14 results on '"Dris El Atmioui"'
Search Results
2. Inhibition of transcription leads to rewiring of locus-specific chromatin proteomes
- Author
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Ila van Kruijsbergen, Tibor van Welsem, Christine E. Cucinotta, Fred van Leeuwen, Tessy Korthout, Deepani W. Poramba-Liyanage, Toshio Tsukiyama, Dris El Atmioui, Huib Ovaa, Graduate School, and Medical Biology
- Subjects
Proteomics ,Proteome ,Transcription, Genetic ,Method ,Repressor ,RNA polymerase II ,Locus (genetics) ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Transcription (biology) ,Yeasts ,RNA polymerase ,Genetics ,Genetics (clinical) ,030304 developmental biology ,Genomic Library ,0303 health sciences ,biology ,Chromatin binding ,Chromatin Assembly and Disassembly ,Chromatin ,Cell biology ,DNA-Binding Proteins ,chemistry ,Genetic Loci ,biology.protein ,Chromatin Immunoprecipitation Sequencing ,RNA Polymerase II ,030217 neurology & neurosurgery ,Protein Binding ,Transcription Factors - Abstract
Transcription of a chromatin template involves the concerted interaction of many different proteins and protein complexes. Analyses of specific factors showed that these interactions change during stress and upon developmental switches. However, how the binding of multiple factors at any given locus is coordinated has been technically challenging to investigate. Here we used Epi-Decoder in yeast to systematically decode, at one transcribed locus, the chromatin binding changes of hundreds of proteins in parallel upon perturbation of transcription. By taking advantage of improved Epi-Decoder libraries, we observed broad rewiring of local chromatin proteomes following chemical inhibition of RNA polymerase. Rapid reduction of RNA polymerase II binding was accompanied by reduced binding of many other core transcription proteins and gain of chromatin remodelers. In quiescent cells, where strong transcriptional repression is induced by physiological signals, eviction of the core transcriptional machinery was accompanied by the appearance of quiescent cell–specific repressors and rewiring of the interactions of protein-folding factors and metabolic enzymes. These results show that Epi-Decoder provides a powerful strategy for capturing the temporal binding dynamics of multiple chromatin proteins under varying conditions and cell states. The systematic and comprehensive delineation of dynamic local chromatin proteomes will greatly aid in uncovering protein–protein relationships and protein functions at the chromatin template.
- Published
- 2020
3. Total Chemical Synthesis of SUMO and SUMO-Based Probes for Profiling the Activity of SUMO-Specific Proteases
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Monique P. C. Mulder, Remco Merkx, Katharina F. Witting, Dharjath S. Hameed, Dris El Atmioui, Lindsey Lelieveld, Frauke Liebelt, Jacques Neefjes, Ilana Berlin, Alfred C. O. Vertegaal, and Huib Ovaa
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0301 basic medicine ,03 medical and health sciences ,030104 developmental biology ,General Medicine ,010402 general chemistry ,01 natural sciences ,0104 chemical sciences - Published
- 2018
4. Generation of the UFM1 Toolkit for Profiling UFM1-Specific Proteases and Ligases
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Huib Ovaa, Monique P. C. Mulder, Katharina F. Witting, Cami Talavera Ormeño, Dris El Atmioui, Christian Kofoed, and Gerbrand J. van der Heden van Noort
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0301 basic medicine ,Proteases ,Activity‐Based Probes ,activity-based probes ,Chemical biology ,chemical biology ,Computational biology ,010402 general chemistry ,01 natural sciences ,Catalysis ,Unmet needs ,03 medical and health sciences ,Activity profiling ,native chemical ligation ,post-translational modifications ,Profiling (information science) ,Humans ,Chromatography, High Pressure Liquid ,chemistry.chemical_classification ,Communication ,Circular Dichroism ,UFM1 ,Proteins ,General Chemistry ,General Medicine ,Native chemical ligation ,Communications ,0104 chemical sciences ,Enzyme ,Electroporation ,030104 developmental biology ,chemistry ,Molecular Probes ,Posttranslational modification ,Electrophoresis, Polyacrylamide Gel ,Protein Processing, Post-Translational ,HeLa Cells ,Peptide Hydrolases - Abstract
Ubiquitin‐fold modifier 1 (UFM1) is a reversible post‐translational modifier that is covalently attached to target proteins through an enzymatic cascade and removed by designated proteases. Abnormalities in this process, referred to as Ufmylation, have been associated with a variety of human diseases. Given this, the UFM1‐specific enzymes represent potential therapeutic targets; however, understanding of their biological function has been hampered by the lack of chemical tools for activity profiling. To address this unmet need, a diversifiable platform for UFM1 activity‐based probes (ABPs) utilizing a native chemical ligation (NCL) strategy was developed, enabling the generation of a variety of tools to profile both UFM1 conjugating and deconjugating enzymes. The use of the probes is demonstrated in vitro and in vivo for monitoring UFM1 enzyme reactivity, opening new research avenues.
