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Select item 114236781.

An APEX2-based proximity-dependent biotinylation assay with temporal specificity to study protein interactions during autophagy in the yeast Saccharomyces cerevisiae

Yasmina Filali-Mouncef, Alexandre Leytens, Prado Vargas Duarte, Mattia Zampieri, Jörn Dengjel, Fulvio Reggiori

Autophagy. 2024; 20(10): 2323–2337. Published online 2024 Jul 3. doi: 10.1080/15548627.2024.2366749

PMCID:: PMC11423678

Abstract Article PDF–1.7M

Select item 108799852.

Structure of the Preholoproteasome Reveals Late Steps in Proteasome Core Particle Biogenesis

Richard M. Walsh, Jr., Shaun Rawson, Helena M. Schnell, Benjamin Velez, Tamayanthi Rajakumar, John Hanna

Nat Struct Mol Biol. Author manuscript; available in PMC 2024 Apr 1.

Published in final edited form as: Nat Struct Mol Biol. 2023 Oct; 30(10): 1516–1524. Published online 2023 Aug 31. doi: 10.1038/s41594-023-01081-w

PMCID:: PMC10879985

Abstract Article PDF–3.5M

Select item 108724773.

Protein interaction network revealed by quantitative proteomic analysis links TFIIB to multiple aspects of the transcription cycle

Michael J. O’Brien, Athar Ansari

Biochim Biophys Acta Proteins Proteom. Author manuscript; available in PMC 2024 Feb 16.

Published in final edited form as: Biochim Biophys Acta Proteins Proteom. 2024 Jan 1; 1872(1): 140968. Published online 2023 Oct 19. doi: 10.1016/j.bbapap.2023.140968

PMCID:: PMC10872477

Abstract Article PDF–1.7M

Select item 108687274.

Adaptive preservation of orphan ribosomal proteins in chaperone-dispersed condensates

Asif Ali, Rania Garde, Olivia C. Schaffer, Jared A. M. Bard, Kabir Husain, Samantha Keyport Kik, Kathleen A. Davis, Sofia Luengo-Woods, Maya G. Igarashi, D. Allan Drummond, Allison H. Squires, David Pincus

Nat Cell Biol. Author manuscript; available in PMC 2024 Feb 15.

Published in final edited form as: Nat Cell Biol. 2023 Nov; 25(11): 1691–1703. Published online 2023 Oct 16. doi: 10.1038/s41556-023-01253-2

PMCID:: PMC10868727

Abstract Article PDF–7.0M

Select item 107001385.

The social and structural architecture of the yeast protein interactome

André C. Michaelis, Andreas-David Brunner, Maximilian Zwiebel, Florian Meier, Maximilian T. Strauss, Isabell Bludau, Matthias Mann

Nature. 2023; 624(7990): 192–200. Published online 2023 Nov 15. doi: 10.1038/s41586-023-06739-5

PMCID:: PMC10700138

Abstract Article PDF–20M

Select item 102922106.

Nuclear pore complexes mediate subtelomeric gene silencing by regulating PCNA levels on chromatin

Sanjeev Kumar Choudhry, Maxwell L. Neal, Song Li, Arti T. Navare, Trevor Van Eeuwen, Richard W. Wozniak, Fred D. Mast, Michael P. Rout, John D. Aitchison

J Cell Biol. 2023 Sep 4; 222(9): e202207060. Published online 2023 Jun 26. doi: 10.1083/jcb.202207060

PMCID:: PMC10292210

Abstract Article PDF–5.9M

Select item 102333687.

A systematic proximity ligation approach to studying protein‐substrate specificity identifies the substrate spectrum of the Ssh1 translocon

Nir Cohen, Naama Aviram, Maya Schuldiner

EMBO J. 2023 Jun; 42(11): e113385. Published online 2023 Apr 19. doi: 10.15252/embj.2022113385

PMCID:: PMC10233368

Abstract Article PDF–1.2M

Select item 95136778.

