All ETDs from UAB

Advisory Committee Chair

Donald D Muccio

Advisory Committee Members

David E Graves

Tracy P Hamilton

Aaron L Lucius

Matthew B Renfrow

Jamil S Saad

Document Type


Date of Award


Degree Name by School

Doctor of Philosophy (PhD) College of Arts and Sciences


Vitamin A metabolites are compounds that perform critical functions for mammalian life. The retinoic acid metabolites of vitamin A regulate genetic transcription. Retinoic acids function by binding to type II nuclear receptor proteins (NRs), which modulates interactions between nuclear receptors and transcription initiation machinery (such as coactivator proteins). It is the focus of this dissertation to expand our understanding of retinoic acids in their interactions with the nuclear receptor protein Retinoid X Receptor alpha (RXR&alpha). Retinoic acids are composed of a trimethylcyclohexenyl ring, polyene chain, and terminal carboxylic acid. The first chapter investigates the energetics of the ring-chain conformation using computational methods. The lowest energy conformer of retinoic acids was found to be a distorted geometry. The steric interactions that favor the distorted conformer over the planar conformer were determined using model molecules. We also explored how ring inversion, polyene chain isomerization, and nature of polar end groups affected the relative energies of the low-energy conformers. RXR&alpha forms heterodimers partnered with other NRs (such as Peroxisome Proliferator-Activated Receptor gamma, PPAR&gamma), and the heterodimer is responsible for modulating activity of target genes. The 9-cis retinoic acid (9cRA) binds to RXR&alpha and regulates its ability to recruit coactivator proteins. The second chapter in this dissertation compares the binding mode of 9cRA to RXR&alpha homodimers with 9cRA binding to RXR&alpha/PPAR&gamma ligand binding domain heterodimers. The results indicate that the 9cRA binding affinity and conformation is similar in RXR&alpha homodimers and RXR&alpha/PPAR&gamma heterodimers, but the surrounding protein environment may differ. We also compare the binding mode of the PPAR agonist Rosiglitazone to homodimers and heterodimers. The third chapter investigates how the presence of 9cRA affects the binding of coactivator protein models (coactivator peptides that model the LxxLL motif) to RXR&alpha homodimers and RXR&alpha/PPAR&gamma heterodimers by isothermal titration calorimetry. Two coactivator peptides were studied and found to bind differently to RXR&alpha and PPAR&gamma. These studies found that the presence of 9cRA increased the stoichiometry of dimer - peptide binding for both RXR&alpha homodimers and RXR&alpha/PPAR&gamma heterodimers. Also, the capability of PPAR&gamma to bind coactivator peptides depended largely on the peptide sequence about the LxxLL motif.