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.