1
|
Tsumagari K, Isobe Y, Imami K, Arita M. Exploring protein lipidation by mass spectrometry-based proteomics. J Biochem 2024; 175:225-233. [PMID: 38102731 PMCID: PMC10908362 DOI: 10.1093/jb/mvad109] [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: 06/30/2023] [Revised: 11/13/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023] Open
Abstract
Protein lipidation is a common co- or post-translational modification that plays a crucial role in regulating the localization, interaction and function of cellular proteins. Dysregulation of lipid modifications can lead to various diseases, including cancer, neurodegenerative diseases and infectious diseases. Therefore, the identification of proteins undergoing lipidation and their lipidation sites should provide insights into many aspects of lipid biology, as well as providing potential targets for therapeutic strategies. Bottom-up proteomics using liquid chromatography/tandem mass spectrometry is a powerful technique for the global analysis of protein lipidation. Here, we review proteomic methods for profiling protein lipidation, focusing on the two major approaches: the use of chemical probes, such as lipid alkyne probes, and the use of enrichment techniques for endogenous lipid-modified peptides. The challenges facing these methods and the prospects for developing them further to achieve a comprehensive analysis of lipid modifications are discussed.
Collapse
Affiliation(s)
- Kazuya Tsumagari
- Proteome Homeostasis Research Unit, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yosuke Isobe
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Division of Physiological Chemistry and Metabolism, Graduate School of Pharmaceutical Sciences, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan
- Cellular and Molecular Epigenetics Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Koshi Imami
- Proteome Homeostasis Research Unit, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Makoto Arita
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Division of Physiological Chemistry and Metabolism, Graduate School of Pharmaceutical Sciences, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan
- Cellular and Molecular Epigenetics Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Human Biology-Microbiome-Quantum Research Center (WPI-Bio2Q), Keio University, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| |
Collapse
|
2
|
Ritzefeld M, Zhang L, Xiao Z, Andrei SA, Boyd O, Masumoto N, Rodgers UR, Artelsmair M, Sefer L, Hayes A, Gavriil ES, Raynaud FI, Burke R, Blagg J, Rzepa HS, Siebold C, Magee AI, Lanyon-Hogg T, Tate EW. Design, Synthesis, and Evaluation of Inhibitors of Hedgehog Acyltransferase. J Med Chem 2024; 67:1061-1078. [PMID: 38198226 PMCID: PMC10823475 DOI: 10.1021/acs.jmedchem.3c01363] [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: 07/28/2023] [Revised: 11/08/2023] [Accepted: 12/12/2023] [Indexed: 01/12/2024]
Abstract
Hedgehog signaling is involved in embryonic development and cancer growth. Functional activity of secreted Hedgehog signaling proteins is dependent on N-terminal palmitoylation, making the palmitoyl transferase Hedgehog acyltransferase (HHAT), a potential drug target and a series of 4,5,6,7-tetrahydrothieno[3,2-c]pyridines have been identified as HHAT inhibitors. Based on structural data, we designed and synthesized 37 new analogues which we profiled alongside 13 previously reported analogues in enzymatic and cellular assays. Our results show that a central amide linkage, a secondary amine, and (R)-configuration at the 4-position of the core are three key factors for inhibitory potency. Several potent analogues with low- or sub-μM IC50 against purified HHAT also inhibit Sonic Hedgehog (SHH) palmitoylation in cells and suppress the SHH signaling pathway. This work identifies IMP-1575 as the most potent cell-active chemical probe for HHAT function, alongside an inactive control enantiomer, providing tool compounds for validation of HHAT as a target in cellular assays.
Collapse
Affiliation(s)
- Markus Ritzefeld
- Department
of Chemistry, Imperial College London, London W12 0BZ, U.K.
| | - Leran Zhang
- Department
of Chemistry, Imperial College London, London W12 0BZ, U.K.
| | - Zhangping Xiao
- Department
of Chemistry, Imperial College London, London W12 0BZ, U.K.
| | | | - Olivia Boyd
- Department
of Chemistry, Imperial College London, London W12 0BZ, U.K.
| | - Naoko Masumoto
- Department
of Chemistry, Imperial College London, London W12 0BZ, U.K.
| | - Ursula R. Rodgers
- National
Heart and Lung Institute, Imperial College
London, London SW7 2AZ, U.K.
| | - Markus Artelsmair
- Department
of Chemistry, Imperial College London, London W12 0BZ, U.K.
| | - Lea Sefer
- Division
of Structural Biology, University of Oxford, Oxford OX3 7BN, U.K.
| | - Angela Hayes
- Division
of Cancer Therapeutics, Centre for Cancer Drug Discovery, Institute of Cancer Research, London SM2 5NG, U.K.
| | | | - Florence I. Raynaud
- Division
of Cancer Therapeutics, Centre for Cancer Drug Discovery, Institute of Cancer Research, London SM2 5NG, U.K.
| | - Rosemary Burke
- Division
of Cancer Therapeutics, Centre for Cancer Drug Discovery, Institute of Cancer Research, London SM2 5NG, U.K.
| | - Julian Blagg
- Division
of Cancer Therapeutics, Centre for Cancer Drug Discovery, Institute of Cancer Research, London SM2 5NG, U.K.
| | - Henry S. Rzepa
- Department
of Chemistry, Imperial College London, London W12 0BZ, U.K.
| | - Christian Siebold
- Division
of Structural Biology, University of Oxford, Oxford OX3 7BN, U.K.
| | - Anthony I. Magee
- National
Heart and Lung Institute, Imperial College
London, London SW7 2AZ, U.K.
| | | | - Edward W. Tate
- Department
of Chemistry, Imperial College London, London W12 0BZ, U.K.
| |
Collapse
|
3
|
Bae J, Zhang G, Park H, Warren WS, Wang Q. 15N-Azides as practical and effective tags for developing long-lived hyperpolarized agents. Chem Sci 2021; 12:14309-14315. [PMID: 34760217 DOI: 10.1039/d1sc04647k] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 10/08/2021] [Indexed: 01/24/2023] Open
Abstract
Azide moieties, unique linear species containing three nitrogen atoms, represent an attractive class of molecular tag for hyperpolarized magnetic resonance imaging (HP-MRI). Here we demonstrate (15N)3-azide-containing molecules exhibit long-lasting hyperpolarization lifetimes up to 9.8 min at 1 T with remarkably high polarization levels up to 11.6% in water, thus establishing (15N)3-azide as a powerful spin storage for hyperpolarization. A single (15N)-labeled azide has also been examined as an effective alternative tag with long-lived hyperpolarization. A variety of biologically important molecules are studied in this work, including choline, glucose, amino acid, and drug derivatives, demonstrating great potential of 15N-labeled azides as universal hyperpolarized tags for nuclear magnetic resonance imaging applications.
Collapse
Affiliation(s)
- Junu Bae
- Department of Chemistry, Duke University Durham North Carolina 27708 USA
| | - Guannan Zhang
- Department of Chemistry, Duke University Durham North Carolina 27708 USA
| | - Hyejin Park
- Department of Chemistry, Duke University Durham North Carolina 27708 USA
| | - Warren S Warren
- Department of Chemistry, Duke University Durham North Carolina 27708 USA .,Department of Physics, Duke University Durham North Carolina 27708 USA.,Department of Radiology and Biomedical Engineering, Duke University Durham North Carolina 27708 USA
| | - Qiu Wang
- Department of Chemistry, Duke University Durham North Carolina 27708 USA
| |
Collapse
|
4
|
Suazo KF, Park KY, Distefano MD. A Not-So-Ancient Grease History: Click Chemistry and Protein Lipid Modifications. Chem Rev 2021; 121:7178-7248. [PMID: 33821625 DOI: 10.1021/acs.chemrev.0c01108] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein lipid modification involves the attachment of hydrophobic groups to proteins via ester, thioester, amide, or thioether linkages. In this review, the specific click chemical reactions that have been employed to study protein lipid modification and their use for specific labeling applications are first described. This is followed by an introduction to the different types of protein lipid modifications that occur in biology. Next, the roles of click chemistry in elucidating specific biological features including the identification of lipid-modified proteins, studies of their regulation, and their role in diseases are presented. A description of the use of protein-lipid modifying enzymes for specific labeling applications including protein immobilization, fluorescent labeling, nanostructure assembly, and the construction of protein-drug conjugates is presented next. Concluding remarks and future directions are presented in the final section.
Collapse
Affiliation(s)
- Kiall F Suazo
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Keun-Young Park
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Mark D Distefano
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| |
Collapse
|
5
|
Zhao T, Liu J, Zeng X, Wang W, Li S, Zang T, Peng J, Yang Y. Prediction and collection of protein-metabolite interactions. Brief Bioinform 2021; 22:6130169. [PMID: 33554247 DOI: 10.1093/bib/bbab014] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 01/01/2021] [Accepted: 01/10/2021] [Indexed: 11/14/2022] Open
Abstract
Interactions between proteins and small molecule metabolites play vital roles in regulating protein functions and controlling various cellular processes. The activities of metabolic enzymes, transcription factors, transporters and membrane receptors can all be mediated through protein-metabolite interactions (PMIs). Compared with the rich knowledge of protein-protein interactions, little is known about PMIs. To the best of our knowledge, no existing database has been developed for collecting PMIs. The recent rapid development of large-scale mass spectrometry analysis of biomolecules has led to the discovery of large amounts of PMIs. Therefore, we developed the PMI-DB to provide a comprehensive and accurate resource of PMIs. A total of 49 785 entries were manually collected in the PMI-DB, corresponding to 23 small molecule metabolites, 9631 proteins and 4 species. Unlike other databases that only provide positive samples, the PMI-DB provides non-interaction between proteins and metabolites, which not only reduces the experimental cost for biological experimenters but also facilitates the construction of more accurate algorithms for researchers using machine learning. To show the convenience of the PMI-DB, we developed a deep learning-based method to predict PMIs in the PMI-DB and compared it with several methods. The experimental results show that the area under the curve and area under the precision-recall curve of our method are 0.88 and 0.95, respectively. Overall, the PMI-DB provides a user-friendly interface for browsing the biological functions of metabolites/proteins of interest, and experimental techniques for identifying PMIs in different species, which provides important support for furthering the understanding of cellular processes. The PMI-DB is freely accessible at http://easybioai.com/PMIDB.
