Literature DB >> 24225431

Activity-based diubiquitin probes for elucidating the linkage specificity of deubiquitinating enzymes.

Guorui Li1, Qin Liang, Ping Gong, Adam H Tencer, Zhihao Zhuang.   

Abstract

We report a new class of deubiquitinating enzyme (DUB) probes that resemble the native diubiquitin with a same linkage size and contain a Michael addition acceptor for trapping the DUB active-site cysteine. Both K63- and K48-linked diubiquitin probes were generated using a facile chemical ligation method. The diUb probes were demonstrated to label DUBs from different families and revealed intrinsic linkage specificities of DUBs.

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Year:  2014        PMID： 24225431      PMCID： PMC3918478          DOI： 10.1039/c3cc47382a

Source DB:  PubMed          Journal:  Chem Commun (Camb)        ISSN： 1359-7345            Impact factor:   6.222


  25 in total

1.  A novel active site-directed probe specific for deubiquitylating enzymes reveals proteasome association of USP14.

Authors:  A Borodovsky; B M Kessler; R Casagrande; H S Overkleeft; K D Wilkinson; H L Ploegh
Journal:  EMBO J       Date:  2001-09-17       Impact factor: 11.598

2.  Chemistry-based functional proteomics reveals novel members of the deubiquitinating enzyme family.

Authors:  Anna Borodovsky; Huib Ovaa; Nagamalleswari Kolli; Tudeviin Gan-Erdene; Keith D Wilkinson; Hidde L Ploegh; Benedikt M Kessler
Journal:  Chem Biol       Date:  2002-10

Review 3.  Mechanism and function of deubiquitinating enzymes.

Authors:  Alexander Y Amerik; Mark Hochstrasser
Journal:  Biochim Biophys Acta       Date:  2004-11-29

4.  Structure of the ubiquitin hydrolase UCH-L3 complexed with a suicide substrate.

Authors:  Shahram Misaghi; Paul J Galardy; Wim J N Meester; Huib Ovaa; Hidde L Ploegh; Rachelle Gaudet
Journal:  J Biol Chem       Date:  2004-11-05       Impact factor: 5.157

Review 5.  Tagging and detection strategies for activity-based proteomics.

Authors:  Amir M Sadaghiani; Steven Hl Verhelst; Matthew Bogyo
Journal:  Curr Opin Chem Biol       Date:  2006-12-13       Impact factor: 8.822

Review 6.  Active-site directed probes to report enzymatic action in the ubiquitin proteasome system.

Authors:  Huib Ovaa
Journal:  Nat Rev Cancer       Date:  2007-07-19       Impact factor: 60.716

7.  Structural basis for specific cleavage of Lys 63-linked polyubiquitin chains.

Authors:  Yusuke Sato; Azusa Yoshikawa; Atsushi Yamagata; Hisatoshi Mimura; Masami Yamashita; Kayoko Ookata; Osamu Nureki; Kazuhiro Iwai; Masayuki Komada; Shuya Fukai
Journal:  Nature       Date:  2008-08-31       Impact factor: 49.962

Review 8.  Activity-based protein profiling: from enzyme chemistry to proteomic chemistry.

Authors:  Benjamin F Cravatt; Aaron T Wright; John W Kozarich
Journal:  Annu Rev Biochem       Date:  2008       Impact factor: 23.643

9.  Evidence for bidentate substrate binding as the basis for the K48 linkage specificity of otubain 1.

Authors:  Tao Wang; Luming Yin; Eric M Cooper; Ming-Yih Lai; Seth Dickey; Cecile M Pickart; David Fushman; Keith D Wilkinson; Robert E Cohen; Cynthia Wolberger
Journal:  J Mol Biol       Date:  2009-01-13       Impact factor: 5.469

10.  Structural basis and specificity of human otubain 1-mediated deubiquitination.

Authors:  Mariola J Edelmann; Alexander Iphöfer; Masato Akutsu; Mikael Altun; Katalin di Gleria; Holger B Kramer; Edda Fiebiger; Sirano Dhe-Paganon; Benedikt M Kessler
Journal:  Biochem J       Date:  2009-03-01       Impact factor: 3.857
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  25 in total

