Conformational Ensembles from Experimental Data and Computer Simulations

Conformational Ensembles from Experimental Data and Computer Simulations

Poster Abstracts

1-POS Board 1 Integrative Modelling of Nuclear Receptor Proteins Jérôme Eberhardt, Roland H. Stote, Annick Dejaegere . IGBMC - Strasbourg University, Illkirch, France.

Nuclear hormone receptors (NRs) are ligand-dependent transcriptional regulators that have a central role in regulating development and homeostasis in metazoan. Their molecular regulation is linked to their ability to undergo allosteric structural changes upon signaling hormone binding, which leads to activation or repression of regulated genes. Besides ligand binding, nuclear receptors are regulated by different signals including post-translational modifications. However, for these latter signaling events, the underlying molecular mechanism of regulation is still poorly understood. Although structural snapshots of essential structures along the regulation pathway of NRs have been obtained largely by crystallographic studies of their structured DNA binding (DBD) and ligand binding (LBD) domains, regulation is also linked to changes in the structural dynamics of the receptor. The characterization of these structural dynamical effects is crucial to our understanding of the allosteric mechanisms occurring in these receptors. In recent years, mass spectrometry based hydrogen-deuterium (HDXMS) exchange has emerged as the method of choice to characterize NRs structural dynamics. However, even if empirical correlations have been established between HDXMS and functional effects of NRs ligands, the underlying conformational landscape has not been characterized. We use molecular simulations coupled with experimental data to characterize the conformational dynamics of nuclear receptors and their role in functional regulation. In particular, we identified transient conformations of the retinoic X receptor (RXR) using accelerated molecular dynamics simulations and showed that phosphorylation of the RXR ligand binding domain affects the underlying conformational landscape. To validate our conformations, we developed a protocol that permits us to calculate hydrogen-deuterium exchange data. This protocol is of general use to interpret HDMX data and to relate the observed exchange to transient conformations.

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