Systematic multi‐level analysis of an organelle proteome reveals new peroxisomal functions

Eden Yifrach, Duncan Holbrook‐Smith, Jérôme Bürgi, Alaa Othman, Miriam Eisenstein, Carlo WT van Roermund, Wouter Visser, Asa Tirosh, Markus Rudowitz, Chen Bibi, Shahar Galor, Uri Weill, Amir Fadel, Yoav Peleg, Ralf Erdmann, Hans R Waterham, Ronald J A Wanders, Matthias Wilmanns, Nicola Zamboni, Maya Schuldiner, Einat Zalckvar

Mol Syst Biol. 2022 Sep; 18(9): e11186. Published online 2022 Sep 27. doi: 10.15252/msb.202211186

PMCID:: PMC9513677

Abstract Article PDF–3.3M

Select item 92098119.

New data and collaborations at the Saccharomyces Genome Database: updated reference genome, alleles, and the Alliance of Genome Resources

Stacia R Engel, Edith D Wong, Robert S Nash, Suzi Aleksander, Micheal Alexander, Eric Douglass, Kalpana Karra, Stuart R Miyasato, Matt Simison, Marek S Skrzypek, Shuai Weng, J Michael Cherry

Genetics. 2022 Apr; 220(4): iyab224. Published online 2021 Dec 13. doi: 10.1093/genetics/iyab224

PMCID:: PMC9209811

Abstract Article PDF–818K

Select item 857106310.

Systems-level effects of allosteric perturbations to a model molecular switch

Tina Perica, Christopher J. P. Mathy, Jiewei Xu, Gwendolyn M. Jang, Yang Zhang, Robyn Kaake, Noah Ollikainen, Hannes Braberg, Danielle L. Swaney, David G. Lambright, Mark J. S. Kelly, Nevan J. Krogan, Tanja Kortemme

Nature. Author manuscript; available in PMC 2022 May 1.

Published in final edited form as: Nature. 2021 Nov; 599(7883): 152–157. Published online 2021 Oct 13. doi: 10.1038/s41586-021-03982-6

PMCID:: PMC8571063

Abstract Article PDF–2.7M

Select item 816058011.

Structures of Chaperone-Associated Assembly Intermediates Reveal Coordinated Mechanisms of Proteasome Biogenesis

Helena M. Schnell, Richard M. Walsh, Jr., Shaun Rawson, Mandeep Kaur, Meera K. Bhanu, Geng Tian, Miguel A. Prado, Angel Guerra-Moreno, Joao A. Paulo, Steven P. Gygi, Jeroen Roelofs, Daniel Finley, John Hanna

Nat Struct Mol Biol. Author manuscript; available in PMC 2021 Nov 1.

Published in final edited form as: Nat Struct Mol Biol. 2021 May; 28(5): 418–425. Published online 2021 Apr 12. doi: 10.1038/s41594-021-00583-9

PMCID:: PMC8160580

Abstract Article PDF–6.2M

Select item 774881612.

Subcellular localization of the J-protein Sis1 regulates the heat shock response

Zoë A. Feder, Asif Ali, Abhyudai Singh, Joanna Krakowiak, Xu Zheng, Vytas P. Bindokas, Donald Wolfgeher, Stephen J. Kron, David Pincus

J Cell Biol. 2021 Jan 4; 220(1): e202005165. Published online 2020 Dec 16. doi: 10.1083/jcb.202005165

PMCID:: PMC7748816

Abstract Article PDF–4.6M

Select item 771875113.

Comprehensive Synthetic Genetic Array Analysis of Alleles That Interact with Mutation of the Saccharomyces cerevisiae RecQ Helicases Hrq1 and Sgs1

Elsbeth Sanders, Phoebe A. Nguyen, Cody M. Rogers, Matthew L. Bochman

G3 (Bethesda) 2020 Dec; 10(12): 4359–4368. Published online 2020 Oct 28. doi: 10.1534/g3.120.401709

PMCID:: PMC7718751

Abstract Article PDF–1.2M

Select item 769987314.

