Assembly of active biomolecular complexes

Protein interaction domains play essential roles in the transport, localization, assembly and functioning of multi-protein complexes. We study the structure function relationships of the five PDZ domains of the protein tyrosine phosphatase PTP-BL and the so-called PAH domains of the transcriptional co-repressor SIN3.

PDZ domains


PDZ 3 figs
Figure 1. Solution structures of the native PDZ domain, the alternative-spliced PDZ domain and analysis of of the orientation of helix a2.

PDZ domains are essential in the targeting and assembly of multi-protein complexes. We studied the five PDZ domains (PDZ1-5) of the protein tyrosine phosphatase PTP-BL by solving the structures of the native PDZ2, an alternatively spliced PDZ2 and the PDZ-APC complex. We also established a direct regulatory PDZ1-PDZ2 interaction, explored the structural requirements for the PDZ2-LIM-domain interaction and probed the PDZ2 folding behavior. We recently also solved the structure of the second PDZ domain of X11α/Mint.

Key publications:

■ Walma, T., Spronk, C.A.E.M., Tessari, M., Aelen, J.M.A., Schepens, J., Hendriks, W. & Vuister, G.W. (2002) “Structure, Dynamics and Binding Characteristics of the Second PDZ Domain of PTP-BL”, J. Mol. Biol. 316, 1101-1110.
■ Walma, T., Aelen, J.M.A., Nabuurs, S., van den Berk, L., Oostendorp, M., Hendriks, W. & Vuister, G.W. (2004) “A closed binding pocket modifies the binding properties of an alternatively spliced form of the second PDZ domain of PTP-BL”, Structure 12, 10-20.

Transcription regulation


PAH domains
Figure 2: Solution structures of the native PAH2 domain, the PAH2-MAD24 complex and the extended interaction motif.


The proteins Sin3A/B are crucial components for the assembly of a co-repressor complex essential for the transition between cell proliferation and differentiation. Sin3A/B each contain three domains (PAH1-3) responsible for interaction with the Sin3 targets. We solved the structures of the native PAH2 and two PAH2 complexes with a 13-mer Mad peptide and 24-mer Mad peptide. These structures allowed us to define a minimal binding motif. We also extensively assessed the changes in dynamic behavior of the PAH2 domain upon peptide binding.

Key publications:

■ Spronk, C.A.E.M., Tessari, M., Kaan, A.M., Jansen, J.F.A., Vermeulen, M., Stunnenberg, H.G & Vuister, G.W. (2000) "The Mad1-Sin3B interaction involves a novel helical fold", Nature Struct. Biol. 7, 1100-1104.
■ Ingen, H. van, Lasonder, E., Jansen, J.F.A., Kaan, A., Spronk, C.A.E.M., Stunnenberg, H.G & Vuister G.W (2004) “Extension of the binding motif of the Sin3 Interacting Domain of the Mad-family proteins”, Biochemistry 43, 46-53.
■ Van Ingen, H., Baltussen, M.A.H, Aelen, J. & Vuister, G.W. (2006) “Role of Structural and Dynamical Plasticity in Sin3: The Free PAH2 Domain is a Folded Module in mSin3B”, J. Mol. Biol. 358, 485-497.