- Department of Biochemistry and Biomedical Sciences, McMaster University, Health Sciences Centre, Hamilton, ON L8S 3L8, Canada
| | - Jenny Yune
- Department of Biochemistry and Biomedical Sciences, McMaster University, Health Sciences Centre, Hamilton, ON L8S 3L8, Canada
| | - Sukhvershjit S Aulakh
- Department of Biochemistry and Biomedical Sciences, McMaster University, Health Sciences Centre, Hamilton, ON L8S 3L8, Canada
| | - Zihao Cao
- Department of Biochemistry and Biomedical Sciences, McMaster University, Health Sciences Centre, Hamilton, ON L8S 3L8, Canada
| | - Alexia Fernandes
- Department of Biochemistry and Biomedical Sciences, McMaster University, Health Sciences Centre, Hamilton, ON L8S 3L8, Canada
| | - Alma Seitova
- Structural Genomics Consortium, University of Toronto, Toronto, ON N5G 1L7, Canada
| | - Yufeng Tong
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Shirley Schreier
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-000, Brazil
| | - Richard M Epand
- Department of Biochemistry and Biomedical Sciences, McMaster University, Health Sciences Centre, Hamilton, ON L8S 3L8, Canada
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12
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Barneda D, Janardan V, Niewczas I, Collins DM, Cosulich S, Clark J, Stephens LR, Hawkins PT. Acyl chain selection couples the consumption and synthesis of phosphoinositides. EMBO J 2022; 41:e110038. [PMID: 35771169 PMCID: PMC9475507 DOI: 10.15252/embj.2021110038] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 05/11/2022] [Accepted: 05/12/2022] [Indexed: 12/12/2022] Open
Abstract
Phosphoinositides (PIPn) in mammalian tissues are enriched in the stearoyl/arachidonoyl acyl chain species ("C38:4"), but its functional significance is unclear. We have used metabolic tracers (isotopologues of inositol, glucose and water) to study PIPn synthesis in cell lines in which this enrichment is preserved to differing relative extents. We show that PIs synthesised from glucose are initially enriched in shorter/more saturated acyl chains, but then rapidly remodelled towards the C38:4 species. PIs are also synthesised by a distinct 're-cycling pathway', which utilises existing precursors and exhibits substantial selectivity for the synthesis of C38:4-PA and -PI. This re-cycling pathway is rapidly stimulated during receptor activation of phospholipase-C, both allowing the retention of the C38:4 backbone and the close coupling of PIPn consumption to its resynthesis, thus maintaining pool sizes. These results suggest that one property of the specific acyl chain composition of PIPn is that of a molecular code, to facilitate 'metabolic channelling' from PIP2 to PI via pools of intermediates (DG, PA and CDP-DG) common to other lipid metabolic pathways.
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Affiliation(s)
- David Barneda
- Signalling Programme, Babraham Institute, Cambridge, UK.,Projects, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Vishnu Janardan
- Cellular Organization and Signalling, National Centre for Biological Sciences, Bangalore, India
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13
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Aulakh SS, Bozelli JC, Epand RM. Exploring the AlphaFold Predicted Conformational Properties of Human Diacylglycerol Kinases. J Phys Chem B 2022; 126:7172-7183. [PMID: 36041230 DOI: 10.1021/acs.jpcb.2c04533] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Diacylglycerol kinases (DGKs) are important enzymes in molecular membrane biology, as they can lower the concentration of diacylglycerol through phosphorylation while at the same time producing phosphatidic acid. Dysfunction of DGK is linked with multiple diseases including cancer and autoimmune disorders. Currently, the high-resolution structures have not been determined for any of the 10 human DGK paralogs, which has made it difficult to gain a more complete understanding of the enzyme's mechanism of action and regulation. In the present study, we have taken advantage of the significant developments in protein structural prediction technology by artificial intelligence (i.e., Alphafold 2.0), to conduct a comprehensive investigation on the properties of all 10 human DGK paralogs. Structural alignment of the predictions reveals that the C1, catalytic, and accessory domains are conserved in their spatial arrangement relative to each other, across all paralogs. This suggests a critical role played by this domain architecture in DGK function. Moreover, docking studies corroborate the existence of a conserved ATP-binding site between the catalytic and accessory domains. Interestingly, the ATP bound to the interdomain cleft was also found to be in proximity of the conserved glycine-rich motif, which in protein kinases has been suggested to function in ATP binding. Lastly, the spatial arrangement of DGK, with respect to the membrane, reveals that most paralogs possess a more energetically favorable interaction with curved membranes. In conclusion, AlphaFold predictions of human DGKs provide novel insights into the enzyme's structural and functional properties while also paving the way for future experimentation.