1.  SARS hCoV papain-like protease is a unique Lys48 linkage-specific di-distributive deubiquitinating enzyme.

Authors:  Miklós Békés; Wioletta Rut; Paulina Kasperkiewicz; Monique P C Mulder; Huib Ovaa; Marcin Drag; Christopher D Lima; Tony T Huang
Journal:  Biochem J       Date:  2015-06-01       Impact factor: 3.857

2.  Cell Lysate-Based AlphaLISA Deubiquitinase Assay Platform for Identification of Small Molecule Inhibitors.

Authors:  Christine A Ott; Bolormaa Baljinnyam; Alexey V Zakharov; Ajit Jadhav; Anton Simeonov; Zhihao Zhuang
Journal:  ACS Chem Biol       Date:  2017-08-24       Impact factor: 5.100

3.  Synthesis of Branched Triubiquitin Active-Site Directed Probes.

Authors:  Jiaan Liu; Yanfeng Li; Kirandeep K Deol; Eric R Strieter
Journal:  Org Lett       Date:  2019-08-09       Impact factor: 6.005

4.  Selenocysteine as a Latent Bioorthogonal Electrophilic Probe for Deubiquitylating Enzymes.

Authors:  Samuel D Whedon; Nagula Markandeya; Ambar S J B Rana; Nicholas A Senger; Caroline E Weller; Frantisek Tureček; Eric R Strieter; Champak Chatterjee
Journal:  J Am Chem Soc       Date:  2016-10-17       Impact factor: 15.419

5.  Linkage-Specific Synthesis of Di-ubiquitin Probes Enabled by the Incorporation of Unnatural Amino Acid ThzK.

Authors:  Han Zhou; Tomaya Carpenter; Xuan Fu; Bo Jin; Britton Ody; Mohammad Sazid Hassan; Savannah E Jacobs; Jenny Cheung; Eve M Nicholson; Mark Turlington; Bo Zhao; Sonja Lorenz; T Ashton Cropp; Jun Yin
Journal:  Chembiochem       Date:  2022-03-19       Impact factor: 3.461

6.  Computational and biochemical studies of isothiocyanates as inhibitors of proteasomal cysteine deubiquitinases in human cancer cells.

Authors:  Zainab Sabry Othman Ahmed; Xin Li; Feng Li; Hassan Ali Cheaito; Kush Patel; El-Sayed Mohammed Mosallam; Gehad Abd El-Fattah Hassan Elbargeesy; Q Ping Dou
Journal:  J Cell Biochem       Date:  2018-07-17       Impact factor: 4.429

7.  Cell-Permeable Activity-Based Ubiquitin Probes Enable Intracellular Profiling of Human Deubiquitinases.

Authors:  Weijun Gui; Christine A Ott; Kun Yang; Jedidiah S Chung; Siqi Shen; Zhihao Zhuang
Journal:  J Am Chem Soc       Date:  2018-09-21       Impact factor: 15.419

Review 8.  Tools for the discovery of biopolymer producing cysteine relays.

Authors:  Peter D Mabbitt
Journal:  Biophys Rev       Date:  2021-03-11

9.  A native chemical ligation handle that enables the synthesis of advanced activity-based probes: diubiquitin as a case study.

Authors:  Monique P C Mulder; Farid El Oualid; Jarno ter Beek; Huib Ovaa
Journal:  Chembiochem       Date:  2014-03-12       Impact factor: 3.164

10.  Non-hydrolyzable Diubiquitin Probes Reveal Linkage-Specific Reactivity of Deubiquitylating Enzymes Mediated by S2 Pockets.

Authors:  Dennis Flierman; Gerbrand J van der Heden van Noort; Reggy Ekkebus; Paul P Geurink; Tycho E T Mevissen; Manuela K Hospenthal; David Komander; Huib Ovaa
Journal:  Cell Chem Biol       Date:  2016-04-07       Impact factor: 8.116
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