The research of the solution-state NMR group is focused on the elucidation of the structure, interactions and dynamcis of (bio)molecules by NMR spectroscopic techniques. NMR spectra can providedetails of the geometry of connected atoms in a molecule, and on the spatial proximity of hydrogen atoms. As one of few experimental techniques, by computer calculations NMR data can be transformed into 3-dimensional molecular structures. Several contributions were made to the methodology and automation of structural analysis by NMR. In addition, the Utrecht NMR group was involved in one of the first protein structure determinations by NMR (lac-repressor headpiece, 1985), and we determined the first structure of a protein-DNA complex (1987). Similar studies have been conducted on other DNA binding domains, including those of nuclear hormone receptors, nuclear excision DNA repair complexes. Currently, our research focus lies on NMR studies on large nucleosomes.
Illuminating the nucleosome using methyl group based NMR
The repeating unit of chromatin, 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 techniques use the ultra-sensitive observation of methyl-groups in the proteins to produce beautiful high-quality spectra. This in turn allows us to use these methyl groups as probes to monitor the structure, dynamics and interactions of the nucleosome.
Structural basis of epigenetic recognition
The post-translational modification of histone proteins is a key mechanism in epigenetics. The majority of these chemical marks on chromatin serve as binding platforms for so-called reader proteins that in turn coordinate the functional state of chromatin. These protein-nucleosome interactions have in recent years become targets for the development of so-called ‘epigenetic drugs’.
The structural basis of reader-nucleosome interactions is an important focus of our research. Using tricks from chemical biology, we produce of nucleosomes that are decorated with specific epigenetic modifications. These tailor-made nucleosome can then be interrogated to reveal the molecular mechanism of epigenetic read-out.
Using this approach, we uncovered an unexpected role for the nucleosomal DNA in driving the recognition of an epigenetic mark. We determined the complex structure between a reader protein and a complete nucleosomes carrying an epigenetic mark at lysine 36 in histone H3. Importantly, this structure showed how the binding affinity of the reader protein for the trimethylated lysine is strongly enhanced by additional binding to the nucleosomal DNA, underscoring the potential of our studies to discover new concepts in chromatin biology.
Integrative modeling of biomolecular assemblies. For many interesting systems, including nucleosome complexes, only sparse or low-resolution data may be available. Using integrative computational tools we can combine the data to generate meaningful atomic models of these systems.
Protein dynamics. Motions in proteins can be crucial for their function. Because of its sensitivity to motions on a very wide range of time scales, NMR is very well suited to not only study structure-function relationships, but also the role of dynamics herein.
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.