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Items: 1 to 20 of 37

1.
Assessment of community efforts to advance network-based prediction of protein–protein interactions
Xu-Wen Wang, Lorenzo Madeddu, Kerstin Spirohn, Leonardo Martini, Adriano Fazzone, Luca Becchetti, Thomas P. Wytock, István A. Kovács, Olivér M. Balogh, Bettina Benczik, Mátyás Pétervári, Bence Ágg, Péter Ferdinandy, Loan Vulliard, Jörg Menche, Stefania Colonnese, Manuela Petti, Gaetano Scarano, Francesca Cuomo, Tong Hao, Florent Laval, Luc Willems, Jean-Claude Twizere, Marc Vidal, Michael A. Calderwood, Enrico Petrillo, Albert-László Barabási, Edwin K. Silverman, Joseph Loscalzo, Paola Velardi, Yang-Yu Liu
Nat Commun. 2023; 14: 1582. Published online 2023 Mar 22. doi: 10.1038/s41467-023-37079-7
PMCID:
PMC10033937
AbstractArticlePDF–1.5M
2.
Elucidation of ubiquitin-conjugating enzymes that interact with RBR-type ubiquitin ligases using a liquid–liquid phase separation–based method
Ryota Hayashida, Reika Kikuchi, Kenichiro Imai, Waka Kojima, Tatsuya Yamada, Miho Iijima, Hiromi Sesaki, Keiji Tanaka, Noriyuki Matsuda, Koji Yamano
J Biol Chem. 2023 Feb; 299(2): 102822. Published online 2022 Dec 21. doi: 10.1016/j.jbc.2022.102822
PMCID:
PMC9860496
AbstractArticlePDF–6.6M
3.
Divergent self-association properties of paralogous proteins TRIM2 and TRIM3 regulate their E3 ligase activity
Diego Esposito, Jane Dudley-Fraser, Acely Garza-Garcia, Katrin Rittinger
Nat Commun. 2022; 13: 7583. Published online 2022 Dec 8. doi: 10.1038/s41467-022-35300-7
PMCID:
PMC9732051
AbstractArticlePDF–4.5M
4.
Enzymatic analysis of WWP2 E3 ubiquitin ligase using protein microarrays identifies autophagy-related substrates
Hanjie Jiang, Claire Y. Chiang, Zan Chen, Sara Nathan, Gabriel D’Agostino, Joao A. Paulo, Guang Song, Heng Zhu, Sandra B. Gabelli, Philip A. Cole
J Biol Chem. 2022 May; 298(5): 101854. Published online 2022 Mar 21. doi: 10.1016/j.jbc.2022.101854
PMCID:
PMC9034101
AbstractArticlePDF–3.7M
5.
Histone deacetylase inhibitors inhibit cervical cancer growth through Parkin acetylation-mediated mitophagy
Xin Sun, Yuhan Shu, Guiqin Ye, Caixia Wu, Mengting Xu, Ruilan Gao, Dongsheng Huang, Jianbin Zhang
Acta Pharm Sin B. 2022 Feb; 12(2): 838–852. Published online 2021 Jul 21. doi: 10.1016/j.apsb.2021.07.003
PMCID:
PMC8897022
AbstractArticlePDF–3.0M
6.
Reconstitution of human CMG helicase ubiquitylation by CUL2LRR1 and multiple E2 enzymes
Thanh Thi Le, Johanna Ainsworth, Cristian Polo Rivera, Thomas Macartney, Karim P.M. Labib
Biochem J. 2021 Jul 30; 478(14): 2825–2842. Prepublished online 2021 Jun 29. Published online 2021 Jul 23. doi: 10.1042/BCJ20210315
PMCID:
PMC8331092
AbstractArticlePDF–1.9M
7.
Dual Proteome-scale Networks Reveal Cell-specific Remodeling of the Human Interactome
Edward L. Huttlin, Raphael J. Bruckner, Jose Navarrete-Perea, Joe R. Cannon, Kurt Baltier, Fana Gebreab, Melanie P. Gygi, Alexandra Thornock, Gabriela Zarraga, Stanley Tam, John Szpyt, Brandon M. Gassaway, Alexandra Panov, Hannah Parzen, Sipei Fu, Arvene Golbazi, Eila Maenpaa, Keegan Stricker, Sanjukta Guha Thakurta, Tian Zhang, Ramin Rad, Joshua Pan, David P. Nusinow, Joao A. Paulo, Devin K. Schweppe, Laura Pontano Vaites, J. Wade Harper, Steven P. Gygi
Cell. Author manuscript; available in PMC 2022 May 27.
Published in final edited form as: Cell. 2021 May 27; 184(11): 3022–3040.e28. Published online 2021 May 6. doi: 10.1016/j.cell.2021.04.011
PMCID:
PMC8165030
AbstractArticlePDF–2.2M
8.
