Analysing the rearrangement of holo-TFIID with cross-linking/mass spectrometry

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Coactivators like the transcriptional factor IID (TFIID) are multi-protein complexes that impact transcription through interactions with the core transcription machinery and regulatory proteins, as well as by modifying chromatin. Recent studies suggest that TFIID processes these signals by changing its conformation, resulting in a rearranged structure of DNA bound-TFIID. The conformational flexibility of TFIID and its megadalton size have so far prevented the acquisition of high-resolution structures of the entire complex.The host lab has pioneered a novel approach using cross-linking and mass spectrometry (CLMS) to obtain structural insights of proteins and their complexes in solution. This method is especially well suited to study structural changes in complex environments. Using state-of-the-art integrative structural approaches that combine cross-linking/mass spectrometry, cryo-electron microscopy and X-ray, I will acquire high-resolution structures of TFIID. This in vitro study will be complemented by the structural analysis of TFIID complexes in their native environment. I will cross-link TFIID in living cells to avoid the loss of weak interactions, conformational rearrangements during biochemical purification or artefacts from recombinant expression. My aim is to elucidate a central step in transcription control and to learn a cutting edge technique. Structural analyses in cells by the technologies implemented in my work here have the potential to fundamentally change the way structural biology is conducted, allowing its migration from highly restrictive in vitro conditions towards more native environments.