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Affiliation(s)
- Sukhvershjit S Aulakh
- Department of Biochemistry and Biomedical Sciences, Health Sciences Centre, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - José Carlos Bozelli
- Department of Biochemistry and Biomedical Sciences, Health Sciences Centre, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Richard M Epand
- Department of Biochemistry and Biomedical Sciences, Health Sciences Centre, McMaster University, Hamilton, ON L8S 4K1, Canada
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14
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Cooke M, Kazanietz MG. Overarching roles of diacylglycerol signaling in cancer development and antitumor immunity. Sci Signal 2022; 15:eabo0264. [PMID: 35412850 DOI: 10.1126/scisignal.abo0264] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Diacylglycerol (DAG) is a lipid second messenger that is generated in response to extracellular stimuli and channels intracellular signals that affect mammalian cell proliferation, survival, and motility. DAG exerts a myriad of biological functions through protein kinase C (PKC) and other effectors, such as protein kinase D (PKD) isozymes and small GTPase-regulating proteins (such as RasGRPs). Imbalances in the fine-tuned homeostasis between DAG generation by phospholipase C (PLC) enzymes and termination by DAG kinases (DGKs), as well as dysregulation in the activity or abundance of DAG effectors, have been widely associated with tumor initiation, progression, and metastasis. DAG is also a key orchestrator of T cell function and thus plays a major role in tumor immunosurveillance. In addition, DAG pathways shape the tumor ecosystem by arbitrating the complex, dynamic interaction between cancer cells and the immune landscape, hence representing powerful modifiers of immune checkpoint and adoptive T cell-directed immunotherapy. Exploiting the wide spectrum of DAG signals from an integrated perspective could underscore meaningful advances in targeted cancer therapy.
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Affiliation(s)
- Mariana Cooke
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Medicine, Einstein Medical Center Philadelphia, Philadelphia, PA 19141, USA
| | - Marcelo G Kazanietz
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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15
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Ma Q, Srinivasan L, Gabelli SB, Raben DM. Elusive structure of mammalian DGKs. Adv Biol Regul 2022; 83:100847. [PMID: 34922895 PMCID: PMC8858910 DOI: 10.1016/j.jbior.2021.100847] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 01/03/2023]
Abstract
Mammalian diacylglycerol kinases (DGKs) are a group of enzymes that catalyze the ATP-dependent phosphorylation of diacylglycerol (DAG) to produce phosphatidic acid (PtdOH). In doing so, they modulate the levels of these two important signaling lipids. Currently, ten mammalian DGKs are organized into five classes that vary with respect to domain organization, regulation, and cellular/subcellular distribution. As lipids play critical roles in cells, it is not surprising that there is increasing interest in understanding the mechanism underlying the catalysis and regulation of lipid modulating enzymes such as DGKs. However, there are no solved 3D structures for any of the eukaryotic DGKs. In this review, we summarize what is known and the current challenges in determining the structures of these important enzymes. In addition to gain critical insights into their mechanisms of catalysis and regulation, DGK structures will provide a platform for the design of isoform specific inhibitors.
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Affiliation(s)
- Qianqian Ma
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore Maryland
| | - Lakshmi Srinivasan
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore Maryland
| | - Sandra B. Gabelli
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore Maryland,Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore Maryland,Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore Maryland,Corresponding author: Sandra B. Gabelli (), Daniel M. Raben ()
| | - Daniel M. Raben
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore Maryland,Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore Maryland,Corresponding author: Sandra B. Gabelli (), Daniel M. Raben ()
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16
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Ware TB, Hsu KL. Advances in chemical proteomic evaluation of lipid kinases-DAG kinases as a case study. Curr Opin Chem Biol 2021; 65:101-108. [PMID: 34311404 PMCID: PMC8671151 DOI: 10.1016/j.cbpa.2021.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/24/2021] [Accepted: 06/18/2021] [Indexed: 10/20/2022]
Abstract
Advancements in chemical proteomics and mass spectrometry lipidomics are providing new opportunities to understand lipid kinase activity, specificity, and regulation on a global cellular scale. Here, we describe recent developments in chemical biology of lipid kinases with a focus on those members that phosphorylate diacylglycerols. We further discuss future implications of how these mass spectrometry-based approaches can be adapted for studies of additional lipid kinase members with the aim of bridging the gap between protein and lipid kinase-focused investigations.