The Proteasome Activators Blm10/PA200 Enhance the Proteasomal Degradation of N-Terminal Huntingtin

Azzam Aladdin, Yanhua Yao, Ciyu Yang, Günther Kahlert, Marvi Ghani, Nikolett Király, Anita Boratkó, Karen Uray, Gunnar Dittmar, Krisztina Tar

Biomolecules. 2020 Nov; 10(11): 1581. Published online 2020 Nov 20. doi: 10.3390/biom10111581

PMCID:: PMC7699873

Abstract Article PDF–7.2M

Select item 766412215.

The Capture of a Disabled Proteasome Identifies Erg25 as a Substrate for Endoplasmic Reticulum Associated Degradation

Teresa M. Buck, Xuemei Zeng, Pamela S. Cantrell, Richard T. Cattley, Zikri Hasanbasri, Megan E. Yates, Diep Nguyen, Nathan A. Yates, Jeffrey L. Brodsky

Mol Cell Proteomics. 2020 Nov; 19(11): 1896–1909. Published online 2020 Aug 31. doi: 10.1074/mcp.RA120.002050

PMCID:: PMC7664122

Abstract Article PDF–1.2M

Select item 751569416.

RNA-binding and prion domains: the Yin and Yang of phase separation

Nieves Lorenzo Gotor, Alexandros Armaos, Giulia Calloni, Marc Torrent Burgas, R Martin Vabulas, Natalia Sanchez De Groot, Gian Gaetano Tartaglia

Nucleic Acids Res. 2020 Sep 25; 48(17): 9491–9504. Published online 2020 Aug 28. doi: 10.1093/nar/gkaa681

PMCID:: PMC7515694

Abstract Article PDF–3.1M

Select item 727317717.

Chaperone-Mediated Protein Disaggregation Triggers Proteolytic Clearance of Intra-nuclear Protein Inclusions

Fabian den Brave, Lucas V. Cairo, Chandhuru Jagadeesan, Carmen Ruger-Herreros, Axel Mogk, Bernd Bukau, Stefan Jentsch

Cell Rep. 2020 Jun 2; 31(9): 107680. Published online 2020 Jun 2. doi: 10.1016/j.celrep.2020.107680

PMCID:: PMC7273177

Abstract Article

Select item 726367518.

Dbf4-Dependent Kinase (DDK)-Mediated Proteolysis of CENP-A Prevents Mislocalization of CENP-A in Saccharomyces cerevisiae

Jessica R. Eisenstatt, Lars Boeckmann, Wei-Chun Au, Valerie Garcia, Levi Bursch, Josefina Ocampo, Michael Costanzo, Michael Weinreich, Robert A. Sclafani, Anastasia Baryshnikova, Chad L. Myers, Charles Boone, David J. Clark, Richard Baker, Munira A. Basrai

G3 (Bethesda) 2020 Jun; 10(6): 2057–2068. Published online 2020 Apr 15. doi: 10.1534/g3.120.401131

PMCID:: PMC7263675

Abstract Article PDF–1.8M

Select item 703273219.

Skp, Cullin, F-box (SCF)-Met30 and SCF-Cdc4-Mediated Proteolysis of CENP-A Prevents Mislocalization of CENP-A for Chromosomal Stability in Budding Yeast

Wei-Chun Au, Tianyi Zhang, Prashant K. Mishra, Jessica R. Eisenstatt, Robert L. Walker, Josefina Ocampo, Anthony Dawson, Jack Warren, Michael Costanzo, Anastasia Baryshnikova, Karin Flick, David J. Clark, Paul S. Meltzer, Richard E. Baker, Chad Myers, Charles Boone, Peter Kaiser, Munira A. Basrai

PLoS Genet. 2020 Feb; 16(2): e1008597. Published online 2020 Feb 7. doi: 10.1371/journal.pgen.1008597