The solution NMR group is formed by Dr. Hugo van Ingen and his team. Research in the Van Ingen group focusses on the molecular basis of chromatin function using an integrative approach of modern NMR, biochemistry and computation. Next to working on NMR methodology and theory, the group also collaborates with and supports users of the solution NMR Facility via iNEXT-Discovery and INSTRUCT, building on the long and rich history of the Utrecht NMR group.
Van Ingen Team
Current team members
Ulric le Paige (PD), Vincenzo Lobbia (PhD), Petrit Sadiku (MSc intern), Christina Trueba Sanches (MSc intern)
Velten Horn, Pepscan
Clara van Emmerik, MRC Holland
Heyi Zhang, Scientific Volume Imaging
Ivan Corbeski, talented Post-Doc for hire
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 and 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 together with our collegues of the solid-state NMR team 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.
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. The challenging nature of these systems makes them perfect for NMR-driven integrative structural biology. With the unique sensitivity of NMR spectroscopy to structure and dynamics, we hope to create a new perspective on protein-nucleosome complexes.
NMR methodology and theory
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.
The Utrecht NMR group was established by prof. dr. Rob Kaptein and prof. dr. Rolf Boelens, who made several key contributions to the methodology and automation of structural analysis by NMR. The Utrecht NMR group of Kaptein and Boelens determined one of the first protein structures by NMR (lac-repressor headpiece, 1985), and the first structure of a protein-DNA complex (1987). Their studies on the interaction of the bacterial Lac-repressor with DNA revealed new insights into recognition of specific and non-specific DNA sequences and the associated structural transitions of the protein.