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Affiliation(s)
- Timothy B Ware
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, United States
| | - Ku-Lung Hsu
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, United States; Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA 22908, United States; Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, United States; University of Virginia Cancer Center, University of Virginia, Charlottesville, VA 22903, USA.
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17
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Bustamante A, Rivera R, Floor M, Babul J, Baez M. Single-molecule optical tweezers reveals folding steps of the domain swapping mechanism of a protein. Biophys J 2021; 120:4809-4818. [PMID: 34555362 PMCID: PMC8595740 DOI: 10.1016/j.bpj.2021.09.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 05/15/2021] [Accepted: 09/15/2021] [Indexed: 11/18/2022] Open
Abstract
Domain swapping is a mechanism of protein oligomerization by which two or more subunits exchange structural elements to generate an intertwined complex. Numerous studies support a diversity of swapping mechanisms in which structural elements can be exchanged at different stages of the folding pathway of a subunit. Here, we used single-molecule optical tweezers technique to analyze the swapping mechanism of the forkhead DNA-binding domain of human transcription factor FoxP1. FoxP1 populates folded monomers in equilibrium with a swapped dimer. We generated a fusion protein linking two FoxP1 domains in tandem to obtain repetitive mechanical folding and unfolding trajectories. Thus, by stretching the same molecule several times, we detected either the independent folding of each domain or the elusive swapping step between domains. We found that a swapped dimer can be formed directly from fully or mostly folded monomer. In this situation, the interaction between the monomers in route to the domain-swapped dimer is the rate-limiting step. This approach is a useful strategy to test the different proposed domain swapping mechanisms for proteins with relevant physiological functions.
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Affiliation(s)
- Andres Bustamante
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Rodrigo Rivera
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Martin Floor
- Bioinformatics and Medical Statistics Group, Faculty of Science and Technology, Universitat de Vic - Universitat Central de Catalunya, Vic, Spain; Department of Basic Sciences, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Sant Cugat del Vallès, Spain
| | - Jorge Babul
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Mauricio Baez
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile.
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18
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Sakane F, Hoshino F, Ebina M, Sakai H, Takahashi D. The Roles of Diacylglycerol Kinase α in Cancer Cell Proliferation and Apoptosis. Cancers (Basel) 2021; 13:cancers13205190. [PMID: 34680338 PMCID: PMC8534027 DOI: 10.3390/cancers13205190] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 10/14/2021] [Accepted: 10/14/2021] [Indexed: 02/02/2023] Open
Abstract
Simple Summary Diacylglycerol (DG) kinase (DGK) phosphorylates DG to generate phosphatidic acid (PA). DGKα is highly expressed in several refractory cancer cells, including melanoma, hepatocellular carcinoma, and glioblastoma cells, attenuates apoptosis, and promotes proliferation. In cancer cells, PA produced by DGKα plays an important role in proliferation/antiapoptosis. In addition to cancer cells, DGKα is highly abundant in T cells and induces a nonresponsive state (anergy), representing the main mechanism by which advanced cancers avoid immune action. In T cells, DGKα induces anergy through DG consumption. Therefore, a DGKα-specific inhibitor is expected to be a dual effective anticancer treatment that inhibits cancer cell proliferation and simultaneously activates T cell function. Moreover, the inhibition of DGKα synergistically enhances the anticancer effects of programmed cell death-1/programmed cell death ligand 1 blockade. Taken together, DGKα inhibition provides a promising new treatment strategy for refractory cancers. Abstract Diacylglycerol (DG) kinase (DGK) phosphorylates DG to generate phosphatidic acid (PA). The α isozyme is activated by Ca2+ through its EF-hand motifs and tyrosine phosphorylation. DGKα is highly expressed in several refractory cancer cells including melanoma, hepatocellular carcinoma, and glioblastoma cells. In melanoma cells, DGKα is an antiapoptotic factor that activates nuclear factor-κB (NF-κB) through the atypical protein kinase C (PKC) ζ-mediated phosphorylation of NF-κB. DGKα acts as an enhancer of proliferative activity through the Raf–MEK–ERK pathway and consequently exacerbates hepatocellular carcinoma progression. In glioblastoma and melanoma cells, DGKα attenuates apoptosis by enhancing the phosphodiesterase (PDE)-4A1–mammalian target of the rapamycin pathway. As PA activates PKCζ, Raf, and PDE, it is likely that PA generated by DGKα plays an important role in the proliferation/antiapoptosis of cancer cells. In addition to cancer cells, DGKα is highly abundant in T cells and induces a nonresponsive state (anergy), which represents the main mechanism by which advanced cancers escape immune action. In T cells, DGKα attenuates the activity of Ras-guanyl nucleotide-releasing protein, which is activated by DG and avoids anergy through DG consumption. Therefore, a DGKα-specific inhibitor is expected to be a dual effective anticancer treatment that inhibits cancer cell proliferation and simultaneously enhances T cell functions. Moreover, the inhibition of DGKα synergistically enhances the anticancer effects of programmed cell death-1/programmed cell death ligand 1 blockade. Taken together, DGKα inhibition provides a promising new treatment strategy for refractory cancers.