- Published
- 2018
5. Total Chemical Synthesis of SUMO and SUMO-Based Probes for Profiling the Activity of SUMO-Specific Proteases
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Frauke Liebelt, Dris El Atmioui, Ilana Berlin, Huib Ovaa, Remco Merkx, Katharina F. Witting, Dharjath S. Hameed, Monique P. C. Mulder, Alfred C.O. Vertegaal, Lindsey T. Lelieveld, and Jacques Neefjes
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0301 basic medicine ,Models, Molecular ,Proteases ,proteolysis ,medicine.medical_treatment ,Proteolysis ,Activity‐Based Protein Profiling ,genetic processes ,macromolecular substances ,environment and public health ,Catalysis ,law.invention ,Substrate Specificity ,03 medical and health sciences ,In vivo ,Confocal microscopy ,law ,medicine ,post-translational modifications ,Humans ,Solid-Phase Synthesis Techniques ,activity-based protein profiling ,chemistry.chemical_classification ,Protease ,Microscopy, Confocal ,medicine.diagnostic_test ,Communication ,Activity-based proteomics ,General Chemistry ,In vitro ,Communications ,enzymes and coenzymes (carbohydrates) ,030104 developmental biology ,Enzyme ,chemistry ,Biochemistry ,Microscopy, Fluorescence ,SUMO ,solid-phase peptide synthesis ,health occupations ,Small Ubiquitin-Related Modifier Proteins ,Peptides ,HeLa Cells ,Peptide Hydrolases - Abstract
SUMO is a post‐translational modifier critical for cell cycle progression and genome stability that plays a role in tumorigenesis, thus rendering SUMO‐specific enzymes potential pharmacological targets. However, the systematic generation of tools for the activity profiling of SUMO‐specific enzymes has proven challenging. We developed a diversifiable synthetic platform for SUMO‐based probes by using a direct linear synthesis method, which permits N‐ and C‐terminal labelling to incorporate dyes and reactive warheads, respectively. In this manner, activity‐based probes (ABPs) for SUMO‐1, SUMO‐2, and SUMO‐3‐specific proteases were generated and validated in cells using gel‐based assays and confocal microscopy. We further expanded our toolbox with the synthesis of a K11‐linked diSUMO‐2 probe to study the proteolytic cleavage of SUMO chains. Together, these ABPs demonstrate the versatility and specificity of our synthetic SUMO platform for in vitro and in vivo characterization of the SUMO protease family.
