The Nucleosome Remodeling and Deacetylase (NuRD) complex is a ~1-MDa transcriptional co-regulator that is found in all complex animals and is essential for normal development. The complex displays both nucleosome remodeling and histone deacetylase activities and has strong links to cancer biology.

Although it is known that the NuRD complex is made up of ~10 protein subunits (namely CHD3/4, HDAC1/2, MTA1/2/3, RBBP4/7, p66α/β and MBD2/3), neither its exact stoichiometry nor arrangement of the subunits within the complex is known. Given its central importance throughout the animal kingdom, knowledge of NuRD structure and function will provide broad insight into mechanisms of eukaryotic gene regulation.

To this end, we have undertaken a program of research to probe the structure of the NuRD complex. Substantial progress has been made through a combination of pair-wise interaction pulldowns, single-particle electron microscopy (EM), blue-native PAGE, X-ray crystallography, NMR spectroscopy and mass spectrometry (MS). Our goal is to combine all these data, particularly the MS data with EM-derived structural envelopes, to derive the first glimpse of the NuRD structure.

In this presentation, I will focus on our implementation of mass spectrometry based approaches to provide absolute quantification of subunit stoichiometry and to derive inter-protein distance constraints, both of which are critical to our integrative effort to understand NuRD structure and function.