Collapse
Affiliation(s)
- Tianyi Zhao
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Inner Mongolia, 010010, China.,Department of Computer Science, Harbin Institute of Technology, Harbin, 150001, China
| | - Jinxin Liu
- Department of Computer Science, Harbin Institute of Technology, Harbin, 150001, China
| | - Xi Zeng
- School of Computer Science, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Wei Wang
- School of Computer Science, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Sheng Li
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, 430000, China
| | - Tianyi Zang
- Department of Computer Science, Harbin Institute of Technology, Harbin, 150001, China
| | - Jiajie Peng
- School of Computer Science, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Yang Yang
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Inner Mongolia, 010010, China
| |
Collapse
|
6
|
Zhu Y, Willems LI, Salas D, Cecioni S, Wu WB, Foster LJ, Vocadlo DJ. Tandem Bioorthogonal Labeling Uncovers Endogenous Cotranslationally O-GlcNAc Modified Nascent Proteins. J Am Chem Soc 2020; 142:15729-15739. [PMID: 32870666 DOI: 10.1021/jacs.0c04121] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Hundreds of nuclear, cytoplasmic, and mitochondrial proteins within multicellular eukaryotes have hydroxyl groups of specific serine and threonine residues modified by the monosaccharide N-acetylglucosamine (GlcNAc). This modification, known as O-GlcNAc, has emerged as a central regulator of both cell physiology and human health. A key emerging function of O-GlcNAc appears to be to regulate cellular protein homeostasis. We previously showed, using overexpressed model proteins, that O-GlcNAc modification can occur cotranslationally and that this process prevents premature degradation of such nascent polypeptide chains. Here, we use tandem metabolic engineering strategies to label endogenously occurring nascent polypeptide chains within cells using O-propargyl-puromycin (OPP) and target the specific subset of nascent chains that are cotranslationally glycosylated with O-GlcNAc by metabolic saccharide engineering using tetra-O-acetyl-2-N-azidoacetyl-2-deoxy-d-galactopyranose (Ac4GalNAz). Using various combinations of sequential chemoselective ligation strategies, we go on to tag these analytes with a series of labels, allowing us to define conditions that enable their robust labeling. Two-step enrichment of these glycosylated nascent chains, combined with shotgun proteomics, allows us to identify a set of endogenous cotranslationally O-GlcNAc modified proteins. Using alternative targeted methods, we examine three of these identified proteins and further validate their cotranslational O-GlcNAcylation. These findings detail strategies to enable isolation and identification of extremely low abundance endogenous analytes present within complex protein mixtures. Moreover, this work opens the way to studies directed at understanding the roles of O-GlcNAc and other cotranslational protein modifications and should stimulate an improved understanding of the role of O-GlcNAc in cytoplasmic protein quality control and proteostasis.
Collapse
Affiliation(s)
- Yanping Zhu
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Lianne I Willems
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Daniela Salas
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.,Michael Smith Laboratories and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia Canada
| | - Samy Cecioni
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Weifeng B Wu
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Leonard J Foster
- Michael Smith Laboratories and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia Canada
| | - David J Vocadlo
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| |
Collapse
|
7
|
Ward JA, Pinto-Fernandez A, Cornelissen L, Bonham S, Díaz-Sáez L, Riant O, Huber KVM, Kessler BM, Feron O, Tate EW. Re-Evaluating the Mechanism of Action of α,β-Unsaturated Carbonyl DUB Inhibitors b-AP15 and VLX1570: A Paradigmatic Example of Unspecific Protein Cross-linking with Michael Acceptor Motif-Containing Drugs. J Med Chem 2020; 63:3756-3762. [PMID: 32109059 PMCID: PMC7152998 DOI: 10.1021/acs.jmedchem.0c00144] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
Deubiquitinating
enzymes (DUBs) are a growing target class across
multiple disease states, with several inhibitors now reported. b-AP15
and VLX1570 are two structurally related USP14/UCH-37 inhibitors.
Through a proteomic approach, we demonstrate that these compounds
target a diverse range of proteins, resulting in the formation of
higher molecular weight (MW) complexes. Activity-based proteome profiling
identified CIAPIN1 as a submicromolar covalent target of VLX1570,
and further analysis demonstrated that high MW complex formation leads
to aggregation of CIAPIN1 in intact cells. Our results suggest that
in addition to DUB inhibition, these compounds induce nonspecific
protein aggregation, providing molecular explanation for general cellular
toxicity.
Collapse
Affiliation(s)
- Jennifer A Ward
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, U.K.,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, U.K.,Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, London W12 0BZ, U.K
| | - Adan Pinto-Fernandez
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, U.K.,Pole of Pharmacology and Therapeutics (FATH), Institut de Recherche Expérimentale et Clinique (IREC), UCLouvain, 57 Avenue Hippocrate B1.57.04, Brussels B-1200, Belgium
| | - Loïc Cornelissen
- Institute of Condensed Matter and Nanosciences, MOST Division, Place Louis Pasteur, UCLouvain, Louvain-la-Neuve B-1348, Belgium
| | - Sarah Bonham
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, U.K
| | - Laura Díaz-Sáez
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, U.K.,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, U.K
| | - Olivier Riant
- Institute of Condensed Matter and Nanosciences, MOST Division, Place Louis Pasteur, UCLouvain, Louvain-la-Neuve B-1348, Belgium
| | - Kilian V M Huber
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, U.K.,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, U.K
| | - Benedikt M Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, U.K
| | - Olivier Feron
- Pole of Pharmacology and Therapeutics (FATH), Institut de Recherche Expérimentale et Clinique (IREC), UCLouvain, 57 Avenue Hippocrate B1.57.04, Brussels B-1200, Belgium
| | - Edward W Tate
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, London W12 0BZ, U.K
| |
Collapse
|
8
|
Li Y, Lou Z, Li H, Yang H, Zhao Y, Fu H. Bioorthogonal Ligation and Cleavage by Reactions of Chloroquinoxalines with
ortho
‐Dithiophenols. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201913620] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Youshan Li
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education)Department of ChemistryTsinghua University Beijing 100084 China
| | - Zhenbang Lou
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education)Department of ChemistryTsinghua University Beijing 100084 China
| | - Hongyun Li
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education)Department of ChemistryTsinghua University Beijing 100084 China
| | - Haijun Yang
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education)Department of ChemistryTsinghua University Beijing 100084 China
| | - Yufen Zhao
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education)Department of ChemistryTsinghua University Beijing 100084 China
| | - Hua Fu
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education)Department of ChemistryTsinghua University Beijing 100084 China
| |
Collapse
|
9
|
Bioorthogonal Ligation and Cleavage by Reactions of Chloroquinoxalines with
ortho
‐Dithiophenols. Angew Chem Int Ed Engl 2020; 59:3671-3677. [DOI: 10.1002/anie.201913620] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 12/04/2019] [Indexed: 01/10/2023]
|
10
|
Faletrov YV, Efimova VS, Horetski MS, Tugaeva KV, Frolova NS, Lin Q, Isaeva LV, Rubtsov MA, Sluchanko NN, Novikova LA, Shkumatov VM. New 20-hydroxycholesterol-like compounds with fluorescent NBD or alkyne labels: Synthesis, in silico interactions with proteins and uptake by yeast cells. Chem Phys Lipids 2019; 227:104850. [PMID: 31836520 DOI: 10.1016/j.chemphyslip.2019.104850] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 12/03/2019] [Accepted: 12/04/2019] [Indexed: 01/07/2023]
Abstract
20-hydroxycholesterol is a signaling oxysterol with immunomodulating functions and, thus, structural analogues with reporter capabilities could be useful for studying and modulating the cellular processes concerned. We have synthesized three new 20-hydroxycholesterol-like pregn-5-en-3β-ol derivatives with fluorescent 7-nitrobenzofurazan (NBD) or Raman-sensitive alkyne labels in their side-chains. In silico computations demonstrated the compounds possess good membrane permeability and can bind within active sites of known 20-hydroxycholesterol targets (e.g. Smoothened and yeast Osh4) and some other sterol-binding proteins (human LXRβ and STARD1; yeast START-kins Lam4S2 and Lam2S2). Having found good predicted membrane permeability and binding to some yeast proteins, we tested the compounds on microorganisms. Fluorescent microscopy indicated the uptake of the steroids by both Saccharomyces cerevisiae and Yarrowia lipolytica, whereas only S. cerevisiae demonstrated conversion of the compounds into 3-O-acetates, likely because 3-O-acetyltransferase Atf2p is present only in its genome. The new compounds provide new options to study the uptake, intracellular distribution and metabolism of sterols in yeast cells as well as might be used as ligands for sterol-binding proteins.
Collapse
Affiliation(s)
- Yaroslav V Faletrov
- Research Institute for Physical Chemical Problems, Belarusian State University, Leningradskaya str. 14, Minsk, Belarus; Faculty of Chemistry, Belarusian State University, Leningradskaya str. 14, Minsk, Belarus
| | - Vera S Efimova
- Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, 1/40, 119234 Moscow, Russia; Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, 1/12, 119234 Moscow, Russia
| | - Matvey S Horetski
- Research Institute for Physical Chemical Problems, Belarusian State University, Leningradskaya str. 14, Minsk, Belarus; Faculty of Chemistry, Belarusian State University, Leningradskaya str. 14, Minsk, Belarus
| | - Kristina V Tugaeva
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Pr. 33, Moscow, 119071, Russia; Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, 1/12, 119234 Moscow, Russia
| | - Nina S Frolova
- Research Institute for Physical Chemical Problems, Belarusian State University, Leningradskaya str. 14, Minsk, Belarus
| | - Quingquing Lin
- Faculty of Chemistry, Belarusian State University, Leningradskaya str. 14, Minsk, Belarus
| | - Ludmila V Isaeva
- Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, 1/40, 119234 Moscow, Russia
| | - Mikhail A Rubtsov
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, 1/12, 119234 Moscow, Russia; Sechenov First Moscow State Medical University (Sechenov University), Moscow, 119991, Russia; Lomonosov Moscow State University, Laboratoire Franco-Russe de Recherches en Oncologie, Moscow, 119234, Russia
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Pr. 33, Moscow, 119071, Russia; Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, 1/12, 119234 Moscow, Russia
| | - Ludmila A Novikova
- Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, 1/40, 119234 Moscow, Russia
| | - Vladimir M Shkumatov
- Research Institute for Physical Chemical Problems, Belarusian State University, Leningradskaya str. 14, Minsk, Belarus; Faculty of Chemistry, Belarusian State University, Leningradskaya str. 14, Minsk, Belarus.
| |
Collapse
|
11
|
Zhang X, Xu Z, Moumin DS, Ciulla DA, Owen TS, Mancusi RA, Giner JL, Wang C, Callahan BP. Protein-Nucleic Acid Conjugation with Sterol Linkers Using Hedgehog Autoprocessing. Bioconjug Chem 2019; 30:2799-2804. [PMID: 31600061 PMCID: PMC7045895 DOI: 10.1021/acs.bioconjchem.9b00550] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Hedgehog (Hh) precursor proteins contain an autoprocessing domain called HhC whose native function is protein cleavage and C-terminal glycine sterylation. The transformation catalyzed by HhC occurs in cis from a precursor protein and exhibits wide tolerance toward both sterol and protein substrates. Here, we repurpose HhC as a 1:1 protein-nucleic acid ligase, with the sterol serving as a molecular linker. A procedure is described for preparing HhC-active sterylated DNA, called steramers, using aqueous compatible chemistry and commercial reagents. Steramers have KM values of 7-11 μM and reaction t1/2 values of ∼10 min. Modularity of the HhC/steramer method is demonstrated using four different proteins along with structured and unstructured sterylated nucleic acids. The resulting protein-DNA conjugates retain the native solution properties and biochemical function. Unlike self-tagging domains, HhC does not remain fused to the conjugate; rather, enzymatic activity is mechanistically coupled to conjugate release. That unique feature of HhC, coupled with efficient kinetics and substrate tolerance, may ease access and open new applications for these suprabiological chimeras.
