Research in the group of Hugo van Ingen focusses primarily on the molecular basis of chromatin function. We are mostly interested in the interactions of histone proteins and nucleosomes with other chromatin factors such as chaperones, remodelers, or proteins that control epigenetics. We aspire to create a new perspective on protein-nucleosome complexes, afforded by the unique sensitivity of NMR spectroscopy to structure, dynamics and interactions. We apply and develop new approaches to tackle these challenging systems. Next to the nucleosome-focused research, we also engage in collaborative projects ranging from protein interaction studies to NMR theory.

Team

PhD students: Ivan Corbeski (joined with prof. dr. Rolf Boelens), Velten Horn, Ulric le Paige, Clara van Emmerik, Heyi Zhang, Vincenzo Lobbia

Molecular basis of chromatin function

The packaging of DNA into chromatin represents one of the most fundamental layers of cell biology. Chromatin provides the required structural compaction of the DNA to fit in the nucleus, and plays crucial roles in controlling cell fate and protecting genomic integrity. These functions ultimately depend on the interactions of a wide range of proteins with the nucleosome, chromatin’s fundamental building block. But how these proteins recognize, bind and perturb nucleosomes? We aim to answer this question, and to thereby provide a guide for the rational search for new therapeutics.

The nucleosome is a 200,000 Da supramolecular assembly of roughly one part DNA and one part protein. The massive size of the nucleosome calls for state-of-the-art NMR techniques that are tailored for such high-molecular weight systems. These can be applied both in solution, as in a sediment. In solution, the methyl-TROSY approach allows the ultra-sensitive observation of methyl-groups in the proteins to produce beautiful high-quality spectra. In the sediment, we showed, in close collaboration with the Utrecht solid-state NMR group, that ¹H-detected solid-state NMR can give high quality spectra of the nucleosome core. In both cases, the NMR signals act as molecular probes to monitor the structure, dynamics and interactions of the nucleosome.

Protein dynamics

Proteins and nucleic acids have inherently dynamic structures. Nature exploits these dynamics to make the impossible possible like tunneling through the activation barrier of a chemcial reaction or ligand binding to the inside of a protein. Conformational dynamics also play a key role in molecular recognition and protein folding. NMR has a a unique set of tools to detect and analyze such motions at atomic resolution over a wide range of time scales. We apply and develop these methods for a better understanding of protein function in general and chromatin in particular.

NMR theory and methodology.

As the saying goes, in theory there is no difference between theory and practice. In practice, this is only true for NMR. Well, at least practically true. NMR is essentially an applied form of quantum mechanics, allowing one to accurately design and simulate experiments.

As it turns out, our group has spent considerable time on analyzing the effects of strong coupling in NMR experiments and spectra. Strong coupling occurs when the J-coupling is small compared to the frequency separation and is probably best known for the roofing effect in AB-type spectra. While strong coupling has been studied intensively since the late 50’s, there are still fundamental and new aspects to be discovered in this fascinating corner of spectroscopy.