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For: Guerrero C, Tagwerker C, Kaiser P, Huang L. An Integrated Mass Spectrometry-based Proteomic Approach. Mol Cell Proteomics 2006;5:366-78. [PMID: 16284124 DOI: 10.1074/mcp.m500303-mcp200] [Citation(s) in RCA: 223] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
Number Cited by Other Article(s)
1
Wu D, Ouyang Q, Wang H, Mao Y. A kinetic model for USP14 regulated substrate degradation in 26S proteasome. PLoS Comput Biol 2025;21:e1012761. [PMID: 40315273 PMCID: PMC12068737 DOI: 10.1371/journal.pcbi.1012761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2024] [Revised: 05/12/2025] [Accepted: 03/17/2025] [Indexed: 05/04/2025]  Open
2
Ouyang H, How CY, Wang X, Yu C, Luo A, Huang L, Chen Y. Crosslinking-mediated Interactome Analysis Identified PHD2-HIF1α Interaction Hotspots and the Role of PHD2 in Regulating Protein Neddylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.16.628769. [PMID: 39763868 PMCID: PMC11702602 DOI: 10.1101/2024.12.16.628769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2025]
3
Breckels LM, Hutchings C, Ingole KD, Kim S, Lilley KS, Makwana MV, McCaskie KJA, Villanueva E. Advances in spatial proteomics: Mapping proteome architecture from protein complexes to subcellular localizations. Cell Chem Biol 2024;31:1665-1687. [PMID: 39303701 DOI: 10.1016/j.chembiol.2024.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 08/12/2024] [Accepted: 08/20/2024] [Indexed: 09/22/2024]
4
Chandrasekharan G, Unnikrishnan M. High throughput methods to study protein-protein interactions during host-pathogen interactions. Eur J Cell Biol 2024;103:151393. [PMID: 38306772 DOI: 10.1016/j.ejcb.2024.151393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 01/18/2024] [Accepted: 01/21/2024] [Indexed: 02/04/2024]  Open
5
Sahoo MP, Lavy T, Cohen N, Sahu I, Kleifeld O. Activity-Guided Proteomic Profiling of Proteasomes Uncovers a Variety of Active (and Inactive) Proteasome Species. Mol Cell Proteomics 2024;23:100728. [PMID: 38296025 PMCID: PMC10907802 DOI: 10.1016/j.mcpro.2024.100728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 01/11/2024] [Accepted: 01/24/2024] [Indexed: 02/29/2024]  Open
6
Kovacs M, Geltinger F, Schartel L, Pöschl S, Briza P, Paschinger M, Boros K, Felder TK, Wimmer H, Duschl J, Rinnerthaler M. Ola1p trafficking indicates an interaction network between mitochondria, lipid droplets, and stress granules in times of stress. J Lipid Res 2023;64:100473. [PMID: 37949369 PMCID: PMC10757043 DOI: 10.1016/j.jlr.2023.100473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 09/25/2023] [Accepted: 11/01/2023] [Indexed: 11/12/2023]  Open
7
Zhong B, An Y, Gao H, Zhao L, Li X, Liang Z, Zhang Y, Zhao Q, Zhang L. In vivo cross-linking-based affinity purification and mass spectrometry for targeting intracellular protein-protein interactions. Anal Chim Acta 2023;1265:341273. [PMID: 37230567 DOI: 10.1016/j.aca.2023.341273] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/28/2023] [Accepted: 04/23/2023] [Indexed: 05/27/2023]
8
Choi WH, Yun Y, Byun I, Kim S, Lee S, Sim J, Levi S, Park SH, Jun J, Kleifeld O, Kim KP, Han D, Chiba T, Seok C, Kwon YT, Glickman MH, Lee MJ. ECPAS/Ecm29-mediated 26S proteasome disassembly is an adaptive response to glucose starvation. Cell Rep 2023;42:112701. [PMID: 37384533 DOI: 10.1016/j.celrep.2023.112701] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 05/07/2023] [Accepted: 06/09/2023] [Indexed: 07/01/2023]  Open
9