Collapse
Affiliation(s)
- Xiaoyu Zhang
- Chemistry Department, Binghamton University, Binghamton, New York 13902, United States
| | - Zihan Xu
- Chemistry Department, Binghamton University, Binghamton, New York 13902, United States
| | - Dina S. Moumin
- Chemistry Department, Binghamton University, Binghamton, New York 13902, United States
| | - Daniel A. Ciulla
- Chemistry Department, Binghamton University, Binghamton, New York 13902, United States
| | - Timothy S. Owen
- Chemistry Department, Binghamton University, Binghamton, New York 13902, United States
| | - Rebecca A. Mancusi
- Chemistry Department, Binghamton University, Binghamton, New York 13902, United States
| | - José-Luis Giner
- Department of Chemistry, State University of New York - ESF, Syracuse, New York 13210, United States
| | - Chunyu Wang
- Biology Department, Rensselaer Polytechnic Institute, 110 8th Street, Troy, New York 12180, United States
| | - Brian P. Callahan
- Chemistry Department, Binghamton University, Binghamton, New York 13902, United States
| |
Collapse
|
12
|
Poocza L, Cipriani F, Alonso M, Rodríguez-Cabello JC. Hydrophobic Cholesteryl Moieties Trigger Substrate Cell-Membrane Interaction of Elastin-Mimetic Protein Coatings in Vitro. ACS OMEGA 2019; 4:10818-10827. [PMID: 31460179 PMCID: PMC6648790 DOI: 10.1021/acsomega.9b00548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 05/15/2019] [Indexed: 06/10/2023]
Abstract
A cellular coating based on hydrophobic interactions of an elastin-like recombinamer (ELR) with the cell membrane is presented. It is well-documented that biophysical properties such as net charge, hydrophobicity, and protein-driven cell-ligand (integrin binding) interactions influence the interaction of polymers, proteins or peptides with model membranes and biological cells. Most studies to enhance membrane-substrate interactions have focused on the introduction of positively charged groups to foster electrostatic interactions with the negatively charged membrane. Herein, we present an antagonistic approach based on ELRs with varying amounts of hydrophobic cholesteryl groups (ELRCTAs). The ability of the membranes to stabilize cholesteryl groups is hypothesized to assist the coordination of hydrophobic ELRs with the membrane. The main objective was to generate a defined cellular coating of a recombinant protein that allows for total sequence control and less host, or batch-to-batch, variation as a substitute for the existing coatings like alginate, polyelectrolytes, collagens, and fibronectin. We used an in vitro cell-binding assay to quantify cell-substrate interactions, showing enhanced cellular recognition and matrix distribution with an increasing number of cholesteryl groups incorporated. These novel materials and the versatile nature of their protein sequence have great potential as cellular markers, drug carriers, or hydrophobic cell-binding domains.
Collapse
Affiliation(s)
- Leander Poocza
- Bioforge, University of Valladolid CIBER-BNN, Paseo de Belén 19, 47011 Valladolid, Spain
| | - Filippo Cipriani
- Technical
Proteins Nanobiotechnology S.L., Paseo de Belén 9A, 47011 Valladolid, Spain
| | - Matilde Alonso
- Bioforge, University of Valladolid CIBER-BNN, Paseo de Belén 19, 47011 Valladolid, Spain
| | | |
Collapse
|
13
|
Kallemeijn WW, Lueg GA, Faronato M, Hadavizadeh K, Goya Grocin A, Song OR, Howell M, Calado DP, Tate EW. Validation and Invalidation of Chemical Probes for the Human N-myristoyltransferases. Cell Chem Biol 2019; 26:892-900.e4. [PMID: 31006618 PMCID: PMC6593224 DOI: 10.1016/j.chembiol.2019.03.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 02/20/2019] [Accepted: 03/06/2019] [Indexed: 12/15/2022]
Abstract
On-target, cell-active chemical probes are of fundamental importance in chemical and cell biology, whereas poorly characterized probes often lead to invalid conclusions. Human N-myristoyltransferase (NMT) has attracted increasing interest as target in cancer and infectious diseases. Here we report an in-depth comparison of five compounds widely applied as human NMT inhibitors, using a combination of quantitative whole-proteome N-myristoylation profiling, biochemical enzyme assays, cytotoxicity, in-cell protein synthesis, and cell-cycle assays. We find that N-myristoylation is unaffected by 2-hydroxymyristic acid (100 μM), D-NMAPPD (30 μM), or Tris-DBA palladium (10 μM), with the latter compounds causing cytotoxicity through mechanisms unrelated to NMT. In contrast, drug-like inhibitors IMP-366 (DDD85646) and IMP-1088 delivered complete and specific inhibition of N-myristoylation in a range of cell lines at 1 μM and 100 nM, respectively. This study enables the selection of appropriate on-target probes for future studies and suggests the need for reassessment of previous studies that used off-target compounds.
Collapse
Affiliation(s)
- Wouter W Kallemeijn
- Department of Chemistry, Imperial College London, Molecular Research Science Hub, 80 Wood Lane, London W12 0BZ, UK
| | - Gregor A Lueg
- Department of Chemistry, Imperial College London, Molecular Research Science Hub, 80 Wood Lane, London W12 0BZ, UK; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Monica Faronato
- Department of Chemistry, Imperial College London, Molecular Research Science Hub, 80 Wood Lane, London W12 0BZ, UK; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Kate Hadavizadeh
- Department of Chemistry, Imperial College London, Molecular Research Science Hub, 80 Wood Lane, London W12 0BZ, UK
| | - Andrea Goya Grocin
- Department of Chemistry, Imperial College London, Molecular Research Science Hub, 80 Wood Lane, London W12 0BZ, UK
| | - Ok-Ryul Song
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Michael Howell
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Dinis P Calado
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, King's College London, London SE1 9RT, UK
| | - Edward W Tate
- Department of Chemistry, Imperial College London, Molecular Research Science Hub, 80 Wood Lane, London W12 0BZ, UK; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
| |
Collapse
|
14
|
Tapodi A, Clemens DM, Uwineza A, Jarrin M, Goldberg MW, Thinon E, Heal WP, Tate EW, Nemeth-Cahalan K, Vorontsova I, Hall JE, Quinlan RA. BFSP1 C-terminal domains released by post-translational processing events can alter significantly the calcium regulation of AQP0 water permeability. Exp Eye Res 2019; 185:107585. [PMID: 30790544 PMCID: PMC6713518 DOI: 10.1016/j.exer.2019.02.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 01/26/2019] [Accepted: 02/03/2019] [Indexed: 01/20/2023]
Abstract
BFSP1 (beaded filament structural protein 1, filensin) is a cytoskeletal protein expressed in the eye lens. It binds AQP0 in vitro and its C-terminal sequences have been suggested to regulate the water channel activity of AQP0. A myristoylated fragment from the C-terminus of BFSP1 was found in AQP0 enriched fractions. Here we identify BFSP1 as a substrate for caspase-mediated cleavage at several C-terminal sites including D433. Cleavage at D433 exposes a cryptic myristoylation sequence (434–440). We confirm that this sequence is an excellent substrate for both NMT1 and 2 (N-myristoyl transferase). Thus caspase cleavage may promote formation of myristoylated fragments derived from the BFSP1 C-terminus (G434-S665). Myristoylation at G434 is not required for membrane association. Biochemical fractionation and immunogold labeling confirmed that C-terminal BFSP1 fragments containing the myristoylation sequence colocalized with AQP0 in the same plasma membrane compartments of lens fibre cells. To determine the functional significance of the association of BFSP1 G434-S665 sequences with AQP0, we measured AQP0 water permeability in Xenopus oocytes co-transfected with transcripts expressing both AQP0 and various C-terminal domain fragments of BFSP1 generated by caspase cleavage. We found that different fragments dramatically alter the response of AQP0 to different concentrations of Ca2+. The complete C-terminal fragment (G434-S665) eliminates calcium regulation altogether. Shorter fragments can enhance regulation by elevated calcium or reverse the response, indicative of the regulatory potential of BFSP1 with respect to AQP0. In particular, elimination of the myristoylation site by the mutation G434A reverses the order of water permeability sensitivity to different Ca2+ concentrations.
Collapse
Affiliation(s)
- Antal Tapodi
- Department of Biosciences, The University of Durham, South Road, Durham, DH1 3LE, UK
| | | | - Alice Uwineza
- Department of Biosciences, The University of Durham, South Road, Durham, DH1 3LE, UK
| | - Miguel Jarrin
- Department of Biosciences, The University of Durham, South Road, Durham, DH1 3LE, UK
| | - Martin W Goldberg
- Department of Biosciences, The University of Durham, South Road, Durham, DH1 3LE, UK
| | - Emmanuelle Thinon
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, Wood Lane, London, W12 0BZ, UK; Institute of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, Wood Lane, London, W12 0BZ, UK
| | - William P Heal
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, Wood Lane, London, W12 0BZ, UK; Institute of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, Wood Lane, London, W12 0BZ, UK
| | - Edward W Tate
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, Wood Lane, London, W12 0BZ, UK; Institute of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, Wood Lane, London, W12 0BZ, UK
| | | | | | - James E Hall
- Physiology and Biophysics, UC Irvine, Irvine, CA, USA.
| | - Roy A Quinlan
- Department of Biosciences, The University of Durham, South Road, Durham, DH1 3LE, UK; Biophysical Sciences Institute, The University of Durham, South Road, Durham, DH1 3LE, UK.
| |
Collapse
|
15
|
The Cellular Senescence-Inhibited Gene Is Essential for PPM1A Myristoylation To Modulate Transforming Growth Factor β Signaling. Mol Cell Biol 2018; 38:MCB.00414-18. [PMID: 30201805 DOI: 10.1128/mcb.00414-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 09/05/2018] [Indexed: 12/16/2022] Open
Abstract
The cellular senescence-inhibited gene (CSIG) is implicated in important biological processes, including cellular senescence and apoptosis. Our work showed that CSIG is involved in the myristoylation of the serine/threonine protein phosphatase PPM1A. Previous research has shown that myristoylation is necessary for PPM1A to dephosphorylate Smad2 and Smad3. However, the control and the biological significance of the myristoylation remain poorly understood. In this study, we found that CSIG knockdown disturbs PPM1A myristoylation and reduces the dephosphorylation by PPM1A of its substrate Smad2. By regulating PPM1A myristoylation, CSIG is involved in modulating the signaling of transforming growth factor β (TGF-β). Further study of the mechanism indicated that CSIG facilitates the interaction between N-myristoyltransferase 1 (NMT1) and PPM1A. Taking the data together, we found that CSIG is a regulator of PPM1A myristoylation and TGF-β signaling. By promoting the myristoylation of PPM1A, CSIG enhanced the phosphatase activity of PPM1A and further inhibited TGF-β signaling. This work not only extends the biological significance of CSIG but also provides new ideas and a reference for the study of the regulatory mechanism of myristoylation.
Collapse
|
16
|
El-Zaatari BM, Cole SM, Bischoff DJ, Kloxin CJ. Copper Ligand and Anion Effects: Controlling the Kinetics of the Photoinitiated Copper(I) Catalyzed Azide-Alkyne Cycloaddition Polymerization. Polym Chem 2018; 9:4772-4780. [PMID: 31031838 PMCID: PMC6483394 DOI: 10.1039/c8py01004h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The kinetics of photoinduced copper(I) catalyzed azide-alkyne cycloaddition (CuAAC) polymerizations were assessed as a function of copper(II) amine-based ligands. Copper(II) bromide ligated with 1,1,4,7,10,10-hexamethylenetetramine (HMTETA) exhibited the fastest kinetics in both Norrish type(I) and type(II) photoinitiating systems. A characteristic induction period is observed with these polymerizations and is manipulated by adding an external tertiary amine in Norrish Type(II) photoinitating systems or by changing the anion of the copper(II) salt. Halides, specifically bromide and chloride, exhibit the fastest kinetics with the smallest induction period in comparison with organic anions, such as bistriflimide and triflate. The temporal control of the photo-CuAAC polymerization is affected by pre-ligation of the copper catalyst, by the presence of certain anions such as acetate, and by specific ligands such as tetramethylethylenediamine (TMEDA).
