Wong, Wai Keet (2015) Visualization of localized movement of vitamin d receptor using molecular dynamic simulation approach / Wong Wai Keet. Masters thesis, University of Malaya.
Abstract
Research on treatments of rickets had led to the discovery of Vitamin D back in the early nineties. Vitamin D is synthesised through exposure of skin to sunlight and then transported to liver and kidney for activation process. Recent research showed that there are quite a number of targeted cells which uptake Vitamin D through the intra-cellular receptor, Vitamin D receptor (VDR). The purpose of this study is to visualise the changes of VDR during the present of Vitamin D. Molecular dynamic simulation was implemented to carry out this study. PDB file (1DB1) of the latest entry in PDB was obtained. Parameters were being set to resemble the biological environment which surrounds the receptor. Movement of atoms were bound to CHARMM with restrains applied. Data obtained were all plotted for stability check and to validate the surrounding did resemble the actual biological environment. Thousands of frames were produced and combined to produce a movie. The results showed localize movement of VDR throughout a two nanoseconds time period. The structure maintained a stable energy state and all environmental factors were kept at a constant state. Throughout the simulation, eight thousands frames were obtained. Snapshots of certain important frames were done and localize movement of the VDR were clearly seen within the movie and the images.
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