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For: Páleníková P, Harbour ME, Ding S, Fearnley IM, Van Haute L, Rorbach J, Scavetta R, Minczuk M, Rebelo-Guiomar P. Quantitative density gradient analysis by mass spectrometry (qDGMS) and complexome profiling analysis (ComPrAn) R package for the study of macromolecular complexes. Biochim Biophys Acta Bioenerg 2021;1862:148399. [PMID: 33592209 PMCID: PMC8047798 DOI: 10.1016/j.bbabio.2021.148399] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/05/2021] [Accepted: 02/07/2021] [Indexed: 11/28/2022]
Number Cited by Other Article(s)
1
Tahir M, Hussain S, Alarfaj FK. An Integrated Multi-Model Framework Utilizing Convolutional Neural Networks Coupled with Feature Extraction for Identification of 4mC Sites in DNA Sequences. Comput Biol Med 2024;183:109281. [PMID: 39461102 DOI: 10.1016/j.compbiomed.2024.109281] [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: 05/29/2024] [Revised: 09/19/2024] [Accepted: 10/14/2024] [Indexed: 10/29/2024]
2
van Strien J, Evers F, Cabrera-Orefice A, Delhez I, Kooij TWA, Huynen MA. Analysis of Complexome Profiles with the Gaussian Interaction Profiler (GIP) Reveals Novel Protein Complexes in Plasmodium falciparum. J Proteome Res 2024;23:4467-4479. [PMID: 39262370 PMCID: PMC11459595 DOI: 10.1021/acs.jproteome.4c00414] [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: 05/11/2024] [Revised: 07/30/2024] [Accepted: 09/04/2024] [Indexed: 09/13/2024]
3
Mutti CD, Van Haute L, Minczuk M. The catalytic activity of methyltransferase METTL15 is dispensable for its role in mitochondrial ribosome biogenesis. RNA Biol 2024;21:23-30. [PMID: 38913872 PMCID: PMC11197891 DOI: 10.1080/15476286.2024.2369374] [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] [Revised: 05/03/2024] [Accepted: 06/11/2024] [Indexed: 06/26/2024]  Open
4
Páleníková P, Minczuk M, Rebelo-Guiomar P. Protocol to study human mitochondrial ribosome using quantitative density gradient analysis by mass spectrometry and complexome profiling analysis. STAR Protoc 2023;4:102605. [PMID: 37976156 PMCID: PMC10692952 DOI: 10.1016/j.xpro.2023.102605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/22/2023] [Accepted: 09/07/2023] [Indexed: 11/19/2023]  Open
5
Potter A, Cabrera-Orefice A, Spelbrink JN. Let's make it clear: systematic exploration of mitochondrial DNA- and RNA-protein complexes by complexome profiling. Nucleic Acids Res 2023;51:10619-10641. [PMID: 37615582 PMCID: PMC10602928 DOI: 10.1093/nar/gkad697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 07/18/2023] [Accepted: 08/11/2023] [Indexed: 08/25/2023]  Open
6
van Strien J, Evers F, Lutikurti M, Berendsen SL, Garanto A, van Gemert GJ, Cabrera-Orefice A, Rodenburg RJ, Brandt U, Kooij TWA, Huynen MA. Comparative Clustering (CompaCt) of eukaryote complexomes identifies novel interactions and sheds light on protein complex evolution. PLoS Comput Biol 2023;19:e1011090. [PMID: 37549177 PMCID: PMC10434966 DOI: 10.1371/journal.pcbi.1011090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 08/17/2023] [Accepted: 07/10/2023] [Indexed: 08/09/2023]  Open
7
High-Throughput Proteome Profiling of Plasma and Native Plasma Complexes Using Native Chromatography. Methods Mol Biol 2023;2628:53-79. [PMID: 36781779 DOI: 10.1007/978-1-0716-2978-9_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
8