Collapse
Affiliation(s)
- Bassil M. El-Zaatari
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, DE 19716, USA
| | - Shea M. Cole
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, DE 19716, USA
| | - Derek J. Bischoff
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, DE 19716, USA
| | - Christopher J. Kloxin
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, DE 19716, USA
- Department of Materials Science and Engineering, University of Delaware, 201 DuPont Hall, Newark, DE 19716, USA
| |
Collapse
|
17
|
Akgun B, Hall DG. Boronic Acids as Bioorthogonal Probes for Site‐Selective Labeling of Proteins. Angew Chem Int Ed Engl 2018; 57:13028-13044. [DOI: 10.1002/anie.201712611] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 04/23/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Burcin Akgun
- Department of Chemistry—CCIS 4–010University of Alberta Edmonton Alberta T6G 2G2 Canada
| | - Dennis G. Hall
- Department of Chemistry—CCIS 4–010University of Alberta Edmonton Alberta T6G 2G2 Canada
| |
Collapse
|
18
|
Akgun B, Hall DG. Boronsäuren als bioorthogonale Sonden für zentrenselektives Protein‐Labeling. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201712611] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Burcin Akgun
- Department of Chemistry – CCIS 4-010University of Alberta Edmonton Alberta T6G 2G2 Kanada
| | - Dennis G. Hall
- Department of Chemistry – CCIS 4-010University of Alberta Edmonton Alberta T6G 2G2 Kanada
| |
Collapse
|
19
|
Chen B, Sun Y, Niu J, Jarugumilli GK, Wu X. Protein Lipidation in Cell Signaling and Diseases: Function, Regulation, and Therapeutic Opportunities. Cell Chem Biol 2018; 25:817-831. [PMID: 29861273 PMCID: PMC6054547 DOI: 10.1016/j.chembiol.2018.05.003] [Citation(s) in RCA: 156] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 10/06/2017] [Accepted: 05/01/2018] [Indexed: 01/08/2023]
Abstract
Protein lipidation is an important co- or posttranslational modification in which lipid moieties are covalently attached to proteins. Lipidation markedly increases the hydrophobicity of proteins, resulting in changes to their conformation, stability, membrane association, localization, trafficking, and binding affinity to their co-factors. Various lipids and lipid metabolites serve as protein lipidation moieties. The intracellular concentrations of these lipids and their derivatives are tightly regulated by cellular metabolism. Therefore, protein lipidation links the output of cellular metabolism to the regulation of protein function. Importantly, deregulation of protein lipidation has been linked to various diseases, including neurological disorders, metabolic diseases, and cancers. In this review, we highlight recent progress in our understanding of protein lipidation, in particular, S-palmitoylation and lysine fatty acylation, and we describe the importance of these modifications for protein regulation, cell signaling, and diseases. We further highlight opportunities and new strategies for targeting protein lipidation for therapeutic applications.
Collapse
Affiliation(s)
- Baoen Chen
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, 149, 13th St., Charlestown, MA 02129, USA
| | - Yang Sun
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, 149, 13th St., Charlestown, MA 02129, USA
| | - Jixiao Niu
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, 149, 13th St., Charlestown, MA 02129, USA
| | - Gopala K Jarugumilli
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, 149, 13th St., Charlestown, MA 02129, USA
| | - Xu Wu
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, 149, 13th St., Charlestown, MA 02129, USA.
| |
Collapse
|
20
|
Jiang H, Zhang X, Chen X, Aramsangtienchai P, Tong Z, Lin H. Protein Lipidation: Occurrence, Mechanisms, Biological Functions, and Enabling Technologies. Chem Rev 2018; 118:919-988. [PMID: 29292991 DOI: 10.1021/acs.chemrev.6b00750] [Citation(s) in RCA: 283] [Impact Index Per Article: 47.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Protein lipidation, including cysteine prenylation, N-terminal glycine myristoylation, cysteine palmitoylation, and serine and lysine fatty acylation, occurs in many proteins in eukaryotic cells and regulates numerous biological pathways, such as membrane trafficking, protein secretion, signal transduction, and apoptosis. We provide a comprehensive review of protein lipidation, including descriptions of proteins known to be modified and the functions of the modifications, the enzymes that control them, and the tools and technologies developed to study them. We also highlight key questions about protein lipidation that remain to be answered, the challenges associated with answering such questions, and possible solutions to overcome these challenges.
Collapse
Affiliation(s)
- Hong Jiang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Xiaoyu Zhang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Xiao Chen
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Pornpun Aramsangtienchai
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Zhen Tong
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Hening Lin
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| |
Collapse
|
21
|
Gao X, Hannoush RN. A Decade of Click Chemistry in Protein Palmitoylation: Impact on Discovery and New Biology. Cell Chem Biol 2017; 25:236-246. [PMID: 29290622 DOI: 10.1016/j.chembiol.2017.12.002] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 11/10/2017] [Accepted: 11/30/2017] [Indexed: 12/17/2022]
Abstract
Protein palmitoylation plays diverse roles in regulating the trafficking, stability, and activity of cellular proteins. The advent of click chemistry has propelled the field of protein palmitoylation forward by providing specific, sensitive, rapid, and easy-to-handle methods for studying protein palmitoylation. This year marks the 10th anniversary since the first click chemistry-based fatty acid probes for detecting protein lipid modifications were reported. The goal of this review is to highlight key biological advancements in the field of protein palmitoylation during the past 10 years. In particular, we discuss the impact of click chemistry on enabling protein palmitoylation proteomics methods, uncovering novel lipid modifications on proteins and elucidating their functions, as well as the development of non-radioactive biochemical and enzymatic assays. In addition, this review provides context for building and exploring new research avenues in protein palmitoylation through the use of clickable fatty acid probes.
Collapse
Affiliation(s)
- Xinxin Gao
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, CA, USA
| | - Rami N Hannoush
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, CA, USA.
| |
Collapse
|
22
|
Akgun B, Li C, Hao Y, Lambkin G, Derda R, Hall DG. Synergic “Click” Boronate/Thiosemicarbazone System for Fast and Irreversible Bioorthogonal Conjugation in Live Cells. J Am Chem Soc 2017; 139:14285-14291. [DOI: 10.1021/jacs.7b08693] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Burcin Akgun
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Caishun Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Yubin Hao
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Gareth Lambkin
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Ratmir Derda
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Dennis G. Hall
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| |
Collapse
|
23
|
Chen JJ, Boehning D. Protein Lipidation As a Regulator of Apoptotic Calcium Release: Relevance to Cancer. Front Oncol 2017; 7:138. [PMID: 28706877 PMCID: PMC5489567 DOI: 10.3389/fonc.2017.00138] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 06/16/2017] [Indexed: 12/16/2022] Open
Abstract
Calcium is a critical regulator of cell death pathways. One of the most proximal events leading to cell death is activation of plasma membrane and endoplasmic reticulum-resident calcium channels. A large body of evidence indicates that defects in this pathway contribute to cancer development. Although we have a thorough understanding of how downstream elevations in cytosolic and mitochondrial calcium contribute to cell death, it is much less clear how calcium channels are activated upstream of the apoptotic stimulus. Recently, it has been shown that protein lipidation is a potent regulator of apoptotic signaling. Although classically thought of as a static modification, rapid and reversible protein acylation has emerged as a new signaling paradigm relevant to many pathways, including calcium release and cell death. In this review, we will discuss the role of protein lipidation in regulating apoptotic calcium signaling with direct therapeutic relevance to cancer.
Collapse
Affiliation(s)
- Jessica J Chen
- Department of Biochemistry and Molecular Biology, McGovern Medical School, UTHealth, Houston, TX, United States
| | - Darren Boehning
- Department of Biochemistry and Molecular Biology, McGovern Medical School, UTHealth, Houston, TX, United States
| |
Collapse
|
24
|
Ward JA, McLellan L, Stockley M, Gibson KR, Whitlock GA, Knights C, Harrigan JA, Jacq X, Tate EW. Quantitative Chemical Proteomic Profiling of Ubiquitin Specific Proteases in Intact Cancer Cells. ACS Chem Biol 2016; 11:3268-3272. [PMID: 27779380 DOI: 10.1021/acschembio.6b00766] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Deubiquitinating enzymes play an important role in a plethora of therapeutically relevant processes and are emerging as pioneering drug targets. Herein, we present a novel probe, Ubiquitin Specific Protease (USP) inhibitor, alongside an alkyne-tagged activity-based probe analogue. Activity-based proteome profiling identified 12 USPs, including USP4, USP16, and USP33, as inhibitor targets using submicromolar probe concentrations. This represents the first intact cell activity-based profiling of deubiquitinating enzymes. Further analysis demonstrated functional inhibition of USP33 and identified a synergistic relationship in combination with ATR inhibition, consistent with USP4 inhibition.
Collapse
Affiliation(s)
- Jennifer A. Ward
- Department of Chemistry, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Lauren McLellan
- MISSION Therapeutics, Ltd., Moneta,
Babraham Research Campus, Cambridge, CB22 3AT, United Kingdom
| | - Martin Stockley
- MISSION Therapeutics, Ltd., Moneta,
Babraham Research Campus, Cambridge, CB22 3AT, United Kingdom
| | - Karl R. Gibson
- Sandexis Medicinal Chemistry, Ltd., Innovation House, Discovery Park, Ramsgate Road, Sandwich, Kent, CT13 9ND, United Kingdom
| | - Gavin A. Whitlock
- Sandexis Medicinal Chemistry, Ltd., Innovation House, Discovery Park, Ramsgate Road, Sandwich, Kent, CT13 9ND, United Kingdom
| | - Charlotte Knights
- MISSION Therapeutics, Ltd., Moneta,
Babraham Research Campus, Cambridge, CB22 3AT, United Kingdom
| | - Jeanine A. Harrigan
- MISSION Therapeutics, Ltd., Moneta,
Babraham Research Campus, Cambridge, CB22 3AT, United Kingdom
| | - Xavier Jacq
- MISSION Therapeutics, Ltd., Moneta,
Babraham Research Campus, Cambridge, CB22 3AT, United Kingdom
| | - Edward W. Tate
- Department of Chemistry, Imperial College London, London, SW7 2AZ, United Kingdom
| |
Collapse
|
25
|
Rodgers U, Lanyon-Hogg T, Masumoto N, Ritzefeld M, Burke R, Blagg J, Magee AI, Tate EW. Characterization of Hedgehog Acyltransferase Inhibitors Identifies a Small Molecule Probe for Hedgehog Signaling by Cancer Cells. ACS Chem Biol 2016; 11:3256-3262. [PMID: 27779865 PMCID: PMC5349656 DOI: 10.1021/acschembio.6b00896] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 10/13/2016] [Indexed: 01/01/2023]
Abstract
The Sonic Hedgehog (Shh) signaling pathway plays a critical role during embryonic development and cancer progression. N-terminal palmitoylation of Shh by Hedgehog acyltransferase (Hhat) is essential for efficient signaling, raising interest in Hhat as a novel drug target. A recently identified series of dihydrothienopyridines has been proposed to function via this mode of action; however, the lead compound in this series (RUSKI-43) was subsequently shown to possess cytotoxic activity unrelated to canonical Shh signaling. To identify a selective chemical probe for cellular studies, we profiled three RUSKI compounds in orthogonal cell-based assays. We found that RUSKI-43 exhibits off-target cytotoxicity, masking its effect on Hhat-dependent signaling, hence results obtained with this compound in cells should be treated with caution. In contrast, RUSKI-201 showed no off-target cytotoxicity, and quantitative whole-proteome palmitoylation profiling with a bioorthogonal alkyne-palmitate reporter demonstrated specific inhibition of Hhat in cells. RUSKI-201 is the first selective Hhat chemical probe in cells and should be used in future studies of Hhat catalytic function.