A reference map of the human binary protein interactome
Katja Luck, Dae-Kyum Kim, Luke Lambourne, Kerstin Spirohn, Bridget E. Begg, Wenting Bian, Ruth Brignall, Tiziana Cafarelli, Francisco J. Campos-Laborie, Benoit Charloteaux, Dongsic Choi, Atina G. Coté, Meaghan Daley, Steven Deimling, Alice Desbuleux, Amélie Dricot, Marinella Gebbia, Madeleine F. Hardy, Nishka Kishore, Jennifer J. Knapp, István A. Kovács, Irma Lemmens, Miles W. Mee, Joseph C. Mellor, Carl Pollis, Carles Pons, Aaron D. Richardson, Sadie Schlabach, Bridget Teeking, Anupama Yadav, Mariana Babor, Dawit Balcha, Omer Basha, Christian Bowman-Colin, Suet-Feung Chin, Soon Gang Choi, Claudia Colabella, Georges Coppin, Cassandra D’Amata, David De Ridder, Steffi De Rouck, Miquel Duran-Frigola, Hanane Ennajdaoui, Florian Goebels, Liana Goehring, Anjali Gopal, Ghazal Haddad, Elodie Hatchi, Mohamed Helmy, Yves Jacob, Yoseph Kassa, Serena Landini, Roujia Li, Natascha van Lieshout, Andrew MacWilliams, Dylan Markey, Joseph N. Paulson, Sudharshan Rangarajan, John Rasla, Ashyad Rayhan, Thomas Rolland, Adriana San-Miguel, Yun Shen, Dayag Sheykhkarimli, Gloria M. Sheynkman, Eyal Simonovsky, Murat Taşan, Alexander Tejeda, Vincent Tropepe, Jean-Claude Twizere, Yang Wang, Robert J. Weatheritt, Jochen Weile, Yu Xia, Xinping Yang, Esti Yeger-Lotem, Quan Zhong, Patrick Aloy, Gary D. Bader, Javier De Las Rivas, Suzanne Gaudet, Tong Hao, Janusz Rak, Jan Tavernier, David E. Hill, Marc Vidal, Frederick P. Roth, Michael A. Calderwood
Nature. Author manuscript; available in PMC 2020 Oct 8.
Published in final edited form as: Nature. 2020 Apr; 580(7803): 402–408. Published online 2020 Apr 8. doi: 10.1038/s41586-020-2188-x
PMCID:
PMC7169983
AbstractArticlePDF–5.4M
9.
Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations
Robert Fragoza, Jishnu Das, Shayne D. Wierbowski, Jin Liang, Tina N. Tran, Siqi Liang, Juan F. Beltran, Christen A. Rivera-Erick, Kaixiong Ye, Ting-Yi Wang, Li Yao, Matthew Mort, Peter D. Stenson, David N. Cooper, Xiaomu Wei, Alon Keinan, John C. Schimenti, Andrew G. Clark, Haiyuan Yu
Nat Commun. 2019; 10: 4141. Published online 2019 Sep 12. doi: 10.1038/s41467-019-11959-3
PMCID:
PMC6742646
AbstractArticlePDF–1.2M
10.
Analysis of the Zn-Binding Domains of TRIM32, the E3 Ubiquitin Ligase Mutated in Limb Girdle Muscular Dystrophy 2H
Elisa Lazzari, Medhat S. El-Halawany, Matteo De March, Floriana Valentino, Francesco Cantatore, Chiara Migliore, Silvia Onesti, Germana Meroni
Cells. 2019 Mar; 8(3): 254. Published online 2019 Mar 16. doi: 10.3390/cells8030254
PMCID:
PMC6468550
AbstractArticlePDF–5.1M
11.
The MALDI-TOF E2/E3 Ligase Assay as Universal Tool for Drug Discovery in the Ubiquitin Pathway
Virginia De Cesare, Clare Johnson, Victoria Barlow, James Hastie, Axel Knebel, Matthias Trost
Cell Chem Biol. 2018 Sep 20; 25(9): 1117–1127.e4. doi: 10.1016/j.chembiol.2018.06.004
PMCID:
PMC6162346
AbstractArticle
12.
Real-time tracking of complex ubiquitination cascades using a fluorescent confocal on-bead assay
Joanna Koszela, Nhan T. Pham, David Evans, Stefan Mann, Irene Perez-Pi, Steven Shave, Derek F. J. Ceccarelli, Frank Sicheri, Mike Tyers, Manfred Auer
BMC Biol. 2018; 16: 88. Published online 2018 Aug 10. doi: 10.1186/s12915-018-0554-z
PMCID:
PMC6086040
AbstractArticlePDF–1.4M
13.
Ubiquitination of STING at lysine 224 controls IRF3 activation
Guoxin Ni, Hiroyasu Konno, Glen N. Barber
Sci Immunol. Author manuscript; available in PMC 2017 Oct 25.
