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Select item 110623591.

ATG8 proteins are co-factors for human dopaminergic neuronal transcriptional control: implications for neuronal resilience in Parkinson disease

Natalia Jiménez-Moreno, Jon D. Lane

Autophagy. 2024; 20(4): 955–957. Published online 2023 Jun 20. doi: 10.1080/15548627.2023.2221958

PMCID:: PMC11062359

Abstract Article PDF–440K

Select item 108832802.

Systematic discovery of protein interaction interfaces using AlphaFold and experimental validation

Chop Yan Lee, Dalmira Hubrich, Julia K Varga, Christian Schäfer, Mareen Welzel, Eric Schumbera, Milena Djokic, Joelle M Strom, Jonas Schönfeld, Johanna L Geist, Feyza Polat, Toby J Gibson, Claudia Isabelle Keller Valsecchi, Manjeet Kumar, Ora Schueler-Furman, Katja Luck

Mol Syst Biol. 2024 Feb; 20(2): 75–97. Published online 2024 Jan 15. doi: 10.1038/s44320-023-00005-6

PMCID:: PMC10883280

Abstract Article PDF–3.4M

Select item 103338843.

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

Abstract Article PDF–5.0M

Select item 102374224.

TRIM67 drives tumorigenesis in oligodendrogliomas through Rho GTPase-dependent membrane blebbing

Engin Demirdizen, Ruslan Al-Ali, Ashwin Narayanan, Xueyuan Sun, Julianna Patricia Varga, Bianca Steffl, Manuela Brom, Damir Krunic, Claudia Schmidt, Gabriele Schmidt, Felix Bestvater, Julian Taranda, Şevin Turcan

Neuro Oncol. 2023 Jun; 25(6): 1031–1043. Published online 2022 Nov 22. doi: 10.1093/neuonc/noac233

PMCID:: PMC10237422

Abstract Article PDF–23M

Select item 101516155.

Cross-linking mass spectrometry discovers, evaluates, and corroborates structures and protein–protein interactions in the human cell

Tara K. Bartolec, Xabier Vázquez-Campos, Alexander Norman, Clement Luong, Marcus Johnson, Richard J. Payne, Marc R. Wilkins, Joel P. Mackay, Jason K. K. Low

Proc Natl Acad Sci U S A. 2023 Apr 25; 120(17): e2219418120. Published online 2023 Apr 18. doi: 10.1073/pnas.2219418120

PMCID:: PMC10151615

Abstract Article PDF–2.9M

Select item 97979886.

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

Abstract Article PDF–6.9M

Select item 94509797.

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

Abstract Article PDF–6.3M

Select item 93569368.

Neuronal-specific septin-3 binds Atg8/LC3B, accumulates and localizes to autophagosomes during induced autophagy

Vilmos Tóth, Henrietta Vadászi, Lilla Ravasz, Dániel Mittli, Dominik Mátyás, Tamás Molnár, András Micsonai, Tamás Szaniszló, Péter Lőrincz, Réka Á. Kovács, Tünde Juhász, Tamás Beke-Somfai, Gábor Juhász, Balázs András Györffy, Katalin A. Kékesi, József Kardos

Cell Mol Life Sci. 2022 Sep; 79(9): 471. Published online 2022 Aug 6. doi: 10.1007/s00018-022-04488-8

PMCID:: PMC9356936

Abstract Article PDF–6.9M

Select item 92792859.

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

Abstract Article PDF–2.5M

Select item 919674710.

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

Abstract Article PDF–3.1M

Select item 911973611.

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

Abstract Article PDF–3.3M

Select item 903739712.

The V-ATPase complex regulates non-canonical Atg8-family protein lipidation through ATG16L1 recruitment

Lewis Timimi, Carmen Figueras-Novoa, Elena Marcassa, Oliver Florey, J Kenneth Baillie, Rupert Beale, Rachel Ulferts

Autophagy. 2022; 18(3): 707–708. Published online 2022 Mar 8. doi: 10.1080/15548627.2022.2029233

PMCID:: PMC9037397

Abstract Article PDF–715K

Select item 895155613.

A BioID-Derived Proximity Interactome for SARS-CoV-2 Proteins

Danielle G. May, Laura Martin-Sancho, Valesca Anschau, Sophie Liu, Rachel J. Chrisopulos, Kelsey L. Scott, Charles T. Halfmann, Ramon Díaz Peña, Dexter Pratt, Alexandre R. Campos, Kyle J. Roux

Viruses. 2022 Mar; 14(3): 611. Published online 2022 Mar 15. doi: 10.3390/v14030611

PMCID:: PMC8951556

Abstract Article PDF–4.4M

Select item 876207814.

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

Abstract Article PDF–2.4M

Select item 851385315.

The proximal proteome of 17 SARS-CoV-2 proteins links to disrupted antiviral signaling and host translation

Jordan M. Meyers, Muthukumar Ramanathan, Ronald L. Shanderson, Aimee Beck, Laura Donohue, Ian Ferguson, Margaret G. Guo, Deepti S. Rao, Weili Miao, David Reynolds, Xue Yang, Yang Zhao, Yen-Yu Yang, Catherine Blish, Yinsheng Wang, Paul A. Khavari

PLoS Pathog. 2021 Oct; 17(10): e1009412. Published online 2021 Oct 1. doi: 10.1371/journal.ppat.1009412

PMCID:: PMC8513853

Abstract Article PDF–4.1M

Select item 836418116.

Protein interaction landscapes revealed by advanced in vivo cross-linking–mass spectrometry

Andrew Wheat, Clinton Yu, Xiaorong Wang, Anthony M. Burke, Ilan E. Chemmama, Robyn M. Kaake, Peter Baker, Scott D. Rychnovsky, Jing Yang, Lan Huang

Proc Natl Acad Sci U S A. 2021 Aug 10; 118(32): e2023360118. Published online 2021 Aug 4. doi: 10.1073/pnas.2023360118

PMCID:: PMC8364181

Abstract Article PDF–3.0M

Select item 822039117.

PRISMA and BioID disclose a motifs-based interactome of the intrinsically disordered transcription factor C/EBPα

Evelyn Ramberger, Valeria Sapozhnikova, Elisabeth Kowenz-Leutz, Karin Zimmermann, Nathalie Nicot, Petr V. Nazarov, Daniel Perez-Hernandez, Ulf Reimer, Philipp Mertins, Gunnar Dittmar, Achim Leutz

iScience. 2021 Jun 25; 24(6): 102686. Published online 2021 Jun 4. doi: 10.1016/j.isci.2021.102686

PMCID:: PMC8220391

Abstract Article PDF–4.4M

Select item 820233018.

Phosphorylation of the LIR Domain of SCOC Modulates ATG8 Binding Affinity and Specificity

Martina Wirth, Stephane Mouilleron, Wenxin Zhang, Eva Sjøttem, Yakubu Princely Abudu, Ashish Jain, Hallvard Lauritz Olsvik, Jack-Ansgar Bruun, Minoo Razi, Harold B.J. Jefferies, Rebecca Lee, Dhira Joshi, Nicola O'Reilly, Terje Johansen, Sharon A. Tooze

J Mol Biol. 2021 Jun 25; 433(13): 166987. doi: 10.1016/j.jmb.2021.166987

Correction in:: J Mol Biol. 2021 Jul 23; 433(15): 167049.

PMCID:: PMC8202330

Abstract Article

Select item 816503019.

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

Abstract Article PDF–2.2M

Select item 812213820.

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

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