Collapse
Affiliation(s)
- Ursula
R. Rodgers
- Molecular
Medicine Section, National Heart & Lung
Institute, Imperial College London, London SW7 2AZ, United
Kingdom
| | - Thomas Lanyon-Hogg
- Department
of Chemistry, Imperial College London, London SW7 2AZ, United Kingdom
| | - Naoko Masumoto
- Department
of Chemistry, Imperial College London, London SW7 2AZ, United Kingdom
| | - Markus Ritzefeld
- Department
of Chemistry, Imperial College London, London SW7 2AZ, United Kingdom
| | - Rosemary Burke
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London, SW7 3RP, United Kingdom
| | - Julian Blagg
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, London, SW7 3RP, United Kingdom
| | - Anthony I. Magee
- Molecular
Medicine Section, National Heart & Lung
Institute, Imperial College London, London SW7 2AZ, United
Kingdom
| | - Edward W. Tate
- Department
of Chemistry, Imperial College London, London SW7 2AZ, United Kingdom
| |
Collapse
|
26
|
Wright MH, Paape D, Price HP, Smith DF, Tate EW. Global Profiling and Inhibition of Protein Lipidation in Vector and Host Stages of the Sleeping Sickness Parasite Trypanosoma brucei. ACS Infect Dis 2016; 2:427-441. [PMID: 27331140 PMCID: PMC4906374 DOI: 10.1021/acsinfecdis.6b00034] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Indexed: 01/05/2023]
Abstract
The enzyme N-myristoyltransferase (NMT) catalyzes the essential fatty acylation of substrate proteins with myristic acid in eukaryotes and is a validated drug target in the parasite Trypanosoma brucei, the causative agent of African trypanosomiasis (sleeping sickness). N-Myristoylation typically mediates membrane localization of proteins and is essential to the function of many. However, only a handful of proteins are experimentally validated as N-myristoylated in T. brucei. Here, we perform metabolic labeling with an alkyne-tagged myristic acid analogue, enabling the capture of lipidated proteins in insect and host life stages of T. brucei. We further compare this with a longer chain palmitate analogue to explore the chain length-specific incorporation of fatty acids into proteins. Finally, we combine the alkynyl-myristate analogue with NMT inhibitors and quantitative chemical proteomics to globally define N-myristoylated proteins in the clinically relevant bloodstream form parasites. This analysis reveals five ARF family small GTPases, calpain-like proteins, phosphatases, and many uncharacterized proteins as substrates of NMT in the parasite, providing a global view of the scope of this important protein modification and further evidence for the crucial and pleiotropic role of NMT in the cell.
Collapse
Affiliation(s)
- Megan H. Wright
- Department of Chemistry, Imperial College London, London SW7 2AZ, United Kingdom
| | - Daniel Paape
- Centre for Immunology and Infection, Department
of Biology, University of York, York YO10 5DD, United Kingdom
| | - Helen P. Price
- Centre for Immunology and Infection, Department
of Biology, University of York, York YO10 5DD, United Kingdom
| | - Deborah F. Smith
- Centre for Immunology and Infection, Department
of Biology, University of York, York YO10 5DD, United Kingdom
| | - Edward W. Tate
- Department of Chemistry, Imperial College London, London SW7 2AZ, United Kingdom
| |
Collapse
|
27
|
Jan HM, Chen YC, Shih YY, Huang YC, Tu Z, Ingle AB, Liu SW, Wu MS, Gervay-Hague J, Mong KKT, Chen YR, Lin CH. Metabolic labelling of cholesteryl glucosides in Helicobacter pylori reveals how the uptake of human lipids enhances bacterial virulence. Chem Sci 2016; 7:6208-6216. [PMID: 30034762 PMCID: PMC6024656 DOI: 10.1039/c6sc00889e] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 05/28/2016] [Indexed: 12/30/2022] Open
Abstract
Helicobacter pylori infects approximately half of the human population and is the main cause of various gastric diseases. This pathogen is auxotrophic for cholesterol, which it converts upon uptake to various cholesteryl α-glucoside derivatives, including cholesteryl 6'-acyl and 6'-phosphatidyl α-glucosides (CAGs and CPGs). Owing to a lack of sensitive analytical methods, it is not known if CAGs and CPGs play distinct physiological roles or how the acyl chain component affects function. Herein we established a metabolite-labelling method for characterising these derivatives qualitatively and quantitatively with a femtomolar detection limit. The development generated an MS/MS database of CGds, allowing for profiling of all the cholesterol-derived metabolites. The subsequent analysis led to the unprecedented information that these bacteria acquire phospholipids from the membrane of epithelial cells for CAG biosynthesis. The resulting increase in longer or/and unsaturated CAG acyl chains helps to promote lipid raft formation and thus delivery of the virulence factor CagA into the host cell, supporting the idea that the host/pathogen interplay enhances bacterial virulence. These findings demonstrate an important connection between the chain length of CAGs and the bacterial pathogenicity.
Collapse
Affiliation(s)
- Hau-Ming Jan
- Institute of Biological Chemistry , Academia Sinica , No. 128 Academia Road Section 2, Nan-Kang , Taipei , 11529 , Taiwan . .,Institute of Biochemical Sciences and Department of Chemistry , National Taiwan University , Taipei , 10617 , Taiwan
| | - Yi-Chi Chen
- Institute of Biological Chemistry , Academia Sinica , No. 128 Academia Road Section 2, Nan-Kang , Taipei , 11529 , Taiwan . .,Institute of Biochemical Sciences and Department of Chemistry , National Taiwan University , Taipei , 10617 , Taiwan
| | - Yu-Yin Shih
- Institute of Biological Chemistry , Academia Sinica , No. 128 Academia Road Section 2, Nan-Kang , Taipei , 11529 , Taiwan .
| | - Yu-Chen Huang
- Agriculture Biotechnology Research Center , Academia Sinica , Taipei , 11529 , Taiwan
| | - Zhijay Tu
- Institute of Biological Chemistry , Academia Sinica , No. 128 Academia Road Section 2, Nan-Kang , Taipei , 11529 , Taiwan .
| | - Arun B Ingle
- Department of Applied Chemistry , National Chiao-Tung University , Hsin-Chu 300 , Taiwan
| | - Sheng-Wen Liu
- Institute of Biological Chemistry , Academia Sinica , No. 128 Academia Road Section 2, Nan-Kang , Taipei , 11529 , Taiwan .
| | - Ming-Shiang Wu
- Division of Gastroenterology , Department of Internal Medicine , National Taiwan University Hospital , Taipei , 10002 , Taiwan
| | | | - Kwok-Kong Tony Mong
- Department of Applied Chemistry , National Chiao-Tung University , Hsin-Chu 300 , Taiwan
| | - Yet-Ran Chen
- Agriculture Biotechnology Research Center , Academia Sinica , Taipei , 11529 , Taiwan
| | - Chun-Hung Lin
- Institute of Biological Chemistry , Academia Sinica , No. 128 Academia Road Section 2, Nan-Kang , Taipei , 11529 , Taiwan . .,Institute of Biochemical Sciences and Department of Chemistry , National Taiwan University , Taipei , 10617 , Taiwan
| |
Collapse
|
28
|
Chen W, Smeekens JM, Wu R. Systematic study of the dynamics and half-lives of newly synthesized proteins in human cells. Chem Sci 2016; 7:1393-1400. [PMID: 29910897 PMCID: PMC5975921 DOI: 10.1039/c5sc03826j] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 11/15/2015] [Indexed: 12/22/2022] Open
Abstract
Protein dynamics are essential in regulating nearly every cellular event, and aberrant proteostasis is the source of many diseases. It is extraordinarily difficult to globally study protein dynamics and accurately measure their half-lives. Here we have developed a chemical proteomics method integrating protein labeling, click chemistry and multiplexed proteomics, which overcomes current challenges with existing methods. Labeling with both azidohomoalanine (AHA) and heavy lysine allows us to selectively enrich newly synthesized proteins, clearly distinguish them from existing proteins, and reduce the impact of heavy amino acid recycling. Moreover, multiplexed proteomics enables us to quantify proteins at multiple time points simultaneously, thus increasing the accuracy of measuring protein abundance changes and their half-lives. Systematic investigation of newly synthesized protein dynamics will provide insight into proteostasis and the molecular mechanisms of disease.
Collapse
Affiliation(s)
- Weixuan Chen
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience , Georgia Institute of Technology , Atlanta , Georgia 30332 , USA . ; ; Tel: +1-404-385-1515
| | - Johanna M Smeekens
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience , Georgia Institute of Technology , Atlanta , Georgia 30332 , USA . ; ; Tel: +1-404-385-1515
| | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience , Georgia Institute of Technology , Atlanta , Georgia 30332 , USA . ; ; Tel: +1-404-385-1515
| |
Collapse
|
29
|
Abstract
Wnt palmitoylation regulates its secretion and signaling activity in cells. Methods to monitor cellular Wnt palmitoylation are instrumental in investigating Wnt activity, secretion, and its interaction with cellular membrane compartments. This protocol describes a method we have recently developed to detect cellular Wnt palmitoylation. The method, combining click chemistry, bio-orthogonal fatty acid probes, and proximity ligation assay (PLA), provides high sensitivity and subcellular resolution for detection of Wnt palmitoylation. It is also compatible with multiple imaging platforms, and is applicable to detecting palmitoylated forms of other fatty acylated proteins.
Collapse
Affiliation(s)
- Xinxin Gao
- Department of Cell Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390-9039, USA
| | - Rami N Hannoush
- Department of Cell Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390-9039, USA.
| |
Collapse
|
30
|
Lanyon-Hogg T, Masumoto N, Bodakh G, Konitsiotis AD, Thinon E, Rodgers UR, Owens RJ, Magee AI, Tate EW. Click chemistry armed enzyme-linked immunosorbent assay to measure palmitoylation by hedgehog acyltransferase. Anal Biochem 2015; 490:66-72. [PMID: 26334609 PMCID: PMC4615133 DOI: 10.1016/j.ab.2015.08.025] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 08/20/2015] [Accepted: 08/21/2015] [Indexed: 12/30/2022]
Abstract
Hedgehog signaling is critical for correct embryogenesis and tissue development. However, on maturation, signaling is also found to be aberrantly activated in many cancers. Palmitoylation of the secreted signaling protein sonic hedgehog (Shh) by the enzyme hedgehog acyltransferase (Hhat) is required for functional signaling. To quantify this important posttranslational modification, many in vitro Shh palmitoylation assays employ radiolabeled fatty acids, which have limitations in terms of cost and safety. Here we present a click chemistry armed enzyme-linked immunosorbent assay (click-ELISA) for assessment of Hhat activity through acylation of biotinylated Shh peptide with an alkyne-tagged palmitoyl-CoA (coenzyme A) analogue. Click chemistry functionalization of the alkyne tag with azido-FLAG peptide allows analysis through an ELISA protocol and colorimetric readout. This assay format identified the detergent n-dodecyl β-d-maltopyranoside as an improved solubilizing agent for Hhat activity. Quantification of the potency of RU-SKI small molecule Hhat inhibitors by click-ELISA indicated IC50 values in the low- or sub-micromolar range. A stopped assay format was also employed that allows measurement of Hhat kinetic parameters where saturating substrate concentrations exceed the binding capacity of the streptavidin-coated plate. Therefore, click-ELISA represents a nonradioactive method for assessing protein palmitoylation in vitro that is readily expandable to other classes of protein lipidation.