Griffin ME, Thompson JW, Xiao Y, Sweredoski MJ, Aksenfeld RB, Jensen EH, Koldobskaya Y, Schacht AL, Kim TD, Choudhry P, Lomenick B, Garbis SD, Moradian A, Hsieh-Wilson LC. Functional glycoproteomics by integrated network assembly and partitioning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.13.541482. [PMID: 37398272 PMCID: PMC10312638 DOI: 10.1101/2023.06.13.541482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
10
Lin Z, Li R, Han Z, Liu Y, Gao L, Huang S, Miao Y, Miao R. The Universally Conserved Unconventional G Protein YchF Is Critical for Growth and Stress Response. Life (Basel) 2023;13:life13041058. [PMID: 37109587 PMCID: PMC10144078 DOI: 10.3390/life13041058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023]  Open
11
Buneeva OA, Kopylov AT, Medvedev AE. Proteasome Interactome and Its Role in the Mechanisms of Brain Plasticity. BIOCHEMISTRY (MOSCOW) 2023;88:319-336. [PMID: 37076280 DOI: 10.1134/s0006297923030033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
12
Rogawski R, Sharon M. Characterizing Endogenous Protein Complexes with Biological Mass Spectrometry. Chem Rev 2022;122:7386-7414. [PMID: 34406752 PMCID: PMC9052418 DOI: 10.1021/acs.chemrev.1c00217] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Indexed: 01/11/2023]
13
Wippel HH, Chavez JD, Tang X, Bruce JE. Quantitative interactome analysis with chemical cross-linking and mass spectrometry. Curr Opin Chem Biol 2022;66:102076. [PMID: 34393043 PMCID: PMC8837725 DOI: 10.1016/j.cbpa.2021.06.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/17/2021] [Accepted: 06/23/2021] [Indexed: 01/03/2023]
14
Wang Y, Hu Y, Höti N, Huang L, Zhang H. Characterization of In Vivo Protein Complexes via Chemical Cross-Linking and Mass Spectrometry. Anal Chem 2022;94:1537-1542. [PMID: 34962381 PMCID: PMC9006583 DOI: 10.1021/acs.analchem.1c02410] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
15
The Role of the Universally Conserved ATPase YchF/Ola1 in Translation Regulation during Cellular Stress. Microorganisms 2021;10:microorganisms10010014. [PMID: 35056463 PMCID: PMC8779481 DOI: 10.3390/microorganisms10010014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 12/16/2021] [Accepted: 12/20/2021] [Indexed: 11/17/2022]  Open
16
Leissing F, Misch NV, Wang X, Werner L, Huang L, Conrath U, Beckers GJM. Purification of MAP-kinase protein complexes and identification of candidate components by XL-TAP-MS. PLANT PHYSIOLOGY 2021;187:2381-2392. [PMID: 34609515 PMCID: PMC8644975 DOI: 10.1093/plphys/kiab446] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
17
Yu C, Wang X, Li W, Liu Y, Huang L. Developing a Bimolecular Affinity Purification Strategy to Isolate 26S Proteasome Holocomplexes for Complex-Centric Proteomic Analysis. Anal Chem 2021;93:13407-13413. [PMID: 34550675 DOI: 10.1021/acs.analchem.1c03551] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
18
Dannenmaier S, Desroches Altamirano C, Schüler L, Zhang Y, Hummel J, Milanov M, Oeljeklaus S, Koch HG, Rospert S, Alberti S, Warscheid B. Quantitative proteomics identifies the universally conserved ATPase Ola1p as a positive regulator of heat shock response in Saccharomyces cerevisiae. J Biol Chem 2021;297:101050. [PMID: 34571008 PMCID: PMC8531669 DOI: 10.1016/j.jbc.2021.101050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/24/2021] [Accepted: 08/04/2021] [Indexed: 12/02/2022]  Open
19
Li H, Frankenfield AM, Houston R, Sekine S, Hao L. Thiol-Cleavable Biotin for Chemical and Enzymatic Biotinylation and Its Application to Mitochondrial TurboID Proteomics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021;32:2358-2365. [PMID: 33909971 PMCID: PMC8898397 DOI: 10.1021/jasms.1c00079] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
