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Items: 1 to 20 of 78

1.
Proteome-scale characterisation of motif-based interactome rewiring by disease mutations
Johanna Kliche, Leandro Simonetti, Izabella Krystkowiak, Hanna Kuss, Marcel Diallo, Emma Rask, Jakob Nilsson, Norman E Davey, Ylva Ivarsson
Mol Syst Biol. 2024 Sep; 20(9): 1025–1048. Published online 2024 Jul 15. doi: 10.1038/s44320-024-00055-4
PMCID:
PMC11369174
AbstractArticlePDF–2.7M
2.
The transcription factor NRF1 (NFE2L1) activates aggrephagy by inducing p62 and GABARAPL1 after proteasome inhibition to maintain proteostasis
Atsushi Hatanaka, Sota Nakada, Gen Matsumoto, Katsuya Satoh, Iori Aketa, Akira Watanabe, Tomoaki Hirakawa, Tadayuki Tsujita, Tsuyoshi Waku, Akira Kobayashi
Sci Rep. 2023; 13: 14405. Published online 2023 Sep 1. doi: 10.1038/s41598-023-41492-9
PMCID:
PMC10474156
AbstractArticlePDF–2.8M
3.
METTL3 promotes hyperoxia-induced pyroptosis in neonatal bronchopulmonary dysplasia by inhibiting ATG8-mediated autophagy
Lili Xu, Zhan Shi, Zhaojun Pan, Rong Wu
Clinics (Sao Paulo) 2023 Jan-Dec; 78: 100253. Published online 2023 Jul 19. doi: 10.1016/j.clinsp.2023.100253
PMCID:
PMC10387564
AbstractArticlePDF–3.9M
4.
Large‐scale phosphomimetic screening identifies phospho‐modulated motif‐based protein interactions
Johanna Kliche, Dimitriya Hristoforova Garvanska, Leandro Simonetti, Dilip Badgujar, Doreen Dobritzsch, Jakob Nilsson, Norman E Davey, Ylva Ivarsson
Mol Syst Biol. 2023 Jul; 19(7): e11164. Published online 2023 May 23. doi: 10.15252/msb.202211164
PMCID:
PMC10333884
AbstractArticlePDF–5.0M
5.
Ubiquitination regulates ER-phagy and remodelling of endoplasmic reticulum
Alexis González, Adriana Covarrubias-Pinto, Ramachandra M. Bhaskara, Marius Glogger, Santosh K. Kuncha, Audrey Xavier, Eric Seemann, Mohit Misra, Marina E. Hoffmann, Bastian Bräuning, Ashwin Balakrishnan, Britta Qualmann, Volker Dötsch, Brenda A. Schulman, Michael M. Kessels, Christian A. Hübner, Mike Heilemann, Gerhard Hummer, Ivan Dikić
Nature. 2023; 618(7964): 394–401. Published online 2023 May 24. doi: 10.1038/s41586-023-06089-2
PMCID:
PMC10247366
AbstractArticlePDF–24M
6.
ATG8-dependent LMX1B-autophagy crosstalk shapes human midbrain dopaminergic neuronal resilience
Natalia Jiménez-Moreno, Madhu Kollareddy, Petros Stathakos, Joanna J. Moss, Zuriñe Antón, Deborah K. Shoemark, Richard B. Sessions, Ralph Witzgall, Maeve Caldwell, Jon D. Lane
J Cell Biol. 2023 May 1; 222(5): e201910133. Published online 2023 Apr 4. doi: 10.1083/jcb.201910133
PMCID:
PMC10075225
AbstractArticlePDF–8.5M
7.
Multiplexed kinase interactome profiling quantifies cellular network activity and plasticity
Martin Golkowski, Andrea Lius, Tanmay Sapre, Ho-Tak Lau, Taylor Moreno, Dustin J. Maly, Shao-En Ong
Mol Cell. Author manuscript; available in PMC 2023 Apr 4.
Published in final edited form as: Mol Cell. 2023 Mar 2; 83(5): 803–818.e8. Published online 2023 Feb 2. doi: 10.1016/j.molcel.2023.01.015
PMCID:
PMC10072906
AbstractArticlePDF–4.2M
8.
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
9.
TBK1 posphorylation activates LIR-dependent degradation of the inflammation repressor TNIP1
Jianwen Zhou, Nikoline Lander Rasmussen, Hallvard Lauritz Olsvik, Vyacheslav Akimov, Zehan Hu, Gry Evjen, Stéphanie Kaeser-Pebernard, Devanarayanan Siva Sankar, Carole Roubaty, Pauline Verlhac, Nicole van de Beek, Fulvio Reggiori, Yakubu Princely Abudu, Blagoy Blagoev, Trond Lamark, Terje Johansen, Jörn Dengjel
J Cell Biol. 2023 Feb 6; 222(2): e202108144. Published online 2022 Dec 27. doi: 10.1083/jcb.202108144
PMCID:
PMC9797988
AbstractArticlePDF–6.9M
10.
Loss of GABARAPL1 confers ferroptosis resistance to cancer stem‐like cells in hepatocellular carcinoma
Xiaojing Du, Zhuoran Qi, Jinzhi Xu, Mengzhou Guo, Xingxing Zhang, Zhijie Yu, Xin Cao, Jinglin Xia
Mol Oncol. 2022 Oct; 16(20): 3703–3719. Published online 2022 Sep 5. doi: 10.1002/1878-0261.13305
PMCID:
PMC9580891
AbstractArticlePDF–3.3M
11.
