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|Title:||Unraveling tobacco BY-2 protein complexes with BN PAGE/LC-MS/MS and clustering methods||Authors:||Remmerie, Noor
De Vijlder, Thomas
Carpentier, Sebastien C.
De Jaeger, Geert
|Issue Date:||2011||Publisher:||ELSEVIER SCIENCE BV||Source:||JOURNAL OF PROTEOMICS, 74(8). p. 1201-1217||Abstract:||To understand physiological processes, insight into protein complexes is very important. Through a combination of blue native gel electrophoresis and LC-MS/MS, we were able to isolate protein complexes and identify their potential subunits from Nicotiana tabacum cv. Bright Yellow-2. For this purpose, a bioanalytical approach was used that works without a priori knowledge of the interacting proteins. Different clustering methods (e.g., k-means and hierarchical clustering) and a biclustering approach were evaluated according to their ability to group proteins by their migration profile and to correlate the proteins to a specific complex. The biclustering approach was identified as a very powerful tool for the exploration of protein complexes of whole cell lysates since it allows for the promiscuous nature of proteins. Furthermore, it searches for associations between proteins that co-occur frequently throughout the BN gel, which increases the confidence of the putative associations between co-migrating proteins. The statistical significance and biological relevance of the profile clusters were verified using functional gene ontology annotation. The proof of concept for identifying protein complexes by our BN PAGE/LC-MS/MS approach is provided through the analysis of known protein complexes. Both well characterized long-lived protein complexes as well as potential temporary sequential multi-enzyme complexes were characterized. (C) 2011 Elsevier B.V. All rights reserved.||Notes:||[Remmerie, N; De Vijlder, T; Valkenborg, D; Mertens, I; Witters, E] Univ Antwerp, Ctr Prote, B-2020 Antwerp, Belgium [Remmerie, N; De Vijlder, T; Prinsen, E] Univ Antwerp, Dept Biol, Lab Plant Growth & Dev, B-2020 Antwerp, Belgium [Valkenborg, D; Mertens, I; Witters, E] Vlaamse Instelling Technol Onderzoek, B-2400 Mol, Belgium [Valkenborg, D] Hasselt Univ, Interuniv Inst Biostat & Stat Bioinformat, B-3590 Diepenbeek, Belgium [Laukens, K] Univ Antwerp, Dept Math & Comp Sci, Intelligent Syst Lab, B-2020 Antwerp, Belgium [Laukens, K] Biomed Informat Res Ctr Antwerp Biomina, B-2650 Edegem, Belgium [Carpentier, SC; Panis, B] Katholieke Univ Leuven, Dept Biosyst, Div Crop Biotech, B-3001 Heverlee, Belgium [De Jaeger, G] Univ Ghent VIB, Dept Plant Syst Biol, B-9052 Ghent, Belgium [De Jaeger, G] Univ Ghent, Dept Plant Biotechnol & Genet, B-9052 Ghent, Belgium [Blust, R; Witters, E] Univ Antwerp, Dept Biol, Lab Ecophysiol Biochem & Toxicol, B-2020 Antwerp, Belgium Erwin.firstname.lastname@example.org||Keywords:||Blue native gel electrophoresis; Liquid chromatography; Clustering; Data mining; Nicotiana tabacum cv. Bright Yellow-2; Protein complexes||Document URI:||http://hdl.handle.net/1942/12221||ISSN:||1874-3919||e-ISSN:||1876-7737||DOI:||10.1016/j.jprot.2011.03.023||ISI #:||000294591500005||Category:||A1||Type:||Journal Contribution||Validations:||ecoom 2012|
|Appears in Collections:||Research publications|
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