20
Kalathiya U, Padariya M, Faktor J, Coyaud E, Alfaro JA, Fahraeus R, Hupp TR, Goodlett DR. Interfaces with Structure Dynamics of the Workhorses from Cells Revealed through Cross-Linking Mass Spectrometry (CLMS). Biomolecules 2021;11:382. [PMID: 33806612 PMCID: PMC8001575 DOI: 10.3390/biom11030382] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 12/28/2022]  Open
21
Mao Y. Structure, Dynamics and Function of the 26S Proteasome. Subcell Biochem 2021;96:1-151. [PMID: 33252727 DOI: 10.1007/978-3-030-58971-4_1] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
22
Zacharias AO, Fang Z, Rahman A, Talukder A, Cornelius S, Chowdhury SM. Affinity and chemical enrichment strategies for mapping low‐abundance protein modifications and protein‐interaction networks. J Sep Sci 2020;44:310-322. [DOI: 10.1002/jssc.202000930] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 11/24/2020] [Accepted: 11/26/2020] [Indexed: 01/07/2023]
23
Alkafeef SS, Lane S, Yu C, Zhou T, Solis NV, Filler SG, Huang L, Liu H. Proteomic profiling of the monothiol glutaredoxin Grx3 reveals its global role in the regulation of iron dependent processes. PLoS Genet 2020;16:e1008881. [PMID: 32525871 PMCID: PMC7319344 DOI: 10.1371/journal.pgen.1008881] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 06/26/2020] [Accepted: 05/22/2020] [Indexed: 12/12/2022]  Open
24
Liebelt F, Sebastian RM, Moore CL, Mulder MPC, Ovaa H, Shoulders MD, Vertegaal ACO. SUMOylation and the HSF1-Regulated Chaperone Network Converge to Promote Proteostasis in Response to Heat Shock. Cell Rep 2020;26:236-249.e4. [PMID: 30605679 PMCID: PMC6316133 DOI: 10.1016/j.celrep.2018.12.027] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/22/2018] [Accepted: 12/05/2018] [Indexed: 12/21/2022]  Open
25
Zhang J, Zhao R, Yu C, Bryant CLN, Wu K, Liu Z, Ding Y, Zhao Y, Xue B, Pan ZQ, Li C, Huang L, Fang L. IKK-Mediated Regulation of the COP9 Signalosome via Phosphorylation of CSN5. J Proteome Res 2020;19:1119-1130. [PMID: 31950832 DOI: 10.1021/acs.jproteome.9b00626] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
26
Stevens LM, Zhang Y, Volnov Y, Chen G, Stein DS. Isolation of secreted proteins from Drosophila ovaries and embryos through in vivo BirA-mediated biotinylation. PLoS One 2019;14:e0219878. [PMID: 31658274 PMCID: PMC6816556 DOI: 10.1371/journal.pone.0219878] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 10/15/2019] [Indexed: 02/07/2023]  Open
27
Lin DW, Chung BP, Huang JW, Wang X, Huang L, Kaiser P. Microhomology-based CRISPR tagging tools for protein tracking, purification, and depletion. J Biol Chem 2019;294:10877-10885. [PMID: 31138654 DOI: 10.1074/jbc.ra119.008422] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 05/07/2019] [Indexed: 12/26/2022]  Open
28
Thibaudeau TA, Smith DM. A Practical Review of Proteasome Pharmacology. Pharmacol Rev 2019;71:170-197. [PMID: 30867233 PMCID: PMC6423620 DOI: 10.1124/pr.117.015370] [Citation(s) in RCA: 253] [Impact Index Per Article: 42.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]  Open
29
Balasingam N, Brandon HE, Ross JA, Wieden HJ, Thakor N. Cellular roles of the human Obg-like ATPase 1 (hOLA1) and its YchF homologs. Biochem Cell Biol 2019;98:1-11. [PMID: 30742486 DOI: 10.1139/bcb-2018-0353] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]  Open
30
Yu C, Wang X, Huszagh AS, Viner R, Novitsky E, Rychnovsky SD, Huang L. Probing H2O2-mediated Structural Dynamics of the Human 26S Proteasome Using Quantitative Cross-linking Mass Spectrometry (QXL-MS). Mol Cell Proteomics 2019;18:954-967. [PMID: 30723094 DOI: 10.1074/mcp.tir119.001323] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Indexed: 12/15/2022]  Open