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Affiliation(s)
- Fumio Sakane
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba 263-8522, Japan; (F.H.); (M.E.)
- Correspondence: ; Tel.: +81-43-290-3695
| | - Fumi Hoshino
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba 263-8522, Japan; (F.H.); (M.E.)
| | - Masayuki Ebina
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba 263-8522, Japan; (F.H.); (M.E.)
| | - Hiromichi Sakai
- Department of Biosignaling and Radioisotope Experiment, Interdisciplinary Center for Science Research, Organization for Research and Academic Information, Shimane University, Izumo 693-8501, Japan;
| | - Daisuke Takahashi
- Department of Pharmaceutical Health Care and Sciences, Kyushu University, Fukuoka 812-8582, Japan;
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19
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Bozelli JC, Yune J, Takahashi D, Sakane F, Epand RM. Membrane morphology determines diacylglycerol kinase α substrate acyl chain specificity. FASEB J 2021; 35:e21602. [PMID: 33977628 DOI: 10.1096/fj.202100264r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/22/2021] [Accepted: 04/01/2021] [Indexed: 01/06/2023]
Abstract
Diacylglycerol kinases catalyze the ATP-dependent phosphorylation of diacylglycerol (DAG) to produce phosphatidic acid (PA). In humans, the alpha isoform (DGKα) has emerged as a potential target in the treatment of cancer due to its anti-tumor and pro-immune responses. However, its mechanism of action at a molecular level is not fully understood. In this work, a systematic investigation of the role played by the membrane in the regulation of the enzymatic properties of human DGKα is presented. By using a cell-free system with purified DGKα and model membranes of variable physical and chemical properties, it is shown that membrane physical properties determine human DGKα substrate acyl chain specificity. In model membranes with a flat morphology; DGKα presents high enzymatic activity, but it is not able to differentiate DAG molecular species. Furthermore, DGKα enzymatic properties are insensitive to membrane intrinsic curvature. However, in the presence of model membranes with altered morphology, specifically the presence of physically curved membrane structures, DGKα bears substrate acyl chain specificity for palmitic acid-containing DAG. The present results identify changes in membrane morphology as one possible mechanism for the depletion of specific pools of DAG as well as the production of specific pools of PA by DGKα, adding an extra layer of regulation on the interconversion of these two potent lipid-signaling molecules. It is proposed that the interplay between membrane physical (shape) and chemical (lipid composition) properties guarantee a fine-tuned signal transduction system dependent on the levels and molecular species of DAG and PA.
