These authors contributed equally to this work.
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Research Article
LC-MS/MS as an alternative for SDS-PAGE in blue native analysis of protein complexes
Article first published online: 17 AUG 2009
DOI: 10.1002/pmic.200900157
Copyright © 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
Additional Information
How to Cite
Wessels, H. J. C. T., Vogel, R. O., van den Heuvel, L., Smeitink, J. A., Rodenburg, R. J., Nijtmans, L. G. and Farhoud, M. H. (2009), LC-MS/MS as an alternative for SDS-PAGE in blue native analysis of protein complexes. Proteomics, 9: 4221–4228. doi: 10.1002/pmic.200900157
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These authors contributed equally to this work.
Publication History
- Issue published online: 31 AUG 2009
- Article first published online: 17 AUG 2009
- Manuscript Accepted: 16 JUN 2009
- Manuscript Revised: 9 JUN 2009
- Manuscript Received: 8 MAR 2009
Funded by
- Sixth Framework Program Priority 1, project titled “Rational treatment strategies combatting mitochondrial oxidative phosphorylation (OXPHOS) disorders (EUMITOCOMBAT)”. Grant Number: 503116
- Research Council for Earth and Life Sciences (ALW)
- The Netherlands Organization for Scientific Research (NWO)
- Prinses Beatrix Fonds. Grant Number: WAR05-0128
Keywords:
- Blue native;
- Complex I intermediates;
- LC-MS/MS;
- Mitochondrion;
- Respiratory chain complex I;
- Technology
Abstract
Two-dimensional blue native/SDS-PAGE is widely applied to investigate native protein–protein interactions, particularly those within membrane multi-protein complexes. MS has enabled the application of this approach at the proteome scale, typically by analysis of picked protein spots. Here, we investigated the potential of using LC-MS/MS as an alternative for SDS-PAGE in blue native (BN) analysis of protein complexes. By subjecting equal slices from BN gel lanes to label-free semi-quantitative LC-MS/MS, we determined an abundance profile for each protein across the BN gel, and used these profiles to identify potentially interacting proteins by protein correlation profiling. We demonstrate the feasibility of this approach by considering the oxidative phosphorylation complexes I–V in the native human embryonic kidney 293 mitochondrial fraction, showing that the method is capable of detecting both the fully assembled complexes as well as assembly/turnover intermediates of complex I (NADH:ubiquinone oxidoreductase). Using protein correlation profiling with a profile for subunits NDUFS2, 3, 7 and 8 we identified multiple proteins possibly involved in the biogenesis of complex I, including the recently implicated chaperone C6ORF66 and a novel candidate, C3ORF60.