31
Iljina M, Dear AJ, Garcia GA, De S, Tosatto L, Flagmeier P, Whiten DR, Michaels TCT, Frenkel D, Dobson CM, Knowles TPJ, Klenerman D. Quantifying Co-Oligomer Formation by α-Synuclein. ACS NANO 2018;12:10855-10866. [PMID: 30371053 PMCID: PMC6262461 DOI: 10.1021/acsnano.8b03575] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
32
Minic Z, Dahms TES, Babu M. Chromatographic separation strategies for precision mass spectrometry to study protein-protein interactions and protein phosphorylation. J Chromatogr B Analyt Technol Biomed Life Sci 2018;1102-1103:96-108. [PMID: 30380468 DOI: 10.1016/j.jchromb.2018.10.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 10/19/2018] [Accepted: 10/22/2018] [Indexed: 11/30/2022]
33
Jung Y, Seong KM, Baek JH, Kim J. Ssb2 is a novel factor in regulating synthesis and degradation of Gcn4 in Saccharomyces cerevisiae. Mol Microbiol 2018;110:728-740. [PMID: 30039896 DOI: 10.1111/mmi.14088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 07/20/2018] [Accepted: 07/21/2018] [Indexed: 12/17/2022]
34
Sinz A. Cross‐Linking/Mass Spectrometry for Studying Protein Structures and Protein–Protein Interactions: Where Are We Now and Where Should We Go from Here? Angew Chem Int Ed Engl 2018;57:6390-6396. [DOI: 10.1002/anie.201709559] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 12/06/2017] [Indexed: 01/13/2023]
35
Mohr JP, Perumalla P, Chavez JD, Eng JK, Bruce JE. Mango: A General Tool for Collision Induced Dissociation-Cleavable Cross-Linked Peptide Identification. Anal Chem 2018;90:6028-6034. [PMID: 29676898 PMCID: PMC5959040 DOI: 10.1021/acs.analchem.7b04991] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
36
Sinz A. Vernetzung/Massenspektrometrie zur Untersuchung von Proteinstrukturen und Protein‐Protein‐Wechselwirkungen: Wo stehen wir und welchen Weg wollen wir einschlagen? Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201709559] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
37
Yu C, Huang L. Cross-Linking Mass Spectrometry: An Emerging Technology for Interactomics and Structural Biology. Anal Chem 2018;90:144-165. [PMID: 29160693 PMCID: PMC6022837 DOI: 10.1021/acs.analchem.7b04431] [Citation(s) in RCA: 249] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
38
Kandasamy G, Andréasson C. Hsp70-Hsp110 chaperones deliver ubiquitin dependent and independent substrates to the 26S proteasome for proteolysis. J Cell Sci 2018;131:jcs.210948. [DOI: 10.1242/jcs.210948] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 02/14/2018] [Indexed: 02/01/2023]  Open
39
Wang X, Huang L. Dissecting Dynamic and Heterogeneous Proteasome Complexes Using In Vivo Cross-Linking-Assisted Affinity Purification and Mass Spectrometry. Methods Mol Biol 2018;1844:401-410. [PMID: 30242723 DOI: 10.1007/978-1-4939-8706-1_25] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
40
Gagarinova A, Phanse S, Cygler M, Babu M. Insights from protein-protein interaction studies on bacterial pathogenesis. Expert Rev Proteomics 2017;14:779-797. [DOI: 10.1080/14789450.2017.1365603] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
41
Gu ZC, Wu E, Sailer C, Jando J, Styles E, Eisenkolb I, Kuschel M, Bitschar K, Wang X, Huang L, Vissa A, Yip CM, Yedidi RS, Friesen H, Enenkel C. Ubiquitin orchestrates proteasome dynamics between proliferation and quiescence in yeast. Mol Biol Cell 2017;28:2479-2491. [PMID: 28768827 PMCID: PMC5597321 DOI: 10.1091/mbc.e17-03-0162] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 06/16/2017] [Accepted: 07/24/2017] [Indexed: 12/14/2022]  Open
