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eBook details

• Title: Chemistry Paper Abstracts (Author Abstract)
• Author : Journal of the Alabama Academy of Science
• Release Date : January 01, 2008
• Genre: Engineering,Books,Professional & Technical,
• Pages : * pages
• Size : 163 KB

Description

Binding of All-trans Retenoic Acid to Retinoic Acid Receptor. Alexander E. Vaughn, Tracy P. Hamilton, Department of Chemistry, Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294. Members of the retinoid family interact with nuclear receptors(NR). NRs, which are regulated by small molecule signals, regulate transcription. All-trans retinoic acid (RA) and 9-cis-retinoic acid (9cRA) are activators of Retinoic Acid Receptors (RARs). UAB-30, an analog of 9cRA, is a drug targeted to prevent prevent cancer by targeting human RXR-gamma. This study will investigate the binding of RA to the human RAR ligand binding domain (RAR-LBD). The x-ray diffraction structure for the ligand binding domain of human RAR-gamma bound to RA was downloaded from the PDB data bank (Renaud, J.-P.; Rochel, N. R. Nature 1995, 378, 681-689). Waters were removed from this experimental structure and 25 RA molecules were added at random positions. The system was then minimized via molecular dynamics for 7.5ps (all molecular dynamics runs had a timestep of 1 fs). This structure was then solvated using a water box padded with 1.5nm of water molecules, and again minimized for 10ps. Afterwards the protein was brought to a temperature of 310K from 0K by 5K increments every picosecond. This work was made possible in part by a grant of high performance computing resources from the Department of Computer and Information Sciences at the University of Alabama at Birmingham, the School of Natural Sciences and Mathematics at the University of Alabama at Birmingham, and the National Science Foundation Award CNS-0420614.

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