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Showing 1–30 of 30 results
Advanced filters: Author: Huib Ovaa Clear advanced filters

  • Most insights into deubiquitinase (DUB) substrate specificity originate from studies with isolated di-ubiquitins (diUb), but in cells diUbs with different linkage types coexist. Here, the authors develop a mass spectrometric DUB activity assay that can probe all diUbs simultaneously under substrate competition conditions.

    • Bianca D. M. van Tol
    • Bjorn R. van Doodewaerd
    • Paul P. Geurink
    ResearchOpen Access
    Nature Communications
    Volume: 14, P: 1-14

  • Using synthetic ubiquitins with non-natural acceptor site, the authors revealed that the length of lysine side chain in acceptor ubiquitins affects ubiquitin chain linkage specificity with native lysine as the preferred geometry.

    • Joanna Liwocha
    • David T. Krist
    • Brenda A. Schulman
    Research
    Nature Chemical Biology
    Volume: 17, P: 272-279

  • Cryo-electron microscopy of neddylated SCF-family ligases interacting with the RBR-type E3 ligase ARIH1 reveals the steps through which E3–E3 super-assemblies ubiquitylate a diverse set of substrates presented on F-box proteins.

    • Daniel Horn-Ghetko
    • David T. Krist
    • Brenda A. Schulman
    ResearchOpen Access
    Nature
    Volume: 590, P: 671-676

  • Thermal profiling in combination with quantitative proteomics makes it possible to identify cellular membrane protein targets of small molecules.

    • Yves Leestemaker
    • Huib Ovaa
    News & Views
    Nature Methods
    Volume: 12, P: 1127-1128

  • Many viral antigens have been identified in patients with COVID-19 patients, but which of these result in meaningful immune responses is unclear. Here the authors identify a range of SARS-CoV-2 CD8+ T cell responses across patients including a response targeting an epitope of ORF1ab with immunodominant properties.

    • Anastasia Gangaev
    • Steven L. C. Ketelaars
    • Pia Kvistborg
    ResearchOpen Access
    Nature Communications
    Volume: 12, P: 1-14

  • Irreversible covalent inhibitors equipped with reporter groups allow the study of target enzymes based on catalytic activity instead of expression level. This Perspective discusses the design and use of such probes directed at the ubiquitin–proteasome system. Can they identify new cancer therapies that target this system?

    • Huib Ovaa
    Reviews
    Nature Reviews Cancer
    Volume: 7, P: 613-620

  • The interplay of the proteasome and deubiquitinase Ubp6 is crucial for the degradation of ubiquitylated substrates. Here, the authors provide structural insights into the allosteric mechanism by which the activities of both Ubp6 and the proteasome are regulated.

    • Ka Ying Sharon Hung
    • Sven Klumpe
    • Daniel Finley
    ResearchOpen Access
    Nature Communications
    Volume: 13, P: 1-13

  • Biochemical, structural and functional studies on the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) papain-like protease PLpro reveal that it regulates host antiviral responses by preferentially cleaving the ubiquitin-like interferon-stimulated gene 15 protein (ISG15) and identify this protease as a potential therapeutic target for coronavirus disease 2019 (COVID-19).

    • Donghyuk Shin
    • Rukmini Mukherjee
    • Ivan Dikic
    Research
    Nature
    Volume: 587, P: 657-662

  • The specificity of USP18's deconjugating activity toward ISG15, a ubiquitin-like protein induced by interferon, is revealed by structural and biochemistry studies of the mouse proteins.

    • Anja Basters
    • Paul P Geurink
    • Günter Fritz
    Research
    Nature Structural & Molecular Biology
    Volume: 24, P: 270-278

  • Deubiquitinating enzymes (DUBs) are critical regulators of cellular processes by removing ubiquitin from specific targets. Here global kinetic modelling reveals the mechanism by which the low intrinsic activity of USP7 is substantially enhanced on a specific physiological target.

    • Robbert Q. Kim
    • Paul P. Geurink
    • Titia K. Sixma
    ResearchOpen Access
    Nature Communications
    Volume: 10, P: 1-16

  • Though ubiquitin is known to broadly influence endosomal trafficking, few ubiquitin-utilizing enzymes targeting endosomal regulators are known. Here, the authors find that the deubiquitylating enzyme (DUB) USP32 influences endosomal membrane dynamics by deubiquitinating Rab7.

    • Aysegul Sapmaz
    • Ilana Berlin
    • Huib Ovaa
    ResearchOpen Access
    Nature Communications
    Volume: 10, P: 1-18

  • A technique for the site-directed conjugation of antibodies via the small-protein ubiquitin allows for the efficient multivalent conjugation of antibodies and nanobodies to fusions of ubiquitin with molecular or proteinic moieties.