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- 2018
6. SUMO targets the APC/C to regulate transition from metaphase to anaphase
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Sabine A.G. Cuijpers, Edwin Willemstein, René H. Medema, Jonne A. Raaijmakers, Dris El Atmioui, Karolin Eifler, Alfred C.O. Vertegaal, and Huib Ovaa
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0301 basic medicine ,Science ,Ubiquitin-activating enzyme ,genetic processes ,SUMO protein ,General Physics and Astronomy ,Kinesins ,Mitosis ,macromolecular substances ,Ubiquitin-Activating Enzymes ,environment and public health ,General Biochemistry, Genetics and Molecular Biology ,Article ,03 medical and health sciences ,Ubiquitin ,Cell Line, Tumor ,Humans ,Apc4 Subunit, Anaphase-Promoting Complex-Cyclosome ,RNA, Small Interfering ,lcsh:Science ,Metaphase ,Ubiquitins ,Anaphase ,Multidisciplinary ,biology ,Chemistry ,Ubiquitination ,Sumoylation ,General Chemistry ,HCT116 Cells ,Cell biology ,enzymes and coenzymes (carbohydrates) ,030104 developmental biology ,biology.protein ,health occupations ,Small Ubiquitin-Related Modifier Proteins ,Kinesin ,lcsh:Q ,RNA Interference ,Signal transduction ,HeLa Cells ,Signal Transduction - Abstract
Signal transduction by small ubiquitin-like modifier (SUMO) regulates a myriad of nuclear processes. Here we report on the role of SUMO in mitosis in human cell lines. Knocking down the SUMO conjugation machinery results in a delay in mitosis and defects in mitotic chromosome separation. Searching for relevant SUMOylated proteins in mitosis, we identify the anaphase-promoting complex/cyclosome (APC/C), a master regulator of metaphase to anaphase transition. The APC4 subunit is the major SUMO target in the complex, containing SUMO acceptor lysines at positions 772 and 798. SUMOylation is crucial for accurate progression of cells through mitosis and increases APC/C ubiquitylation activity toward a subset of its targets, including the newly identified target KIF18B. Combined, our findings demonstrate the importance of SUMO signal transduction for genome integrity during mitotic progression and reveal how SUMO and ubiquitin cooperate to drive mitosis., Signal transduction by small ubiquitin-like modifier (SUMO) is important for cell cycle progression. Here the authors show that SUMOylation regulates the APC/C complex, a master orchestrator of metaphase to anaphase transition, with consequences for mitotic progression.
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- 2018
7. High-throughput epitope discovery reveals frequent recognition of neo-antigens by CD4+ T cells in human melanoma
- Author
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Dris El Atmioui, Remko Schotte, Els M. E. Verdegaal, John B. A. G. Haanen, Laura Bies, Ton N. Schumacher, Sam Behjati, Hergen Spits, Michael R. Stratton, Marten Visser, Carsten Linnemann, Arno Velds, Jorg J A Calis, Marit M. van Buuren, Sjoerd H. van der Burg, Henk Hilkmann, AII - Amsterdam institute for Infection and Immunity, Cell Biology and Histology, and AGEM - Amsterdam Gastroenterology Endocrinology Metabolism
- Subjects
CD4-Positive T-Lymphocytes ,medicine.medical_treatment ,bcl-X Protein ,Epitopes, T-Lymphocyte ,CD8-Positive T-Lymphocytes ,Biology ,medicine.disease_cause ,General Biochemistry, Genetics and Molecular Biology ,Epitope ,Antigen ,Cancer immunotherapy ,Antigens, Neoplasm ,Cell Line, Tumor ,medicine ,Humans ,Melanoma ,Antigen Presentation ,Mutation ,Cancer ,General Medicine ,Immunotherapy ,medicine.disease ,DNA-Binding Proteins ,Immunology ,Proto-Oncogene Proteins c-bcl-6 ,CD8 - Abstract
Tumor-specific neo-antigens that arise as a consequence of mutations(1,2) are thought to be important for the therapeutic efficacy of cancer immunotherapies(3-5). Accumulating evidence suggests that neo-antigens may be commonly recognized by intratumoral CD8(+) T cells(3-7), but it is unclear whether neoantigen-specific CD4(+) T cells also frequently reside within human tumors. In view of the accepted role of tumor-specific CD4(+) T-cell responses in tumor control(8-10), we addressed whether neo-antigen-specific CD4(+) T-cell reactivity is a common property in human melanoma
- Published
- 2014
8. Tumor Exome Analysis Reveals Neoantigen-Specific T-Cell Reactivity in an Ipilimumab-Responsive Melanoma
- Author
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Daisy Philips, Dris El Atmioui, Ton N. Schumacher, Sam Behjati, Bianca Heemskerk, Michael R. Stratton, Nienke van Rooij, Can Keşmir, Arno Velds, John B. A. G. Haanen, Marja Nieuwland, Pia Kvistborg, Henk Hilkmann, Mireille Toebes, Marit M. van Buuren, Laura J. A. van Dijk, and Ron M. Kerkhoven