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Affiliation(s)
- José Carlos Bozelli
- Department of Biochemistry and Biomedical Sciences, McMaster University, Health Sciences Centre, Hamilton, ON, Canada
| | - Jenny Yune
- Department of Biochemistry and Biomedical Sciences, McMaster University, Health Sciences Centre, Hamilton, ON, Canada
| | - Daisuke Takahashi
- Department of Pharmaceutical Health Care and Sciences, Kyushu University, Fukuoka, Japan
| | - Fumio Sakane
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba, Japan
| | - Richard M Epand
- Department of Biochemistry and Biomedical Sciences, McMaster University, Health Sciences Centre, Hamilton, ON, Canada
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20
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Bozelli JC, Aulakh SS, Epand RM. Membrane shape as determinant of protein properties. Biophys Chem 2021; 273:106587. [PMID: 33865153 DOI: 10.1016/j.bpc.2021.106587] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/26/2021] [Accepted: 03/26/2021] [Indexed: 11/30/2022]
Abstract
Membrane lipids play a role in the modulation of a variety of biological processes. This is often achieved through fine-tuned changes in membrane physical and chemical properties. While some membrane physical properties (e.g., curvature, lipid domains, fluidity) have received increased scientific attention over the years, only recently has membrane shape emerged as an active modulator of protein properties. Biological membranes are mostly found organized into a lipid bilayer arrangement, in which the spontaneous shape is an intrinsically flat, planar morphology (in relation to the size of proteins). However, it is known that many cells and organelles have non-planar morphologies. In addition, perturbations in membrane morphology occur in a variety of biological processes. Recent studies have shown that membrane shape can modulate a variety of biological processes by determining protein properties. While membrane shape generation modulates proteins via changes in membrane mechanical properties, membrane shape recognition regulates proteins by providing the optimal surface for interaction. Hence, membranes have evolved an elegant mechanism to couple mesoscopic perturbations to molecular properties and vice-versa. In this review, the regulation of the enzymatic properties of two isoforms of mammalian diacylglycerol kinase, which play important roles in cellular signal transductions, will be used to exemplify the recent advancements in the field of membrane shape recognition, as well as future challenges and perspectives.
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Affiliation(s)
- José Carlos Bozelli
- Department of Biochemistry and Biomedical Sciences, McMaster University, Health Sciences Centre, Hamilton, Ontario, Canada.
| | - Sukhvershjit S Aulakh
- Department of Biochemistry and Biomedical Sciences, McMaster University, Health Sciences Centre, Hamilton, Ontario, Canada
| | - Richard M Epand
- Department of Biochemistry and Biomedical Sciences, McMaster University, Health Sciences Centre, Hamilton, Ontario, Canada.
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Huang T, Hosseinibarkooie S, Borne AL, Granade ME, Brulet JW, Harris TE, Ferris HA, Hsu KL. Chemoproteomic profiling of kinases in live cells using electrophilic sulfonyl triazole probes. Chem Sci 2021; 12:3295-3307. [PMID: 34164099 PMCID: PMC8179411 DOI: 10.1039/d0sc06623k] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/08/2021] [Indexed: 12/23/2022] Open
Abstract
Sulfonyl-triazoles are a new class of electrophiles that mediate covalent reaction with tyrosine residues on proteins through sulfur-triazole exchange (SuTEx) chemistry. Recent studies demonstrate the broad utility and tunability of SuTEx chemistry for chemical proteomics and protein ligand discovery. Here, we present a strategy for mapping protein interaction networks of structurally complex binding elements using functionalized SuTEx probes. We show that the triazole leaving group (LG) can serve as a releasable linker for embedding hydrophobic fragments to direct molecular recognition while permitting efficient proteome-wide identification of binding sites in live cells. We synthesized a series of SuTEx probes functionalized with a lipid kinase fragment binder for discovery of ligandable tyrosines residing in catalytic and regulatory domains of protein and metabolic kinases in live cells. We performed competition studies with kinase inhibitors and substrates to demonstrate that probe binding is occurring in an activity-dependent manner. Our functional studies led to discovery of probe-modified sites within the C2 domain that were important for downregulation of protein kinase C-alpha in response to phorbol ester activation. Our proof of concept studies highlight the triazole LG of SuTEx probes as a traceless linker for locating protein binding sites targeted by complex recognition elements in live cells.