Stress granules and mTOR are regulated by membrane atg8ylation during lysosomal damage
Jingyue Jia, Fulong Wang, Zambarlal Bhujabal, Ryan Peters, Michal Mudd, Thabata Duque, Lee Allers, Ruheena Javed, Michelle Salemi, Christian Behrends, Brett Phinney, Terje Johansen, Vojo Deretic
J Cell Biol. 2022 Nov 7; 221(11): e202207091. Published online 2022 Sep 30. doi: 10.1083/jcb.202207091
PMCID:
PMC9533235
AbstractArticlePDF–9.7M
12.
HYPK coordinates degradation of polyneddylated proteins by autophagy
Debasish Kumar Ghosh, Akash Ranjan
Autophagy. 2022; 18(8): 1763–1784. Published online 2021 Nov 26. doi: 10.1080/15548627.2021.1997053
PMCID:
PMC9450979
AbstractArticlePDF–6.3M
13.
Scalable multiplex co-fractionation/mass spectrometry platform for accelerated protein interactome discovery
Pierre C. Havugimana, Raghuveera Kumar Goel, Sadhna Phanse, Ahmed Youssef, Dzmitry Padhorny, Sergei Kotelnikov, Dima Kozakov, Andrew Emili
Nat Commun. 2022; 13: 4043. Published online 2022 Jul 13. doi: 10.1038/s41467-022-31809-z
PMCID:
PMC9279285
AbstractArticlePDF–2.5M
14.
Global Proximity Interactome of the Human Macroautophagy Pathway
Yi Xin (Iris) Tu, Andrew M. Sydor, Etienne Coyaud, Estelle M. N. Laurent, Diana Dyer, Nora Mellouk, Jonathan St-Germain, Robert M. Vernon, Julie D. Forman-Kay, Taoyingnan Li, Rong Hua, Kexin Zhao, Neale D. Ridgway, Peter K. Kim, Brian Raught, John H. Brumell
Autophagy. 2022; 18(5): 1174–1186. Published online 2021 Sep 15. doi: 10.1080/15548627.2021.1965711
PMCID:
PMC9196747
AbstractArticlePDF–3.1M
15.
OpenCell: proteome-scale endogenous tagging enables the cartography of human cellular organization
Nathan H. Cho, Keith C. Cheveralls, Andreas-David Brunner, Kibeom Kim, André C. Michaelis, Preethi Raghavan, Hirofumi Kobayashi, Laura Savy, Jason Y. Li, Hera Canaj, James Y.S. Kim, Edna M. Stewart, Christian Gnann, Frank McCarthy, Joana P. Cabrera, Rachel M. Brunetti, Bryant B. Chhun, Greg Dingle, Marco Y. Hein, Bo Huang, Shalin B. Mehta, Jonathan S. Weissman, Rafael Gómez-Sjöberg, Daniel N. Itzhak, Loic A. Royer, Matthias Mann, Manuel D. Leonetti
Science. Author manuscript; available in PMC 2022 Sep 11.
Published in final edited form as: Science. 2022 Mar 11; 375(6585): eabi6983. Published online 2022 Mar 11. doi: 10.1126/science.abi6983
PMCID:
PMC9119736
AbstractArticlePDF–3.3M
16.
An ALS-associated variant of the autophagy receptor SQSTM1/p62 reprograms binding selectivity toward the autophagy-related hATG8 proteins
Andrew Brennan, Robert Layfield, Jed Long, Huw E.L. Williams, Neil J. Oldham, Daniel Scott, Mark S. Searle
J Biol Chem. 2022 Feb; 298(2): 101514. Published online 2021 Dec 18. doi: 10.1016/j.jbc.2021.101514
PMCID:
PMC8762078
AbstractArticlePDF–2.4M
17.
Systematic identification of NF90 target RNAs by iCLIP analysis
Valeria Lodde, Matteo Floris, Rachel Munk, Jennifer L. Martindale, Davide Piredda, Catello Mario Panu Napodano, Francesco Cucca, Sergio Uzzau, Kotb Abdelmohsen, Myriam Gorospe, Ji Heon Noh, M. Laura Idda
Sci Rep. 2022; 12: 364. Published online 2022 Jan 10. doi: 10.1038/s41598-021-04101-1
PMCID:
PMC8748789
AbstractArticlePDF–4.2M
18.
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
19.
Non-canonical autophagy drives alternative ATG8 conjugation to phosphatidylserine
Joanne Durgan, Alf H. Lystad, Katherine Sloan, Sven R. Carlsson, Michael I. Wilson, Elena Marcassa, Rachel Ulferts, Judith Webster, Andrea F. Lopez-Clavijo, Michael J. Wakelam, Rupert Beale, Anne Simonsen, David Oxley, Oliver Florey
Mol Cell. 2021 May 6; 81(9): 2031–2040.e8. doi: 10.1016/j.molcel.2021.03.020
PMCID:
PMC8122138
AbstractArticle
20.
Lack of GABARAP-Type Proteins Is Accompanied by Altered Golgi Morphology and Surfaceome Composition
Julia L. Sanwald, Jochen Dobner, Indra M. Simons, Gereon Poschmann, Kai Stühler, Alina Üffing, Silke Hoffmann, Dieter Willbold
Int J Mol Sci. 2021 Jan; 22(1): 85. Published online 2020 Dec 23. doi: 10.3390/ijms22010085
PMCID:
PMC7795684
AbstractArticlePDF–2.8M

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