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Cancer Research ,business.industry ,T-Lymphocytes ,medicine.medical_treatment ,Melanoma ,Cancer ,Ipilimumab ,Immunotherapy ,medicine.disease ,Immunotherapy, Adoptive ,Article ,Epitope ,Oncology ,Antigen ,Neoplasms ,Immunology ,medicine ,Carcinoma ,Animals ,Humans ,business ,Ataxia telangiectasia and Rad3 related ,medicine.drug - Abstract
The evidence for T-cell–mediated regression of human cancers such as non–small-cell lung carcinoma, renal cell carcinoma, and—in particular—melanoma after immunotherapy is strong. Anti-CTLA4 (ipilimumab) treatment has been approved for treatment of meta-static melanoma,1 and antibody-mediated blockade of PD-1, a second inhibitory receptor on T cells, has shown highly encouraging results in early clinical trials.2,3 Although the clinical activity of these treatments is apparent, it is still unknown which T-cell reactivities are involved in immunotherapy-induced cancer regression.4 T-cell reactivity against nonmutated tumor-associated self-antigens has been analyzed in patients treated with ipilimumab or with autologous tumor-infiltrating T cells, but the magnitude of the T-cell responses observed has been relatively modest.5,6 In part on the basis of such data, recognition of patient-specific mutant epitopes (hereafter referred to as neoantigens) has been suggested to be a potentially important component.7 A potential involvement of mutated epitopes in T-cell control would also fit well with the observation that the mutation load in sun-exposed melanomas is particularly high.8-10 Intriguingly, on the basis of animal model data, it has recently been suggested that (therapy-induced) analysis of T-cell reactivity against patient-specific neoantigens may be feasible through exploitation of cancer genome data.11,12 However, human data have thus far been lacking. Here we report a case of a patient with stage IV melanoma who exhibited a clinical response to ipilimumab treatment. Cancer exome–guided analysis of T-cell reactivity in this patient revealed reactivity against two neoantigens, including a dominant T-cell response against a mutant epitope of the ATR (ataxia telangiectasia and Rad3 related) gene product that increased strongly after ipilimumab treatment. These data provide the first demonstration (to our knowledge) of cancer exome–guided analysis to dissect the effects of melanoma immunotherapy.
- Published
- 2013
9. Target Specificity of the E3 Ligase LUBAC for Ubiquitin and NEMO Relies on Different Minimal Requirements
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Dris El Atmioui, Remco Merkx, Titia K. Sixma, Huib Ovaa, Willem J. van Dijk, and Judith J. Smit
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congenital, hereditary, and neonatal diseases and abnormalities ,Ubiquitin-Protein Ligases ,Lysine ,Enzyme Mechanisms ,Priming (immunology) ,Ubiquitin-conjugating enzyme ,Biochemistry ,Catalysis ,03 medical and health sciences ,0302 clinical medicine ,Ubiquitin ,Multienzyme Complexes ,LUBAC ,NF-κB (NF-KB) ,E3 Ubiquitin Ligase ,Humans ,skin and connective tissue diseases ,Molecular Biology ,030304 developmental biology ,0303 health sciences ,biology ,Ubiquitination ,I-Kappa-B Kinase ,RNF31 ,Cell Biology ,I-kappa B Kinase ,Ubiquitin ligase ,Cell biology ,N-terminus ,biology.protein ,Linear Ubiquitin Chain ,030217 neurology & neurosurgery ,Signal Transduction - Abstract
Background: Linear ubiquitination of NEMO by LUBAC is important for NF-κB activation. Results: HOIP and the “top” of ubiquitin are essential for linear ubiquitination, whereas NEMO ubiquitination additionally requires HOIL-1L. Conclusion: NEMO priming and ubiquitin chain elongation rely on different LUBAC contributions. Significance: Novel insights in the requirements for linear ubiquitin chain formation and target selection., The ubiquitination of NEMO with linear ubiquitin chains by the E3-ligase LUBAC is important for the activation of the canonical NF-κB pathway. NEMO ubiquitination requires a dual target specificity of LUBAC, priming on a lysine on NEMO and chain elongation on the N terminus of the priming ubiquitin. Here we explore the minimal requirements for these specificities. Effective linear chain formation requires a precise positioning of the ubiquitin N-terminal amine in a negatively charged environment on the top of ubiquitin. Whereas the RBR-LDD region on HOIP is sufficient for targeting the ubiquitin N terminus, the priming lysine modification on NEMO requires catalysis by the RBR domain of HOIL-1L as well as the catalytic machinery of the RBR-LDD domains of HOIP. Consequently, target specificity toward NEMO is determined by multiple LUBAC components, whereas linear ubiquitin chain elongation is realized by a specific interplay between HOIP and ubiquitin.