    • Angela F. el Hebieshy
    • Zacharias Wijfjes
    • Ferenc A. Scheeren
    ResearchOpen Access
    Nature Biomedical Engineering
    Volume: 9, P: 1101-1116

  • A ubiquitin analog used as an activity-based probe of ubiquitin conjugation enzymes, E1, E2 and E3 covalently traps these enzymes without transfer to substrates. The probes can be used in structural and functional studies and to visualize enzyme activity in cells.

    • Monique P C Mulder
    • Katharina Witting
    • Huib Ovaa
    Research
    Nature Chemical Biology
    Volume: 12, P: 523-530

  • The tumor suppressor BAP1 is activated by ASXL1 to deubiquitinate mono-ubiquitinated H2A at K119 in Polycomb gene repression. Here, the authors show how BAP1’s C-terminal extension auto-recruits it to nucleosomes, where the DEUBAD domain of ASXL1 increases BAP1’s affinity for ubiquitin to drive deubiquitination.

    • Danny D. Sahtoe
    • Willem J. van Dijk
    • Titia K. Sixma
    ResearchOpen Access
    Nature Communications
    Volume: 7, P: 1-13

  • The enzyme autotaxin (ATX) produces the lipid mediator LPA to stimulate cell migration and proliferation. The crystal structures of rat ATX, in its apo and inhibitor-bound forms, along with functional work, offer insight into substrate specificity and show that ATX interacts with integrins through one of its SMB domains.

    • Jens Hausmann
    • Satwik Kamtekar
    • Anastassis Perrakis
    Research
    Nature Structural & Molecular Biology
    Volume: 18, P: 198-204

  • Anthracycline-based drugs can kill cancer cells by inhibiting topoisomerase II and promoting DNA double-strand breaks. Pang et al. show that anthracyclines also induce eviction of histones from open chromatin regions and, in doing so, modulate DNA repair and apoptosis in human cancer cells.

    • Baoxu Pang
    • Xiaohang Qiao
    • Jacques Neefjes
    ResearchOpen Access
    Nature Communications
    Volume: 4, P: 1-13

  • The European Lead Factory combines assets and experience from major pharma with innovation and agility of academia and SMEs in a collaborative platform to expand access to high-throughput screening. With many successes heading towards the clinic, the organization is broadening its approach to screening and partnering.

    • Philip S. Jones
    • Sylviane Boucharens
    • Jon S. B. de Vlieger
    Comments & Opinion
    Nature Reviews Drug Discovery
    Volume: 21, P: 245-246

  • Deubiquitinating enzymes (DUBs) are essential to modulate ubiquitin signaling. While known DUBs can be grouped into six families, the authors here present biochemical and structural evidence for a seventh DUB family, defining determinants of substrate specificity for two representative enzymes.

    • Thomas Hermanns
    • Christian Pichlo
    • Kay Hofmann
    ResearchOpen Access
    Nature Communications
    Volume: 9, P: 1-13

  • The OTU domain deubiquitinase TRABID specifically hydrolyzes atypical Lys29- and Lys33-linked diubiquitin chains. Structural analysis of TRABID reveals an unpredicted ankyrin-repeat domain that binds ubiquitin and is crucial for TRABID efficiency and linkage specificity in vitro and in vivo.

    • Julien D F Licchesi
    • Juliusz Mieszczanek
    • David Komander
    Research
    Nature Structural & Molecular Biology
    Volume: 19, P: 62-71

  • 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.

    • Karolin Eifler
    • Sabine A. G. Cuijpers
    • Alfred C. O. Vertegaal
    ResearchOpen Access
    Nature Communications
    Volume: 9, P: 1-15

  • This protocol describes the chemical synthesis of different nonhydrolyzable diubiquitin linkages and their use in affinity purification and LC–MS/MS identification of linkage-selective diubiquitin interactors.

    • Xiaofei Zhang
    • Arne H Smits
    • Michiel Vermeulen
    Protocols
    Nature Protocols
    Volume: 13, P: 530-550

  • Humans have evolved innate and adaptive immune systems to survive infection. Chemical approaches have enabled modulation of the immune system to activate or dampen it, leading to the development of new treatments for cancer and autoimmunity.

    • Sander I. van Kasteren
    • Jacques Neefjes
    • Huib Ovaa
    Reviews
    Nature Reviews Chemistry
    Volume: 2, P: 184-193