The DOI matches its Crossref record; 25 of the 25 references it cites were found in a registry or an index.
On Terminal Alkynes That Can React with Active-Site Cysteine Nucleophiles in Proteases
Open accessAbstract
Active-site directed probes are powerful in studies of enzymatic function. We report an active-site directed probe based on a warhead so far considered unreactive. By replacing the C-terminal carboxylate of ubiquitin (Ub) with an alkyne functionality, a selective reaction with the active-site cysteine residue of de-ubiquitinating enzymes was observed. The resulting product was shown to be a quaternary vinyl thioether, as determined by X-ray crystallography. Proteomic analysis of proteins bound to an immobilized Ub alkyne probe confirmed the selectivity toward de-ubiquitinating enzymes. The observed reactivity is not just restricted to propargylated Ub, as highlighted by the selective reaction between caspase-1 (interleukin converting enzyme) and a propargylated peptide derived from IL-1β, a caspase-1 substrate.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Tornøe, C. W., Christensen, C., & Meldal, M. (2002) · The Journal of Organic Chemistry · doi:10.1021/jo011148j · Cited by 8,696
The Ubiquitin-Proteasome Proteolytic Pathway: Destruction for the Sake of Construction
Glickman, M. H., & Ciechanover, A. (2002) · Physiological Reviews · doi:10.1152/physrev.00027.2001 · Cited by 4,237
Komander, D., & Rape, M. (2012) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-060310-170328 · Cited by 3,679
Self-citationRegulation and cellular roles of ubiquitin-specific deubiquitinating enzymes.
Reyes-Turcu, F. E., Ventii, K. H., & Wilkinson, K. D. (2009) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.78.082307.091526 · Cited by 1,396
Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics
Boersema, P. J., Raijmakers, R., Lemeer, S., Mohammed, S., & Heck, A. J. R. (2009) · Nature Protocols · doi:10.1038/nprot.2009.21 · Cited by 1,357
Self-citationNew nitric oxide-releasing zwitterions derived from polyamines
Hrabie, J. A., Klose, J. R., Wink, D. A., & Keefer, L. K. (1993) · The Journal of Organic Chemistry · doi:10.1021/jo00058a030 · Cited by 592
Chemistry-Based Functional Proteomics Reveals Novel Members of the Deubiquitinating Enzyme Family
Borodovsky, A., Ovaa, H., Kolli, N., Gan-Erdene, T., Wilkinson, K. D., Ploegh, H. L., & Kessler, B. M. (2002) · Chemistry & Biology · doi:10.1016/s1074-5521(02)00248-x · Cited by 588
Self-citationUbiquitin-like protein conjugation and the ubiquitin–proteasome system as drug targets
Bedford, L., Lowe, J., Dick, L. R., Mayer, R. J., & Brownell, J. E. (2011) · Nature Reviews Drug Discovery · doi:10.1038/nrd3321 · Cited by 563
Activity-Based Chemical Proteomics Accelerates Inhibitor Development for Deubiquitylating Enzymes
Altun, M., Kramer, H. B., Willems, L. I., McDermott, J. L., Leach, C. A., Goldenberg, S. J., Kumar, K. G. S., Konietzny, R., Fischer, R., Kogan, E., et al. (2011) · Chemistry & Biology · doi:10.1016/j.chembiol.2011.08.018 · Cited by 402
Frias-Staheli, N., Giannakopoulos, N. V., Kikkert, M., Taylor, S. L., Bridgen, A., Paragas, J., Richt, J. A., Rowland, R. R., Schmaljohn, C. S., Lenschow, D. J., et al. (2007) · Cell Host & Microbe · doi:10.1016/j.chom.2007.09.014 · Cited by 365
Cited by
Mevissen, T. E. T., Hospenthal, M. K., Geurink, P. P., Elliott, P. R., Akutsu, M., Arnaudo, N., Ekkebus, R., Kulathu, Y., Wauer, T., El Oualid, F., et al. (2013) · Cell · doi:10.1016/j.cell.2013.05.046 · Cited by 626
Self-citationMechanism and inhibition of the papain‐like protease, PLpro, of SARS‐CoV‐2
Klemm, T., Ebert, G., Calleja, D. J., Allison, C. C., Richardson, L. W., Bernardini, J. P., Lu, B. G., Kuchel, N. W., Grohmann, C., Shibata, Y., et al. (2020) · The EMBO Journal · doi:10.15252/embj.2020106275 · Cited by 485
Self-citationRut, W., Lv, Z., Zmudzinski, M., Patchett, S., Nayak, D., Snipas, S. J., El Oualid, F., Huang, T. T., Bekes, M., Drag, M., et al. (2020) · Science Advances · doi:10.1126/sciadv.abd4596 · Cited by 459
