INVESTIGATION OF STRUCTURAL AND FUNCTIONAL PROPERTIES OF SELECTED RNA OR DNA MOLECULES BY MOLECULAR MODELING METHODS
Project no. 647 · Status: Kapanmış · 2017
Summary
Transcription factors (TF) are proteins which are formed by combinations of many different amino acids. The amino acid sequences in the structure provide three-dimensional structure due to the entalpy value of the external environment and the non-covalent interactions. A protein must be in its optimal 3D conformational structure to perform its function: effectively binding to DNA. In this study, the non-covalent interactions between nucleotide dimer sequences in the single-stranded DNA, known to be effectively bound to REST, and the serine trimer of the DNA binding region of RE-1 (Suppressor Element-1) silencer transcription factor (REST) were investigated by computational methods. For this purpose, Spartan 14 program was used to find serine trimer structures and nucleotide dimer structures by conformational analysis. The MOPAC program with PM6-D3H4 method and Gaussian09 program with ?B97XD/6-311++G(d,p) level were used for optimizations (opt) and frequency (freq) calculations for each investigated conformer. Using the calculated results, the most stable structures were determined using the relative energies. Molecular structures were drawn by Discovery Studio Visualizer 2019. As a result, it was found that serine residues in the active DNA binding region of REST protein can form hydrogen (–H) bonds with DNA, and other non-covalent interactions such as Van der Waals forces were also identified.