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- 2013
10. Corrigendum: High-throughput epitope discovery reveals frequent recognition of neo-antigens by CD4
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Carsten, Linnemann, Marit M, van Buuren, Laura, Bies, Els M E, Verdegaal, Remko, Schotte, Jorg J A, Calis, Sam, Behjati, Arno, Velds, Henk, Hilkmann, Dris, El Atmioui, Marten, Visser, Michael R, Stratton, John B A G, Haanen, Hergen, Spits, Sjoerd H, van der Burg, and Ton N M, Schumacher
- Published
- 2016
11. Synthesis and Evaluation of a Selective Fluorogenic Pup Derived Assay Reagent for Dop, a Potential Drug Target inMycobacterium tuberculosis
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Kristin E. Burns, Dris El Atmioui, Remco Merkx, K. Heran Darwin, Farid El Oualid, Huib Ovaa, and Paul Slobbe
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Pup-proteasome system (PPS) ,Virulence Factors ,Molecular Sequence Data ,Drug target ,protein–protein interactions ,010402 general chemistry ,01 natural sciences ,Biochemistry ,Amidohydrolases ,Substrate Specificity ,Mycobacterium tuberculosis ,03 medical and health sciences ,Hydrolysis ,Bacterial Proteins ,fluorescent probes ,deamidase of Pup (Dop) ,High-Throughput Screening Assays ,Amino Acid Sequence ,Enzyme Inhibitors ,Ubiquitins ,Molecular Biology ,Fluorescent Dyes ,030304 developmental biology ,0303 health sciences ,biology ,Organic Chemistry ,Screening assay ,biology.organism_classification ,Molecular biology ,Communications ,In vitro ,0104 chemical sciences ,3. Good health ,Kinetics ,tuberculosis ,Reagent ,Biocatalysis ,Molecular Medicine ,Peptides ,Conjugate - Abstract
A litter of pups: The synthesis and in vitro evaluation of new Pup-based fluorogenic substrates for Dop, the mycobacterial depupylase, are described. A full-length Pup-amidomethylcoumarin conjugate as well as an amino-terminus-truncated analogue exhibited high sensitivity and specificity towards hydrolysis by Dop. The substrates developed here might find application as high-throughput screening assay reagents for the identification of Dop inhibitors.
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- 2012
12. A chemical switch for the modulation of the functional activity of higher homologues of histamine on the human histamine H3 receptor: effect of various substitutions at the primary amino function
- Author
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Iwan J. P. de Esch, Dris El-Atmioui, Remko A. Bakker, Wiro M. P. B. Menge, Rob Leurs, Herman D. Lim, Marinella Govoni, Henk Timmerman, Medicinal chemistry, and Chemistry and Pharmaceutical Sciences
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Tertiary amine ,Stereochemistry ,Ligands ,Chemical synthesis ,Receptors, G-Protein-Coupled ,Structure-Activity Relationship ,Alicyclic compound ,chemistry.chemical_compound ,SDG 3 - Good Health and Well-being ,Drug Discovery ,Radioligand ,Humans ,Receptors, Histamine H3 ,Inverse agonist ,Amines ,Receptors, Histamine H4 ,chemistry.chemical_classification ,Molecular Structure ,Biological activity ,Biochemistry ,chemistry ,Receptors, Histamine ,Molecular Medicine ,Histamine H3 receptor ,Histamine - Abstract
In an effort to establish the structural requirements for agonism, neutral antagonism, and inverse agonism at the human histamine H(3) receptor (H(3)R) we have prepared a series of higher homologues of histamine in which the terminal nitrogen of the side chain has been either mono- or disubstituted with several aliphatic, alicyclic, and aromatic moieties or incorporated in cyclic systems. The novel ligands have been pharmacologically investigated in vitro for their affinities on the human H(3)R and H(4)R subtypes by radioligand displacement experiments and for their intrinsic H(3)R activities via a CRE-mediated beta-galactosidase reporter gene assay. Subtle changes of the substitution pattern at the side chain nitrogen alter enormously the pharmacological activity of the ligands, resulting in a series of compounds with a wide spectrum of pharmacological activities. Among the several neutral H(3)R antagonists identified within this series, compounds 2b and 2h display an H(3)R affinity in the low nanomolar concentration range (pK(i) values of 8.1 and 8.4, respectively). A very potent and selective H(3)R agonist (1l, pEC(50) = 8.9, alpha = 0.94) and a very potent, though not highly selective, H(3)R inverse agonist (2k, pIC(50) = 8.9, alpha = -0.97) have been identified as well.