Mezentsev Y, Ershov P, Yablokov E, Kaluzhskiy L, Kupriyanov K, Gnedenko O, Ivanov A. Protein Interactome Profiling of Stable Molecular Complexes in Biomaterial Lysate. Int J Mol Sci 2022;23:15697. [PMID: 36555337 PMCID: PMC9779103 DOI: 10.3390/ijms232415697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/05/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022]  Open
9
Fernández-Vizarra E, López-Calcerrada S, Sierra-Magro A, Pérez-Pérez R, Formosa LE, Hock DH, Illescas M, Peñas A, Brischigliaro M, Ding S, Fearnley IM, Tzoulis C, Pitceathly RDS, Arenas J, Martín MA, Stroud DA, Zeviani M, Ryan MT, Ugalde C. Two independent respiratory chains adapt OXPHOS performance to glycolytic switch. Cell Metab 2022;34:1792-1808.e6. [PMID: 36198313 DOI: 10.1016/j.cmet.2022.09.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 06/21/2022] [Accepted: 09/08/2022] [Indexed: 01/11/2023]
10
Arnold S, Braun HP. The complexome profiling approach for direct biochemical analysis of multiprotein assemblies. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2022;1863:148522. [PMID: 34902309 DOI: 10.1016/j.bbabio.2021.148522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
11
Rebelo-Guiomar P, Pellegrino S, Dent KC, Sas-Chen A, Miller-Fleming L, Garone C, Van Haute L, Rogan JF, Dinan A, Firth AE, Andrews B, Whitworth AJ, Schwartz S, Warren AJ, Minczuk M. A late-stage assembly checkpoint of the human mitochondrial ribosome large subunit. Nat Commun 2022;13:929. [PMID: 35177605 PMCID: PMC8854578 DOI: 10.1038/s41467-022-28503-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 01/20/2022] [Indexed: 12/04/2022]  Open
12
Cabrera-Orefice A, Potter A, Evers F, Hevler JF, Guerrero-Castillo S. Complexome Profiling-Exploring Mitochondrial Protein Complexes in Health and Disease. Front Cell Dev Biol 2022;9:796128. [PMID: 35096826 PMCID: PMC8790184 DOI: 10.3389/fcell.2021.796128] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/08/2021] [Indexed: 12/14/2022]  Open
13
Complexome Profiling: Assembly and Remodeling of Protein Complexes. Int J Mol Sci 2021;22:ijms22157809. [PMID: 34360575 PMCID: PMC8346016 DOI: 10.3390/ijms22157809] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 07/13/2021] [Accepted: 07/19/2021] [Indexed: 02/06/2023]  Open
14
van Strien J, Haupt A, Schulte U, Braun HP, Cabrera-Orefice A, Choudhary JS, Evers F, Fernandez-Vizarra E, Guerrero-Castillo S, Kooij TWA, Páleníková P, Pardo M, Ugalde C, Wittig I, Wöhlbrand L, Brandt U, Arnold S, Huynen MA. CEDAR, an online resource for the reporting and exploration of complexome profiling data. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2021;1862:148411. [PMID: 33722514 DOI: 10.1016/j.bbabio.2021.148411] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/02/2021] [Accepted: 03/08/2021] [Indexed: 02/06/2023]
15
D’Souza AR, Van Haute L, Powell CA, Mutti CD, Páleníková P, Rebelo-Guiomar P, Rorbach J, Minczuk M. YbeY is required for ribosome small subunit assembly and tRNA processing in human mitochondria. Nucleic Acids Res 2021;49:5798-5812. [PMID: 34037799 PMCID: PMC8191802 DOI: 10.1093/nar/gkab404] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 04/20/2021] [Accepted: 05/06/2021] [Indexed: 12/12/2022]  Open
16
Gerovac M, Vogel J, Smirnov A. The World of Stable Ribonucleoproteins and Its Mapping With Grad-Seq and Related Approaches. Front Mol Biosci 2021;8:661448. [PMID: 33898526 PMCID: PMC8058203 DOI: 10.3389/fmolb.2021.661448] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 03/04/2021] [Indexed: 12/13/2022]  Open
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