Collapse
Affiliation(s)
- Thomas Lanyon-Hogg
- Institute of Chemical Biology, Department of Chemistry, Imperial College London, South Kensington SW7 2AZ, UK
| | - Naoko Masumoto
- Institute of Chemical Biology, Department of Chemistry, Imperial College London, South Kensington SW7 2AZ, UK
| | - George Bodakh
- Institute of Chemical Biology, Department of Chemistry, Imperial College London, South Kensington SW7 2AZ, UK
| | - Antonio D Konitsiotis
- Molecular Medicine Section, National Heart & Lung Institute, Imperial College London, South Kensington SW7 2AZ, UK
| | - Emmanuelle Thinon
- Institute of Chemical Biology, Department of Chemistry, Imperial College London, South Kensington SW7 2AZ, UK
| | - Ursula R Rodgers
- Molecular Medicine Section, National Heart & Lung Institute, Imperial College London, South Kensington SW7 2AZ, UK
| | - Raymond J Owens
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK; OPPF-UK, The Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell, Oxfordshire, OX11 0FA, UK
| | - Anthony I Magee
- Molecular Medicine Section, National Heart & Lung Institute, Imperial College London, South Kensington SW7 2AZ, UK.
| | - Edward W Tate
- Institute of Chemical Biology, Department of Chemistry, Imperial College London, South Kensington SW7 2AZ, UK.
| |
Collapse
|
31
|
Callahan BP, Wang C. Hedgehog Cholesterolysis: Specialized Gatekeeper to Oncogenic Signaling. Cancers (Basel) 2015; 7:2037-53. [PMID: 26473928 PMCID: PMC4695875 DOI: 10.3390/cancers7040875] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 09/22/2015] [Accepted: 09/28/2015] [Indexed: 12/16/2022] Open
Abstract
Discussions of therapeutic suppression of hedgehog (Hh) signaling almost exclusively focus on receptor antagonism; however, hedgehog's biosynthesis represents a unique and potentially targetable aspect of this oncogenic signaling pathway. Here, we review a key biosynthetic step called cholesterolysis from the perspectives of structure/function and small molecule inhibition. Cholesterolysis, also called cholesteroylation, generates cholesterol-modified Hh ligand via autoprocessing of a hedgehog precursor protein. Post-translational modification by cholesterol appears to be restricted to proteins in the hedgehog family. The transformation is essential for Hh biological activity and upstream of signaling events. Despite its decisive role in generating ligand, cholesterolysis remains conspicuously unexplored as a therapeutic target.
Collapse
Affiliation(s)
- Brian P Callahan
- Chemistry Department, Binghamton University 4400 Vestal Parkway East, Binghamton, NY 13902, USA.
| | - Chunyu Wang
- Biology Department, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA.
| |
Collapse
|
32
|
Ganesan L, Levental I. Pharmacological Inhibition of Protein Lipidation. J Membr Biol 2015; 248:929-41. [PMID: 26280397 DOI: 10.1007/s00232-015-9835-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 08/07/2015] [Indexed: 01/02/2023]
Abstract
Lipid modifications of mammalian proteins are widespread, modifying thousands of targets involved in all aspects of cellular physiology cellular physiology. Broadly, lipidations serve to increase protein hydrophobicity and association with cellular membranes. Often, these modifications are absolutely essential for protein stability and localization, and serve critical roles in dynamic regulation of protein function. A number of lipidated proteins are associated with diseases, including parasite infections, neurological diseases, diabetes, and cancer, suggesting that lipid modifications represent potentially attractive targets for pharmacological intervention. This review briefly describes the various types of posttranslational protein lipid modifications, proteins modified by them, and the enzymatic machinery associated with these. We then discuss several case studies demonstrating successful development of lipidation inhibitors of potential (and more rarely, realized) clinical value. Although this field remains in its infancy, we believe these examples demonstrate the potential utility of targeting protein lipidation as a viable strategy for inhibiting the function of pathogenic proteins.
Collapse
Affiliation(s)
| | - Ilya Levental
- University of Texas Medical School, Houston, TX, USA.
| |
Collapse
|
33
|
Ta DT, Redeker ES, Billen B, Reekmans G, Sikulu J, Noben JP, Guedens W, Adriaensens P. An efficient protocol towards site-specifically clickable nanobodies in high yield: cytoplasmic expression in Escherichia coli combined with intein-mediated protein ligation. Protein Eng Des Sel 2015; 28:351-63. [PMID: 26243885 DOI: 10.1093/protein/gzv032] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 07/01/2015] [Indexed: 11/13/2022] Open
Abstract
In this study, several expression strategies were investigated in order to develop a generic, highly productive and efficient protocol to produce nanobodies modified with a clickable alkyne function at their C-terminus via the intein-mediated protein ligation (IPL) technique. Hereto, the nanobody targeting the vascular cell adhesion molecule 1 (NbVCAM1) was used as a workhorse. The highlights of the protocol can be ascribed to a cytoplasmic expression of the nanobody-intein-chitin-binding domain fusion protein in the Escherichia coli SHuffle(®) T7 cells with a C-terminal extension, i.e. LEY, EFLEY or His6 spacer peptide, in the commonly used Luria-Bertani medium. The combination of these factors led to a high yield (up to 22 mg/l of culture) and nearly complete alkynation efficiency of the C-terminally modified nanobody via IPL. This yield can even be improved to ∼45 mg/l in the EnPresso(®) growth system but this method is more expensive and time-consuming. The resulting alkynated nanobodies retained excellent binding capacity towards the recombinant human VCAM1. The presented protocol benefits from time- and cost-effectiveness, which allows a feasible production up-scaling of generic alkynated nanobodies. The production of high quantities of site-specifically modified nanobodies paves the way to new biosurface applications that demand for a homogeneously oriented nanobody coupling. Prospectively, the alkynated nanobodies can be covalently coupled to a multitude of azide-containing counterparts, e.g. contrast labeling agents, particles or surfaces for numerous innovative applications.
Collapse
Affiliation(s)
- Duy Tien Ta
- Biomolecule Design Group, Institute for Materials Research (IMO), Hasselt University, Agoralaan-Building D, Diepenbeek BE-3590, Belgium Faculty of Food Technology and Biotechnology, Can Tho University of Technology, Can Tho, Vietnam
| | - Erik Steen Redeker
- Maastricht Science Programme, Maastricht University, Maastricht 6200 MD, The Netherlands
| | - Brecht Billen
- Biomolecule Design Group, Institute for Materials Research (IMO), Hasselt University, Agoralaan-Building D, Diepenbeek BE-3590, Belgium
| | - Gunter Reekmans
- Applied and Analytical Chemistry, Institute for Materials Research (IMO), Hasselt University, Agoralaan-Building D, Diepenbeek BE-3590, Belgium
| | - Josephine Sikulu
- Biomolecule Design Group, Institute for Materials Research (IMO), Hasselt University, Agoralaan-Building D, Diepenbeek BE-3590, Belgium
| | - Jean-Paul Noben
- Biomedical Research Institute (Biomed) and School of Life Sciences, Transnationale Universiteit Limburg, Hasselt University, Agoralaan-Building C, Diepenbeek BE-3590, Belgium
| | - Wanda Guedens
- Biomolecule Design Group, Institute for Materials Research (IMO), Hasselt University, Agoralaan-Building D, Diepenbeek BE-3590, Belgium
| | - Peter Adriaensens
- Biomolecule Design Group, Institute for Materials Research (IMO), Hasselt University, Agoralaan-Building D, Diepenbeek BE-3590, Belgium Applied and Analytical Chemistry, Institute for Materials Research (IMO), Hasselt University, Agoralaan-Building D, Diepenbeek BE-3590, Belgium
| |
Collapse
|
34
|
Legionella pneumophila Effector LpdA Is a Palmitoylated Phospholipase D Virulence Factor. Infect Immun 2015. [PMID: 26216420 DOI: 10.1128/iai.00785-15] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Legionella pneumophila is a bacterial pathogen that thrives in alveolar macrophages, causing a severe pneumonia. The virulence of L. pneumophila depends on its Dot/Icm type IV secretion system (T4SS), which delivers more than 300 effector proteins into the host, where they rewire cellular signaling to establish a replication-permissive niche, the Legionella-containing vacuole (LCV). Biogenesis of the LCV requires substantial redirection of vesicle trafficking and remodeling of intracellular membranes. In order to achieve this, several T4SS effectors target regulators of membrane trafficking, while others resemble lipases. Here, we characterized LpdA, a phospholipase D effector, which was previously proposed to modulate the lipid composition of the LCV. We found that ectopically expressed LpdA was targeted to the plasma membrane and Rab4- and Rab14-containing vesicles. Subcellular targeting of LpdA required a C-terminal motif, which is posttranslationally modified by S-palmitoylation. Substrate specificity assays showed that LpdA hydrolyzed phosphatidylinositol, -inositol-3- and -4-phosphate, and phosphatidylglycerol to phosphatidic acid (PA) in vitro. In HeLa cells, LpdA generated PA at vesicles and the plasma membrane. Imaging of different phosphatidylinositol phosphate (PIP) and organelle markers revealed that while LpdA did not impact on membrane association of various PIP probes, it triggered fragmentation of the Golgi apparatus. Importantly, although LpdA is translocated inefficiently into cultured cells, an L. pneumophila ΔlpdA mutant displayed reduced replication in murine lungs, suggesting that it is a virulence factor contributing to L. pneumophila infection in vivo.
Collapse
|
35
|
Nickel S, Serwa RA, Kaschani F, Ninck S, Zweerink S, Tate EW, Kaiser M. Chemoproteomic Evaluation of the Polyacetylene Callyspongynic Acid. Chemistry 2015; 21:10721-8. [PMID: 26079733 DOI: 10.1002/chem.201500934] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Indexed: 01/17/2023]
Abstract
Polyacetylenes are a class of alkyne-containing natural products. Although potent bioactivities and thus possible applications as chemical probes have already been reported for some polyacetylenes, insights into the biological activities or molecular mode of action are still rather limited in most cases. To overcome this limitation, we describe the application of the polyacetylene callyspongynic acid in the development of an experimental roadmap for characterizing potential protein targets of alkyne-containing natural products. To this end, we undertook the first chemical synthesis of callyspongynic acid. We then used in situ chemical proteomics methods to demonstrate extensive callyspongynic acid-mediated chemical tagging of endoplasmic reticulum-associated lipid-metabolizing and modifying enzymes. We anticipate that an elucidation of protein targets of natural products may serve as an effective guide to the development of subsequent biological assays that aim to identify chemical phenotypes and bioactivities.