- Published
- 2006
13. Synthesis of atypical diubiquitin chains
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Farid El, Oualid, Dharjath S, Hameed, Dris El, Atmioui, Henk, Hilkmann, and Huib, Ovaa
- Subjects
Ubiquitination ,Polyubiquitin ,Protein Processing, Post-Translational ,Ubiquitins - Abstract
Post-translational modification of proteins with ubiquitin (Ub) and Ub chains controls numerous biochemical events. Although it has been proven that all Ub-Ub linkages are formed in cells, studies have been limited for a long time to K48 and K63 chains as these can be generated biochemically. Access to the remaining (atypical) Ub-Ub chain types has been hampered by a lack of specific E2 enzymes. In this chapter we present a solution to this problem by using a native chemical ligation approach to obtain all other (i.e. K6, K11, K27, K29 and K33) diubiquitin chains.
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- 2012
14. Ubiquitin-based probes prepared by total synthesis to profile the activity of deubiquitinating enzymes
- Author
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Jacques Neefjes, Boris Rodenko, Remco Merkx, Dris El Atmioui, Ilana Berlin, Annemieke de Jong, Craig N. Robson, Zeliha Yalçin, Huib Ovaa, and Ruud H. Wijdeven
- Subjects
solid-phase synthesis ,Immunoprecipitation ,Biotin ,010402 general chemistry ,01 natural sciences ,Biochemistry ,Deubiquitinating enzyme ,03 medical and health sciences ,Solid-phase synthesis ,fluorescent probes ,Catalytic Domain ,Cell Line, Tumor ,Endopeptidases ,Solid-Phase Synthesis Techniques ,Humans ,Biotinylation ,Molecular Biology ,030304 developmental biology ,Fluorescent Dyes ,activity-based protein profiling ,0303 health sciences ,biology ,Chemistry ,Ubiquitin ,deubiquitinating enzymes ,Organic Chemistry ,Activity-based proteomics ,Ubiquitination ,Full Papers ,3. Good health ,0104 chemical sciences ,biology.protein ,Molecular Medicine ,Intein ,Linker - Abstract
Epitope-tagged active-site-directed probes are widely used to visualize the activity of deubiquitinases (DUBs) in cell extracts, to investigate the specificity and potency of small-molecule DUB inhibitors, and to isolate and identify DUBs by mass spectrometry. With DUBs arising as novel potential drug targets, probes are required that can be produced in sufficient amounts and to meet the specific needs of a given experiment. The established method for the generation of DUB probes makes use of labor-intensive intein-based methods that have inherent limitations concerning the incorporation of unnatural amino acids and the amount of material that can be obtained. Here, we describe the total chemical synthesis of active-site-directed probes and their application to activity-based profiling and identification of functional DUBs. This synthetic methodology allowed the easy incorporation of desired tags for specific applications, for example, fluorescent reporters, handles for immunoprecipitation or affinity pull-down, and cleavable linkers. Additionally, the synthetic method can be scaled up to provide significant amounts of probe. Fluorescent ubiquitin probes allowed faster, in-gel detection of active DUBs, as compared to (immuno)blotting procedures. A biotinylated probe holding a photocleavable linker enabled the affinity pull-down and subsequent mild, photorelease of DUBs. Also, DUB activity levels were monitored in response to overexpression or knockdown, and to inhibition by small molecules. Furthermore, fluorescent probes revealed differential DUB activity profiles in a panel of lung and prostate cancer cells.
- Published
- 2012
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