Biophysical Society Thematic Meeting| Les Houches 2019

Multiscale Modeling of Chromatin: Bridging Experiment with Theory

Tuesday Speaker Abstracts

CAPTURING INTERACTIONS TO THE NUCLEOSOME ACIDIC PATCH BY MULTI- SCALE NMR Hugo van Ingen 1 ; 1 Utrecht University, NMR Group, Utrecht, Utrecht, The Netherlands Chromatin biology is driven by the specific interactions of wide range of protein factors with chromatin. The nucleosome forms the key docking platform for many of these proteins. Ultimately, an understanding of how such nucleosome-protein interaction occur in the native, cellular chromatin context is needed to fully appreciate the molecular basis of chromatin function. Motivated by its applicability across a wide range of sample phases, ranging from dilute solutions to cellular samples, our objective is to develop an NMR-based experimental, multi-scale approach to study nucleosome-protein interactions. Here, we present our recent results on three acidic patch binding proteins, each studied at a different level of complexity. For dilute solutions of mononucleosomes, solution NMR techniques are well suited to obtain atomic- resolution interaction data. Combining NMR, XL-MS and mutagenesis, we determined the structure of DNA repair factor and E3 ligase RNF168 bound to the nucleosome acidic patch. The structure highlights how the E3 directs the E2 enzyme towards to target lysine, thus explaining the ubiquitination specificity [1]. Second, we show that similar interaction data can be obtained in a dense phase formed by sedimented mononucleosomes, mimicking the crowded cellular environment. Here, we used state-of-the-art solid-state NMR to retrieve the binding site of the well-known LANA peptide on the nucleosome [2]. Finally, we discuss the prospects of in-cell NMR to study native chromatin interactions using chromatin factor HMGN2. Together, these results indicate that NMR may be appropriate source for multi-scale interaction data. [1] V. Horn et al. Structural basis of specific H2A K13/K15 ubiquitination by RNF168, revised version submitted. [2] S. Xiang, U.B. le Paige, et al (2018). Site-Specific Studies of Nucleosome Interactions by Solid-State NMR Spectroscopy. Angew. Chem. Int. Ed., vol. 57, p. 1-6


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