Cross‐linking mass spectrometry reveals the structural topology of peripheral NuRD subunits relative to the core complex

Autor: Simone C. Kleinendorst, Cornelia G. Spruijt, Marijke P. Baltissen, Cathrin Gräwe, Michiel Vermeulen
Rok vydání: 2020
Předmět:
Models
Molecular
Protein Conformation
alpha-Helical
0301 basic medicine
CDK2AP2
cross‐linking
Mutually exclusive events
Mass spectrometry
Topology
Proteomics
GATA Transcription Factors
Biochemistry
Histone Deacetylases
Mass Spectrometry
03 medical and health sciences
0302 clinical medicine
Cell Line
Tumor
NuRD
Protein Interaction Mapping
Humans
Nucleosome
Protein Interaction Domains and Motifs
Amino Acid Sequence
Molecular Biology
Topology (chemistry)
Binding Sites
Sequence Homology
Amino Acid
Chemistry
Proteomics and Chromatin Biology
C-terminus
Original Articles
Cell Biology
Mi-2/NuRD complex
Cyclin-Dependent Kinases
Recombinant Proteins
Nucleosomes
Protein Subunits
Cross-Linking Reagents
030104 developmental biology
030220 oncology & carcinogenesis
Protein Conformation
beta-Strand
Original Article
Histone deacetylase
Sequence Alignment
xIP‐MS
HeLa Cells
Mi-2 Nucleosome Remodeling and Deacetylase Complex
Protein Binding
Zdroj: The Febs Journal
FEBS Journal, 288, 10, pp. 3231-3245
FEBS Journal, 288, 3231-3245
ISSN: 1742-4658
1742-464X
DOI: 10.1111/febs.15650
Popis: Thorough purification and cross‐linking of the NuRD complex from multiple angles led to a high‐density interaction network. The core is formed by MTA‐HDAC and RBBP proteins, to which MBD and GATAD2 proteins dock. The latter proteins associate with CHDs, which in turn recruit CDK2AP1 and its paralog CDK2AP2 via their C termini.
The multi‐subunit nucleosome remodeling and deacetylase (NuRD) complex consists of seven subunits, each of which comprises two or three paralogs in vertebrates. These paralogs define mutually exclusive and functionally distinct complexes. In addition, several proteins in the complex are multimeric, which complicates structural studies. Attempts to purify sufficient amounts of endogenous complex or recombinantly reconstitute the complex for structural studies have proven quite challenging. Until now, only substructures of individual domains or proteins and low‐resolution densities of (partial) complexes have been reported. In this study, we comprehensively investigated the relative orientation of different subunits within the NuRD complex using multiple cross‐link IP mass spectrometry (xIP‐MS) experiments. Our results confirm that the core of the complex is formed by MTA, RBBP, and HDAC proteins. Assembly of a copy of MBD and GATAD2 onto this core enables binding of the peripheral CHD and CDK2AP proteins. Furthermore, our experiments reveal that not only CDK2AP1 but also CDK2AP2 interacts with the NuRD complex. This interaction requires the C terminus of CHD proteins. Our data provide a more detailed understanding of the topology of the peripheral NuRD subunits relative to the core complex. Database Proteomics data are available in the PRIDE database under the accession numbers PXD017244 and PXD017378.
Databáze: OpenAIRE
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