Published in final edited form as: Sci Immunol. 2017 May 5; 2(11): eaah7119. doi: 10.1126/sciimmunol.aah7119
PMCID:
PMC5656267
AbstractArticlePDF–2.2M
14.
Structure and catalytic activation of the TRIM23 RING E3 ubiquitin ligase
Daria M. Dawidziak, Jacint G. Sanchez, Jonathan M. Wagner, Barbie K. Ganser-Pornillos, Owen Pornillos
Proteins. Author manuscript; available in PMC 2018 Oct 1.
Published in final edited form as: Proteins. 2017 Oct; 85(10): 1957–1961. Published online 2017 Jul 24. doi: 10.1002/prot.25348
PMCID:
PMC5638660
AbstractArticlePDF–881K
15.
Mammalian APE1 controls miRNA processing and its interactome is linked to cancer RNA metabolism
Giulia Antoniali, Fabrizio Serra, Lisa Lirussi, Mikiei Tanaka, Chiara D’Ambrosio, Shiheng Zhang, Slobodanka Radovic, Emiliano Dalla, Yari Ciani, Andrea Scaloni, Mengxia Li, Silvano Piazza, Gianluca Tell
Nat Commun. 2017; 8: 797. Published online 2017 Oct 6. doi: 10.1038/s41467-017-00842-8
PMCID:
PMC5630600
AbstractArticlePDF–2.3M
16.
Osmotic and Heat Stress-dependent Regulation of MLK4β and MLK3 by the CHIP E3 Ligase in Ovarian Cancer Cells
Natalya A. Blessing, Srimathi Kasturirangan, Evan M. Zink, April L. Schroyer, Deborah N. Chadee
Cell Signal. Author manuscript; available in PMC 2018 Nov 1.
Published in final edited form as: Cell Signal. 2017 Nov; 39: 66–73. Published online 2017 Jul 28. doi: 10.1016/j.cellsig.2017.07.021
PMCID:
PMC5592140
AbstractArticlePDF–1.0M
17.
Architecture of the human interactome defines protein communities and disease networks
Edward L. Huttlin, Raphael J. Bruckner, Joao A. Paulo, Joe R. Cannon, Lily Ting, Kurt Baltier, Greg Colby, Fana Gebreab, Melanie P. Gygi, Hannah Parzen, John Szpyt, Stanley Tam, Gabriela Zarraga, Laura Pontano-Vaites, Sharan Swarup, Anne E. White, Devin K. Schweppe, Ramin Rad, Brian K. Erickson, Robert A. Obar, K.G. Guruharsha, Kejie Li, Spyros Artavanis-Tsakonas, Steven P. Gygi, J. Wade Harper
Nature. Author manuscript; available in PMC 2017 Nov 17.
Published in final edited form as: Nature. 2017 May 25; 545(7655): 505–509. Published online 2017 May 17. doi: 10.1038/nature22366
PMCID:
PMC5531611
AbstractArticlePDF–2.7M
18.
A cascading activity-based probe sequentially targets E1–E2–E3 ubiquitin enzymes
Monique P.C. Mulder, Katharina Witting, Ilana Berlin, Jonathan N. Pruneda, Kuen-Phon Wu, Jer-Gung Chang, Remco Merkx, Johanna Bialas, Marcus Groettrup, Alfred C.O. Vertegaal, Brenda A. Schulman, David Komander, Jacques Neefjes, Farid El Oualid, Huib Ovaa
Nat Chem Biol. Author manuscript; available in PMC 2017 Jan 1.
Published in final edited form as: Nat Chem Biol. 2016 Jul; 12(7): 523–530. Published online 2016 May 16. doi: 10.1038/nchembio.2084
PMCID:
PMC5108872
AbstractArticlePDF–2.4M
19.
Synthesis of Isomeric Phosphoubiquitin Chains Reveals that Phosphorylation Controls Deubiquitinase Activity and Specificity
Nicolas Huguenin-Dezot, Virginia De Cesare, Julien Peltier, Axel Knebel, Yosua Adi Kristaryianto, Daniel T. Rogerson, Yogesh Kulathu, Matthias Trost, Jason W. Chin
Cell Rep. 2016 Jul 26; 16(4): 1180–1193. Published online 2016 Jul 14. doi: 10.1016/j.celrep.2016.06.064
PMCID:
PMC4967478
AbstractArticle
20.
Accumulation of p53 via down-regulation of UBE2D family genes is a critical pathway for cadmium-induced renal toxicity
Jin-Yong Lee, Maki Tokumoto, Yasuyuki Fujiwara, Tatsuya Hasegawa, Yoshiyuki Seko, Akinori Shimada, Masahiko Satoh
Sci Rep. 2016; 6: 21968. Published online 2016 Feb 25. doi: 10.1038/srep21968
PMCID:
PMC4766413
AbstractArticlePDF–2.2M

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