Collapse
Affiliation(s)
- Sabrina Nickel
- Chemische Biologie, ZMB, Universität Duisburg-Essen, Universitätsstr. 2, 45117 Essen (Germany)
| | - Remigiusz A Serwa
- Department of Chemistry, Imperial College London, Exhibition Road, London SW7 2AZ (UK)
| | - Farnusch Kaschani
- Chemische Biologie, ZMB, Universität Duisburg-Essen, Universitätsstr. 2, 45117 Essen (Germany)
| | - Sabrina Ninck
- Chemische Biologie, ZMB, Universität Duisburg-Essen, Universitätsstr. 2, 45117 Essen (Germany)
| | - Susanne Zweerink
- Chemische Biologie, ZMB, Universität Duisburg-Essen, Universitätsstr. 2, 45117 Essen (Germany)
| | - Edward W Tate
- Department of Chemistry, Imperial College London, Exhibition Road, London SW7 2AZ (UK)
| | - Markus Kaiser
- Chemische Biologie, ZMB, Universität Duisburg-Essen, Universitätsstr. 2, 45117 Essen (Germany).
| |
Collapse
|
36
|
Abstract
Protein S-acylation, the only fully reversible posttranslational lipid modification of proteins, is emerging as a ubiquitous mechanism to control the properties and function of a diverse array of proteins and consequently physiological processes. S-acylation results from the enzymatic addition of long-chain lipids, most typically palmitate, onto intracellular cysteine residues of soluble and transmembrane proteins via a labile thioester linkage. Addition of lipid results in increases in protein hydrophobicity that can impact on protein structure, assembly, maturation, trafficking, and function. The recent explosion in global S-acylation (palmitoyl) proteomic profiling as a result of improved biochemical tools to assay S-acylation, in conjunction with the recent identification of enzymes that control protein S-acylation and de-acylation, has opened a new vista into the physiological function of S-acylation. This review introduces key features of S-acylation and tools to interrogate this process, and highlights the eclectic array of proteins regulated including membrane receptors, ion channels and transporters, enzymes and kinases, signaling adapters and chaperones, cell adhesion, and structural proteins. We highlight recent findings correlating disruption of S-acylation to pathophysiology and disease and discuss some of the major challenges and opportunities in this rapidly expanding field.
Collapse
Affiliation(s)
- Luke H Chamberlain
- Strathclyde Institute of Pharmacy and Biomedical Sciences, Strathclyde University, Glasgow, United Kingdom; and Centre for Integrative Physiology, College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Michael J Shipston
- Strathclyde Institute of Pharmacy and Biomedical Sciences, Strathclyde University, Glasgow, United Kingdom; and Centre for Integrative Physiology, College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, United Kingdom
| |
Collapse
|
37
|
Abstract
Cholesterylation is a post-translational attachment of sterol to proteins. This modification has been a characteristic of a single family of hedgehog proteins (Hh). Hh is a well-established morphogenic molecule important in embryonic development. It was also found to be involved in the progression of many cancer types. Herein, we describe the mechanism of biosynthesis of cholesterylated Hh, the role of this unusual modification on protein functions and novel chemical probes, which could be used to specifically target this modification, both in vitro and in vivo.
Collapse
|
38
|
Wright MH, Paape D, Storck EM, Serwa RA, Smith DF, Tate EW. Global analysis of protein N-myristoylation and exploration of N-myristoyltransferase as a drug target in the neglected human pathogen Leishmania donovani. ACTA ACUST UNITED AC 2015; 22:342-54. [PMID: 25728269 PMCID: PMC4372256 DOI: 10.1016/j.chembiol.2015.01.003] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 12/16/2014] [Accepted: 01/13/2015] [Indexed: 10/26/2022]
Abstract
N-Myristoyltransferase (NMT) modulates protein function through the attachment of the lipid myristate to the N terminus of target proteins, and is a promising drug target in eukaryotic parasites such as Leishmania donovani. Only a small number of NMT substrates have been characterized in Leishmania, and a global picture of N-myristoylation is lacking. Here, we use metabolic tagging with an alkyne-functionalized myristic acid mimetic in live parasites followed by downstream click chemistry and analysis to identify lipidated proteins in both the promastigote (extracellular) and amastigote (intracellular) life stages. Quantitative chemical proteomics is used to profile target engagement by NMT inhibitors, and to define the complement of N-myristoylated proteins. Our results provide new insight into the multiple pathways modulated by NMT and the pleiotropic effects of NMT inhibition. This work constitutes the first global experimental analysis of protein lipidation in Leishmania, and reveals the extent of NMT-related biology yet to be explored for this neglected human pathogen.
Collapse
Affiliation(s)
- Megan H Wright
- Department of Chemistry, Imperial College London, London SW7 2AZ, UK.
| | - Daniel Paape
- Centre for Immunology and Infection, Department of Biology, University of York, York YO10 5DD, UK
| | | | - Remigiusz A Serwa
- Department of Chemistry, Imperial College London, London SW7 2AZ, UK
| | - Deborah F Smith
- Centre for Immunology and Infection, Department of Biology, University of York, York YO10 5DD, UK
| | - Edward W Tate
- Department of Chemistry, Imperial College London, London SW7 2AZ, UK.
| |
Collapse
|
39
|
Konitsiotis AD, Jovanović B, Ciepla P, Spitaler M, Lanyon-Hogg T, Tate EW, Magee AI. Topological analysis of Hedgehog acyltransferase, a multipalmitoylated transmembrane protein. J Biol Chem 2015; 290:3293-307. [PMID: 25505265 PMCID: PMC4319003 DOI: 10.1074/jbc.m114.614578] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 12/11/2014] [Indexed: 12/20/2022] Open
Abstract
Hedgehog proteins are secreted morphogens that play critical roles in development and disease. During maturation of the proteins through the secretory pathway, they are modified by the addition of N-terminal palmitic acid and C-terminal cholesterol moieties, both of which are critical for their correct function and localization. Hedgehog acyltransferase (HHAT) is the enzyme in the endoplasmic reticulum that palmitoylates Hedgehog proteins, is a member of a small subfamily of membrane-bound O-acyltransferase proteins that acylate secreted proteins, and is an important drug target in cancer. However, little is known about HHAT structure and mode of function. We show that HHAT is comprised of ten transmembrane domains and two reentrant loops with the critical His and Asp residues on opposite sides of the endoplasmic reticulum membrane. We further show that HHAT is palmitoylated on multiple cytosolic cysteines that maintain protein structure within the membrane. Finally, we provide evidence that mutation of the conserved His residue in the hypothesized catalytic domain results in a complete loss of HHAT palmitoylation, providing novel insights into how the protein may function in vivo.
Collapse
Affiliation(s)
| | | | - Paulina Ciepla
- Department of Chemistry, and Institute of Chemical Biology Imperial College London, Sir Alexander Fleming Building, South Kensington, London SW7 2AZ, United Kingdom
| | - Martin Spitaler
- FILM (Facility for Imaging by Light Microscopy), National Heart and Lung Institute
| | | | - Edward W Tate
- Department of Chemistry, and Institute of Chemical Biology Imperial College London, Sir Alexander Fleming Building, South Kensington, London SW7 2AZ, United Kingdom
| | - Anthony I Magee
- From the Molecular Medicine Section and Institute of Chemical Biology Imperial College London, Sir Alexander Fleming Building, South Kensington, London SW7 2AZ, United Kingdom
| |
Collapse
|
40
|
Tate EW, Kalesh KA, Lanyon-Hogg T, Storck EM, Thinon E. Global profiling of protein lipidation using chemical proteomic technologies. Curr Opin Chem Biol 2015; 24:48-57. [PMID: 25461723 PMCID: PMC4319709 DOI: 10.1016/j.cbpa.2014.10.016] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 10/23/2014] [Indexed: 01/22/2023]
Abstract
Protein lipidation is unique amongst post-translational modifications (PTMs) in enabling direct interaction with cell membranes, and is found in every form of life. Lipidation is important in normal function and in disease, but its intricate interplay with disease context presents a challenging for drug development. Global whole-proteome profiling of protein lipidation lies beyond the range of standard methods, but is well-suited to metabolic tagging with small 'clickable' chemical reporters that do not disrupt metabolism and function; chemoselective reactions are then used to add multifunctional labels exclusively to tagged-lipidated proteins. This chemical proteomic technology has opened up the first quantitative whole-proteome studies of the known major classes of protein lipidation, and the first insights into their full scope in vivo.
Collapse
Affiliation(s)
- Edward W Tate
- Department of Chemistry, Imperial College London, Exhibition Road, London SW7 2AZ, UK.
| | - Karunakaran A Kalesh
- Department of Chemistry, Imperial College London, Exhibition Road, London SW7 2AZ, UK
| | - Thomas Lanyon-Hogg
- Department of Chemistry, Imperial College London, Exhibition Road, London SW7 2AZ, UK
| | - Elisabeth M Storck
- Department of Chemistry, Imperial College London, Exhibition Road, London SW7 2AZ, UK
| | | |
Collapse
|
41
|
Owen TS, Xie XJ, Laraway B, Ngoje G, Wang C, Callahan BP. Active site targeting of hedgehog precursor protein with phenylarsine oxide. Chembiochem 2014; 16:55-8. [PMID: 25418613 DOI: 10.1002/cbic.201402421] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Indexed: 01/19/2023]
Abstract
Hedgehog proteins, signaling molecules implicated in human embryo development and cancer, can be inhibited at the stage of autoprocessing by the trivalent arsenical phenyl arsine oxide (PhAs(III) ). The interaction (apparent Ki , 4 × 10(-7) M) is characterized by an optical binding assay and by NMR spectroscopy. PhAs(III) appears to be the first validated inhibitor of hedgehog autoprocessing, which is unique to hedgehog proteins and essential for biological activity.
Collapse
Affiliation(s)
- Timothy S Owen
- Chemistry Department, Binghamton University, 4400 Vestal Parkway East, Binghamton, New York (USA)
| | | | | | | | | | | |
Collapse
|
42
|
Abstract
Dissecting the subcellular distribution of a fatty-acylated protein is key to the understanding of the molecular mechanisms regulating protein movement and function in a cell. This protocol describes how to perform single-cell imaging of palmitoylation in a fatty-acylated protein of interest with high sensitivity using click chemistry, proximity ligation and fluorescence microscopy. The initial steps in this protocol involve optimization of conditions for (i) metabolic incorporation of an alkynyl analog of palmitic acid into cellular proteins coupled with click chemistry and (ii) detecting a specific protein of interest with primary antibodies using automated fluorescence microscopy, followed by (iii) imaging palmitoylation of the target fatty-acylated protein of interest, such as Wnt, Sonic Hedgehog or H-Ras. Furthermore, we outline strategies for imaging specific fatty-acylated proteins with subcellular organelles and/or total proteome palmitoylation, and we discuss special considerations that need to be given depending on the experimental design. The use of clickable fatty acids with proximity ligation may have promising applications to the investigation of fatty acylation cell biology. The entire protocol takes ∼3 weeks to complete.
Collapse
|
43
|
Global profiling of co- and post-translationally N-myristoylated proteomes in human cells. Nat Commun 2014; 5:4919. [PMID: 25255805 PMCID: PMC4200515 DOI: 10.1038/ncomms5919] [Citation(s) in RCA: 169] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 08/05/2014] [Indexed: 02/08/2023] Open
Abstract
Protein N-myristoylation is a ubiquitous co- and post-translational modification that has been implicated in the development and progression of a range of human diseases. Here, we report the global N-myristoylated proteome in human cells determined using quantitative chemical proteomics combined with potent and specific human N-myristoyltransferase (NMT) inhibition. Global quantification of N-myristoylation during normal growth or apoptosis allowed the identification of >100 N-myristoylated proteins, >95% of which are identified for the first time at endogenous levels. Furthermore, quantitative dose response for inhibition of N-myristoylation is determined for >70 substrates simultaneously across the proteome. Small-molecule inhibition through a conserved substrate-binding pocket is also demonstrated by solving the crystal structures of inhibitor-bound NMT1 and NMT2. The presented data substantially expand the known repertoire of co- and post-translational N-myristoylation in addition to validating tools for the pharmacological inhibition of NMT in living cells. Protein N-myristoylation is a ubiquitous modification implicated in the regulation of multiple cellular processes. Here, Thinon et al. report the development of a general method to identify N-myristoylated proteins in human cells and identify over 100 endogenous post- and co-translational substrates of N-myristoyltransferase.