42
Lu Y, Wu J, Dong Y, Chen S, Sun S, Ma YB, Ouyang Q, Finley D, Kirschner MW, Mao Y. Conformational Landscape of the p28-Bound Human Proteasome Regulatory Particle. Mol Cell 2017;67:322-333.e6. [PMID: 28689658 PMCID: PMC5580496 DOI: 10.1016/j.molcel.2017.06.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 04/14/2017] [Accepted: 06/07/2017] [Indexed: 10/19/2022]
43
Budenholzer L, Cheng CL, Li Y, Hochstrasser M. Proteasome Structure and Assembly. J Mol Biol 2017;429:3500-3524. [PMID: 28583440 DOI: 10.1016/j.jmb.2017.05.027] [Citation(s) in RCA: 265] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 05/22/2017] [Accepted: 05/30/2017] [Indexed: 10/19/2022]
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Rampler E, Coman C, Hermann G, Sickmann A, Ahrends R, Koellensperger G. LILY-lipidome isotope labeling of yeast: in vivo synthesis of 13C labeled reference lipids for quantification by mass spectrometry. Analyst 2017;142:1891-1899. [PMID: 28475182 DOI: 10.1039/c7an00107j] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Wang X, Cimermancic P, Yu C, Schweitzer A, Chopra N, Engel JL, Greenberg C, Huszagh AS, Beck F, Sakata E, Yang Y, Novitsky EJ, Leitner A, Nanni P, Kahraman A, Guo X, Dixon JE, Rychnovsky SD, Aebersold R, Baumeister W, Sali A, Huang L. Molecular Details Underlying Dynamic Structures and Regulation of the Human 26S Proteasome. Mol Cell Proteomics 2017;16:840-854. [PMID: 28292943 PMCID: PMC5417825 DOI: 10.1074/mcp.m116.065326] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Revised: 02/13/2017] [Indexed: 12/28/2022]  Open
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In Vivo Ubiquitin Linkage-type Analysis Reveals that the Cdc48-Rad23/Dsk2 Axis Contributes to K48-Linked Chain Specificity of the Proteasome. Mol Cell 2017;66:488-502.e7. [DOI: 10.1016/j.molcel.2017.04.024] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 03/07/2017] [Accepted: 04/27/2017] [Indexed: 12/28/2022]
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Lössl P, van de Waterbeemd M, Heck AJ. The diverse and expanding role of mass spectrometry in structural and molecular biology. EMBO J 2016;35:2634-2657. [PMID: 27797822 PMCID: PMC5167345 DOI: 10.15252/embj.201694818] [Citation(s) in RCA: 171] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 07/25/2016] [Accepted: 10/07/2016] [Indexed: 12/20/2022]  Open
48
Yu C, Huszagh A, Viner R, Novitsky EJ, Rychnovsky SD, Huang L. Developing a Multiplexed Quantitative Cross-Linking Mass Spectrometry Platform for Comparative Structural Analysis of Protein Complexes. Anal Chem 2016;88:10301-10308. [PMID: 27626298 PMCID: PMC5361889 DOI: 10.1021/acs.analchem.6b03148] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Iljina M, Tosatto L, Choi ML, Sang JC, Ye Y, Hughes CD, Bryant CE, Gandhi S, Klenerman D. Arachidonic acid mediates the formation of abundant alpha-helical multimers of alpha-synuclein. Sci Rep 2016;6:33928. [PMID: 27671749 PMCID: PMC5037366 DOI: 10.1038/srep33928] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 08/31/2016] [Indexed: 12/12/2022]  Open
50
Tsimokha AS, Zaykova JJ, Bottrill A, Barlev NA. Extracellular Proteasomes Are Deficient in 19S Subunits as Revealed by iTRAQ Quantitative Proteomics. J Cell Physiol 2016;232:842-851. [DOI: 10.1002/jcp.25492] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 07/18/2016] [Indexed: 12/31/2022]
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