The Caenorhabditis elegans DAF-12 nuclear receptor: Structure, dynamics, and interaction with ligands

L. ALVAREZ; ARROYO MAÑEZ, P.; D. A. ESTRIN; G. BURTON

PROTEINS: STRUCTURE, FUNCTION AND GENETICS

WILEY-LISS, DIV JOHN WILEY & SONS INC

Lugar: New York; Año: 2012 vol. 80 p. 1798 - 1809

0887-3585

A structure for the ligand binding domain (LBD) of the DAF-12 receptor from Caenorhabditis elegans was obtained fromthe X-ray crystal structure of the receptor LBD from Strongyloides stercoralis bound to (25R)-D7-dafachronic acid (DA)(pdb:3GYU). The model was constructed in the presence of the ligand using a combination of Modeller, Autodock, and mo-lecular dynamics (MD) programs, and then its dynamical behavior was studied by MD. A strong ligand binding mode(LBM) was found, with the three arginines in the ligand binding pocket (LBP) contacting the C-26 carboxylate group of theDA. The quality of the ceDAF-12 model was then evaluated by constructing several ligand systems for which the experimen-tal activity is known. Thus, the dynamical behavior of the ceDAF-12 complex with the more active (25S)-D7-DA showed twodistinct binding modes, one of them being energetically more favorable compared with the 25R isomer. Then the effect ofthe Arg564Cys and Arg598Met mutations on the (25R)-D7-DA binding was analyzed. The MD simulations showed that in thefirst case the complex was unstable, consistent with the lack of transactivation activity of (25R)-D7-DA in this mutant.Instead, in the case of the Arg598Met mutant, known to produce a partial loss of activity, our model predicted smallereffects on the LBM with a more stable MD trajectory. The model also showed that removal of the C-25 methyl does notimpede the simultaneous strong interaction of the carboxylate with the three arginines, predicting that 27-nor-DAs areputative ceDAF-12 ligands.