Collapse
|
44
|
Ciepla P, Konitsiotis AD, Serwa RA, Masumoto N, Leong WP, Dallman MJ, Magee AI, Tate EW. New chemical probes targeting cholesterylation of Sonic Hedgehog in human cells and zebrafish. Chem Sci 2014; 5:4249-4259. [PMID: 25574372 PMCID: PMC4285107 DOI: 10.1039/c4sc01600a] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 07/25/2014] [Indexed: 12/17/2022] Open
Abstract
Alkynyl-cholesterol probes tag and track Hedgehog protein, illuminating the role of protein cholesterylation in secretion, transport complex formation and signalling, and enabling quantitative proteomic analysis, imaging, and detection of cholesterylation in developing zebrafish.
Sonic Hedgehog protein (Shh) is a morphogen molecule important in embryonic development and in the progression of many cancer types in which it is aberrantly overexpressed. Fully mature Shh requires attachment of cholesterol and palmitic acid to its C- and N-termini, respectively. The study of lipidated Shh has been challenging due to the limited array of tools available, and the roles of these posttranslational modifications are poorly understood. Herein, we describe the development and validation of optimised alkynyl sterol probes that efficiently tag Shh cholesterylation and enable its visualisation and analysis through bioorthogonal ligation to reporters. An optimised probe was shown to be an excellent cholesterol biomimetic in the context of Shh, enabling appropriate release of tagged Shh from signalling cells, formation of multimeric transport complexes and signalling. We have used this probe to determine the size of transport complexes of lipidated Shh in culture medium and expression levels of endogenous lipidated Shh in pancreatic ductal adenocarcinoma cell lines through quantitative chemical proteomics, as well as direct visualisation of the probe by fluorescence microscopy and detection of cholesterylated Hedgehog protein in developing zebrafish embryos. These sterol probes provide a set of novel and well-validated tools that can be used to investigate the role of lipidation on activity of Shh, and potentially other members of the Hedgehog protein family.
Collapse
Affiliation(s)
- Paulina Ciepla
- Department of Chemistry , Imperial College London , Exhibition Road , London SW7 2AZ , UK . ; Institute of Chemical Biology , Imperial College London , Exhibition Road , London SW7 2AZ , UK .
| | - Antonios D Konitsiotis
- National Heart and Lung Institute , Imperial College London , Exhibition Road , London SW7 2AZ , UK
| | - Remigiusz A Serwa
- Department of Chemistry , Imperial College London , Exhibition Road , London SW7 2AZ , UK .
| | - Naoko Masumoto
- Department of Chemistry , Imperial College London , Exhibition Road , London SW7 2AZ , UK . ; Institute of Chemical Biology , Imperial College London , Exhibition Road , London SW7 2AZ , UK .
| | - Wai P Leong
- Department of Chemistry , Imperial College London , Exhibition Road , London SW7 2AZ , UK .
| | - Margaret J Dallman
- Institute of Chemical Biology , Imperial College London , Exhibition Road , London SW7 2AZ , UK . ; Department of Life Sciences , Imperial College London , Exhibition Road , London SW7 2AZ , UK
| | - Anthony I Magee
- Institute of Chemical Biology , Imperial College London , Exhibition Road , London SW7 2AZ , UK . ; National Heart and Lung Institute , Imperial College London , Exhibition Road , London SW7 2AZ , UK
| | - Edward W Tate
- Department of Chemistry , Imperial College London , Exhibition Road , London SW7 2AZ , UK . ; Institute of Chemical Biology , Imperial College London , Exhibition Road , London SW7 2AZ , UK .
| |
Collapse
|
45
|
Murai M, Matsunobu K, Kudo S, Ifuku K, Kawamukai M, Miyoshi H. Identification of the Binding Site of the Quinone-Head Group in Mitochondrial Coq10 by Photoaffinity Labeling. Biochemistry 2014; 53:3995-4003. [DOI: 10.1021/bi500347s] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | | | - Makoto Kawamukai
- Faculty of Life and Environmental
Science, Shimane University, 1060 Nishikawatsu, Matsue 690-8504, Japan
| | | |
Collapse
|
46
|
Masuya T, Murai M, Ifuku K, Morisaka H, Miyoshi H. Site-Specific Chemical Labeling of Mitochondrial Respiratory Complex I through Ligand-Directed Tosylate Chemistry. Biochemistry 2014; 53:2307-17. [DOI: 10.1021/bi500205x] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Takahiro Masuya
- Division of Applied Life Sciences, Graduate School of Agriculture, and ‡Division of
Integrated Life Science, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Masatoshi Murai
- Division of Applied Life Sciences, Graduate School of Agriculture, and ‡Division of
Integrated Life Science, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kentaro Ifuku
- Division of Applied Life Sciences, Graduate School of Agriculture, and ‡Division of
Integrated Life Science, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Hironobu Morisaka
- Division of Applied Life Sciences, Graduate School of Agriculture, and ‡Division of
Integrated Life Science, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Hideto Miyoshi
- Division of Applied Life Sciences, Graduate School of Agriculture, and ‡Division of
Integrated Life Science, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| |
Collapse
|
47
|
Patterson DM, Nazarova LA, Prescher JA. Finding the right (bioorthogonal) chemistry. ACS Chem Biol 2014; 9:592-605. [PMID: 24437719 DOI: 10.1021/cb400828a] [Citation(s) in RCA: 531] [Impact Index Per Article: 53.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Bioorthogonal chemistries can be used to tag diverse classes of biomolecules in cells and other complex environments. With over 20 unique transformations now available, though, selecting an appropriate reaction for a given experiment is challenging. In this article, we compare and contrast the most common classes of bioorthogonal chemistries and provide a framework for matching the reactions with downstream applications. We also discuss ongoing efforts to identify novel biocompatible reactions and methods to control their reactivity. The continued expansion of the bioorthogonal toolkit will provide new insights into biomolecule networks and functions and thus refine our understanding of living systems.
Collapse
Affiliation(s)
- David M. Patterson
- Departments of †Chemistry, ‡Molecular Biology & Biochemistry, and §Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
| | - Lidia A. Nazarova
- Departments of †Chemistry, ‡Molecular Biology & Biochemistry, and §Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
| | - Jennifer A. Prescher
- Departments of †Chemistry, ‡Molecular Biology & Biochemistry, and §Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
| |
Collapse
|
48
|
Gao X, Hannoush RN. Method for Cellular Imaging of Palmitoylated Proteins with Clickable Probes and Proximity Ligation Applied to Hedgehog, Tubulin, and Ras. J Am Chem Soc 2014; 136:4544-50. [DOI: 10.1021/ja410068g] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Xinxin Gao
- Department of Early Discovery
Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Rami N. Hannoush
- Department of Early Discovery
Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| |
Collapse
|
49
|
Konitsiotis AD, Chang SC, Jovanović B, Ciepla P, Masumoto N, Palmer CP, Tate EW, Couchman JR, Magee AI. Attenuation of hedgehog acyltransferase-catalyzed sonic Hedgehog palmitoylation causes reduced signaling, proliferation and invasiveness of human carcinoma cells. PLoS One 2014; 9:e89899. [PMID: 24608521 PMCID: PMC3946499 DOI: 10.1371/journal.pone.0089899] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 01/29/2014] [Indexed: 11/19/2022] Open
Abstract
Overexpression of Hedgehog family proteins contributes to the aetiology of many cancers. To be highly active, Hedgehog proteins must be palmitoylated at their N-terminus by the MBOAT family multispanning membrane enzyme Hedgehog acyltransferase (Hhat). In a pancreatic ductal adenocarcinoma (PDAC) cell line PANC-1 and transfected HEK293a cells Hhat localized to the endoplasmic reticulum. siRNA knockdown showed that Hhat is required for Sonic hedgehog (Shh) palmitoylation, for its assembly into high molecular weight extracellular complexes and for functional activity. Hhat knockdown inhibited Hh autocrine and juxtacrine signaling, and inhibited PDAC cell growth and invasiveness in vitro. In addition, Hhat knockdown in a HEK293a cell line constitutively expressing Shh and A549 human non-small cell lung cancer cells inhibited their ability to signal in a juxtacrine/paracrine fashion to the reporter cell lines C3H10T1/2 and Shh-Light2. Our data identify Hhat as a key player in Hh-dependent signaling and tumour cell transformed behaviour.
Collapse
Affiliation(s)
- Antonios D. Konitsiotis
- Molecular Medicine Section, National Heart & Lung Institute, Imperial College London, London, United Kingdom
| | - Shu-Chun Chang
- Molecular Medicine Section, National Heart & Lung Institute, Imperial College London, London, United Kingdom
| | - Biljana Jovanović
- Molecular Medicine Section, National Heart & Lung Institute, Imperial College London, London, United Kingdom
| | - Paulina Ciepla
- Department of Chemistry, Imperial College London, London, United Kingdom
- Institute of Chemical Biology, Imperial College London, London, United Kingdom
| | - Naoko Masumoto
- Department of Chemistry, Imperial College London, London, United Kingdom
- Institute of Chemical Biology, Imperial College London, London, United Kingdom
| | - Christopher P. Palmer
- Institute for Health Research and Policy, London Metropolitan University, London, United Kingdom
| | - Edward W. Tate
- Department of Chemistry, Imperial College London, London, United Kingdom
- Institute of Chemical Biology, Imperial College London, London, United Kingdom
| | - John R. Couchman
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anthony I. Magee
- Molecular Medicine Section, National Heart & Lung Institute, Imperial College London, London, United Kingdom
- Institute of Chemical Biology, Imperial College London, London, United Kingdom
| |
Collapse
|
50
|
Haberkant P, Holthuis JCM. Fat & fabulous: bifunctional lipids in the spotlight. Biochim Biophys Acta Mol Cell Biol Lipids 2014; 1841:1022-30. [PMID: 24440797 DOI: 10.1016/j.bbalip.2014.01.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 01/02/2014] [Accepted: 01/05/2014] [Indexed: 01/25/2023]
Abstract
Understanding biological processes at the mechanistic level requires a systematic charting of the physical and functional links between all cellular components. While protein-protein and protein-nucleic acid networks have been subject to many global surveys, other critical cellular components such as membrane lipids have rarely been studied in large-scale interaction screens. Here, we review the development of photoactivatable and clickable lipid analogues-so-called bifunctional lipids-as novel chemical tools that enable a global profiling of lipid-protein interactions in biological membranes. Recent studies indicate that bifunctional lipids hold great promise in systematic efforts to dissect the elaborate crosstalk between proteins and lipids in live cells and organisms. This article is part of a Special Issue entitled Tools to study lipid functions.
Collapse
Affiliation(s)
- Per Haberkant
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| | - Joost C M Holthuis
- Molecular Cell Biology, University of Osnabrück, Barbarastrasse 13, 49076 Osnabrück, Germany.
| |
Collapse
|