Induced Fit Simulations on Nuclear Receptors

Monika      Nocker; Pietro      Cozzini

doi:10.2174/156802611794863526

Abstract

The large superfamily of nuclear receptors is a family of ligand-activated transcription factors involved in numerous fundamental processes and shows many common characteristics and behaviors. The comprehension of these roles is of fundamental importance to select the right target for receptor structure-based screening. Recently, during the last ten years, several crystallographic structures of nuclear receptors complexed with ligands have been registered in the Protein Data Bank, supplying a structural basis for computational simulations. The macroscopic flexibility of helix12 and local flexibility of some amino acids sidechains within cavities of the Ligand Binding Domain suggest a reason for the behavior of these receptors toward different ligands. Several approaches have been applied in trying to explain this flexibility and to predict how ligand binding can influence complex conformations. In this short review, we present an introduction to the structure and function of nuclear receptors, specifically the estrogen, androgen, glucorticoid, peroxisome proliferator, steroid, thyroid and vitamin D receptors, and a discussion of the state-of-the-art of induced fit approaches for the nuclear receptor family.

Keywords: Nuclear Receptor Superfamily, Ligand Binding Domain, Micro- and macroscopic flexibility, Allosteric effect, closed-agonistic conformation, open antagonistic conformation, Helix H12 positioning, amino acids, helix12, androgen, glucorticoid, thyroid, vitamin D receptors, NRs, vitamin D, retinoids, eicosanoids, A-F, AD, TFIIF, RAP74, GR, DBD, NLS, LBD, X-ray crystallography, LBP, PR, ER, AR, TR, VDR, RAR, PPAR, EERs, NOR1, RXR, HRE, Allosteric Effects, BMS614, NcoR1, HDACs, PXR, DHT, MD, Met895, CPA, WT, LIE analysis, QSAR, Glucocorticoid Receptor, Raloxifene, Cyproterone acetate, Aldosterone, Progesterone, MF, IFD, NALLRYLLD, Cys798