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Originally published In Press as doi:10.1074/mcp.M700306-MCP200 on December 17, 2007.
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Molecular & Cellular Proteomics 7:845-852, 2008.
© 2008 by The American Society for Biochemistry and Molecular Biology, Inc.

Research

Quantitative Proteomics Reveals Regulation of Dynamic Components within TATA-binding Protein (TBP) Transcription Complexes*,S

Florence Mousson{ddagger},§,¶, Annemieke Kolkman§,¶,||,**, W. W. M. Pim Pijnappel{ddagger},{ddagger}{ddagger}, H. Th. Marc Timmers{ddagger},{ddagger}{ddagger},§§ and Albert J. R. Heck||,{ddagger}{ddagger},¶¶

From the {ddagger} Department of Physiological Chemistry, University Medical Centre Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands and || Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands

Affinity purification in combination with isotope labeling of proteins has proven to be a powerful method to discriminate specific from nonspecific interactors. However, in the standard SILAC (stable isotope labeling by amino acids in cell culture) approach dynamic components may easily be assigned as nonspecific. We compared two affinity purification protocols, which in combination revealed information on the dynamics of protein complexes. We focused on the central component in eukaryotic transcription, the human TATA-binding protein, which is involved in different complexes. All known TATA-binding protein-associated factors (TAFs) were detected as specific interactors. Interestingly one of them, BTAF1, exchanged significantly in cell extracts during the affinity purification. The other TAFs did not display this behavior. Cell cycle synchronization showed that BTAF1 exchange was regulated during mitosis. The combination of the two affinity purification protocols allows a quantitative approach to identify transient components in any protein complex.

§§ To whom correspondence may be addressed: Dept. of Physiological Chemistry, University Medical Centre Utrecht, Universiteitsweg 100, P. O. box 85060, 3508 AB Utrecht, The Netherlands. E-mail: h.t.m.timmers{at}umcutrecht.nl

¶¶ To whom correspondence may be addressed: Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands. E-mail: a.j.r.heck{at}uu.nl






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