Chemical proteomics approaches for identifying the cellular targets of natural products
Wright, M. H., & Sieber, S. A. (2016) · Natural Product Reports · doi:10.1039/c6np00001k · Cited by 391
Abdul Rehman, S. A., Kristariyanto, Y. A., Choi, S.-Y., Nkosi, P. J., Weidlich, S., Labib, K., Hofmann, K., & Kulathu, Y. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.05.009 · Cited by 363
Self-citationRapid Covalent-Probe Discovery by Electrophile-Fragment Screening
Resnick, E., Bradley, A., Gan, J., Douangamath, A., Krojer, T., Sethi, R., Geurink, P. P., Aimon, A., Amitai, G., Bellini, D., et al. (2019) · Journal of the American Chemical Society · doi:10.1021/jacs.9b02822 · Cited by 335
Self-citationActivity-Based Profiling of Proteases
Sanman, L. E., & Bogyo, M. (2014) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-060713-035352 · Cited by 330
Mortenson, D. E., Brighty, G. J., Plate, L., Bare, G., Chen, W., Li, S., Wang, H., Cravatt, B. F., Forli, S., Powers, E. T., et al. (2018) · Journal of the American Chemical Society · doi:10.1021/jacs.7b08366 · Cited by 292
Allenamides as Orthogonal Handles for Selective Modification of Cysteine in Peptides and Proteins
Abbas, A., Xing, B., & Loh, T. (2014) · Angewandte Chemie International Edition · doi:10.1002/anie.201403121 · Cited by 117
Privileged Electrophile Sensors: A Resource for Covalent Drug Development
Long, M. J. C., & Aye, Y. (2017) · Cell Chemical Biology · doi:10.1016/j.chembiol.2017.05.023 · Cited by 81
Kooij, R., Liu, S., Sapmaz, A., Xin, B.-T., Janssen, G. M. C., van Veelen, P. A., Ovaa, H., Dijke, P. T., & Geurink, P. P. (2020) · Journal of the American Chemical Society · doi:10.1021/jacs.0c07726 · Cited by 82
Self-citationKinetic analysis of multistep USP7 mechanism shows critical role for target protein in activity.
Kim, R. Q., Geurink, P. P., Mulder, M. P. C., Fish, A., Ekkebus, R., El Oualid, F., van Dijk, W. J., van Dalen, D., Ovaa, H., van Ingen, H., et al. (2019) · Nature Communications · doi:10.1038/s41467-018-08231-5 · Cited by 41
Self-citationRennie, M. L., Gundogdu, M., Arkinson, C., Liness, S., Frame, S., & Walden, H. (2024) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.4c01184 · Cited by 27
Strategies to Investigate Ubiquitination in Huntington's Disease
Sap, K. A., & Reits, E. A. (2020) · Frontiers in Chemistry · doi:10.3389/fchem.2020.00485 · Cited by 25
An integrated workflow for quantitative analysis of the newly synthesized proteome
Borteçen, T., Müller, T., & Krijgsveld, J. (2023) · Nature Communications · doi:10.1038/s41467-023-43919-3 · Cited by 19
Structural insights into ubiquitin chain cleavage by Legionella ovarian tumor deubiquitinases
Kang, S., Kim, G., Choi, M., Jeong, M., van der Heden van Noort, G. J., Roh, S.-H., & Shin, D. (2023) · Life Science Alliance · doi:10.26508/lsa.202201876 · Cited by 9
The structural basis for deubiquitination by the fingerless USP-type effector TssM
Hermanns, T., Uthoff, M., Baumann, U., & Hofmann, K. (2024) · Life Science Alliance · doi:10.26508/lsa.202302422 · Cited by 7
Reprogramming of bacterial virulence by lysine acetylation
Schmöker, O., Girbardt, B., Schulze, S., Palm, G. J., Berndt, L., Hoppen, J., Kara, N., Schöps, X., Al-Abdulla, R., Garz, K., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-72244-8 · Cited by 2
Metadata
- Authors
- Ekkebus, R., van Kasteren, S. I., Kulathu, Y., Scholten, A., Berlin, I., Geurink, P. P., de Jong, A., Goerdayal, S., Neefjes, J., Heck, A. J. R., Komander, D., & Ovaa, H.
- Venue
- Journal of the American Chemical Society
- Publisher
- American Chemical Society (ACS)
- Published
- 2013-02-15
- Volume
- 135
- Issue
- 8
- Pages
- 2867-2870
- ISSN
- 0002-7863 (ISSN-L)
- 1520-5126
- OpenAlex
- W2099598643
- Cited by
- 347
- References
- 25
- FWCI
- 9.68
- Type
- journal article
- Language
- en
- Open access
- hybrid
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.