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Affiliation(s)
- Tao Huang
- Department of Chemistry, University of Virginia McCormick Road, P.O. Box 400319 Charlottesville Virginia 22904 USA +1-434-297-4864
| | | | - Adam L Borne
- Department of Pharmacology, University of Virginia School of Medicine Charlottesville Virginia 22908 USA
| | - Mitchell E Granade
- Department of Pharmacology, University of Virginia School of Medicine Charlottesville Virginia 22908 USA
| | - Jeffrey W Brulet
- Department of Chemistry, University of Virginia McCormick Road, P.O. Box 400319 Charlottesville Virginia 22904 USA +1-434-297-4864
| | - Thurl E Harris
- Department of Pharmacology, University of Virginia School of Medicine Charlottesville Virginia 22908 USA
| | - Heather A Ferris
- Department of Medicine, University of Virginia School of Medicine Charlottesville Virginia 22903 USA
| | - Ku-Lung Hsu
- Department of Chemistry, University of Virginia McCormick Road, P.O. Box 400319 Charlottesville Virginia 22904 USA +1-434-297-4864
- Department of Pharmacology, University of Virginia School of Medicine Charlottesville Virginia 22908 USA
- University of Virginia Cancer Center, University of Virginia Charlottesville VA 22903 USA
- Department of Molecular Physiology and Biological Physics, University of Virginia Charlottesville Virginia 22908 USA
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22
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de Mos J, Jakob A, Becker-Baldus J, Heckel A, Glaubitz C. Light-Induced Uncaging for Time-Resolved Observations of Biochemical Reactions by MAS NMR Spectroscopy. Chemistry 2020; 26:6789-6792. [PMID: 32240561 PMCID: PMC7317521 DOI: 10.1002/chem.202000770] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Indexed: 12/23/2022]
Abstract
Light‐induced activation of biomolecules by uncaging of photolabile protection groups has found many applications for triggering biochemical reactions with minimal perturbations directly within cells. Such an approach might also offer unique advantages for solid‐state NMR experiments on membrane proteins for initiating reactions within or at the membrane directly within the closed MAS rotor. Herein, we demonstrate that the integral membrane protein E. coli diacylglycerol kinase (DgkA), which catalyzes the phosphorylation of diacylglycerol, can be controlled by light under MAS‐NMR conditions. Uncaging of NPE‐ATP or of lipid substrate NPE‐DOG by in situ illumination triggers its enzymatic activity, which can be monitored by real‐time 31P‐MAS NMR. This proof‐of‐concept illustrates that combining MAS‐NMR with uncaging strategies and illumination methods offers new possibilities for controlling biochemical reactions at or within lipid bilayers.
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Affiliation(s)
- Julian de Mos
- Institute for Biophysical Chemistry and Centre for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Andreas Jakob
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt am Main, Germany
| | - Johanna Becker-Baldus
- Institute for Biophysical Chemistry and Centre for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Alexander Heckel
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt am Main, Germany
| | - Clemens Glaubitz
- Institute for Biophysical Chemistry and Centre for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
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23
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Live-cell lipid biochemistry reveals a role of diacylglycerol side-chain composition for cellular lipid dynamics and protein affinities. Proc Natl Acad Sci U S A 2020; 117:7729-7738. [PMID: 32213584 PMCID: PMC7149225 DOI: 10.1073/pnas.1912684117] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Every cell produces thousands of lipid species, but studying the function of individual lipids in living cells is almost impossible with existing methodologies. Addressing this experimental bottleneck, we developed a strategy to quantify dissociation constants for lipid–protein interactions and transmembrane flip-flop rates of native lipids in live-cell experiments. Using a combination of plasma membrane-specific photochemical probes and mathematical modeling, we demonstrate that, for diacylglycerols as a model lipid class, the inherent lipid structural diversity caused by variations in acyl chain composition determines lipid protein affinities and transbilayer kinetics. In fact, subtle chemical differences change these values by orders of magnitude. Our approach represents a generally applicable method for elucidating the biological function of single lipid species on subcellular scales. Every cell produces thousands of distinct lipid species, but insight into how lipid chemical diversity contributes to biological signaling is lacking, particularly because of a scarcity of methods for quantitatively studying lipid function in living cells. Using the example of diacylglycerols, prominent second messengers, we here investigate whether lipid chemical diversity can provide a basis for cellular signal specification. We generated photo-caged lipid probes, which allow acute manipulation of distinct diacylglycerol species in the plasma membrane. Combining uncaging experiments with mathematical modeling, we were able to determine binding constants for diacylglycerol–protein interactions, and kinetic parameters for diacylglycerol transbilayer movement and turnover in quantitative live-cell experiments. Strikingly, we find that affinities and kinetics vary by orders of magnitude due to diacylglycerol side-chain composition. These differences are sufficient to explain differential recruitment of diacylglycerol binding proteins and, thus, differing downstream phosphorylation patterns. Our approach represents a generally applicable method for elucidating the biological function of single lipid species on subcellular scales in quantitative live-cell experiments.
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