CONFORMATIONAL CHANGE OF Bacillus subtilis a-AMYLASE BASED ON MOLECULAR DYNAMICS ANALYSIS

• Main Author: KOSIM (NIM 20506009), MUHTAR
• Format: Theses
• Language: Indonesia
• Online Access: https://digilib.itb.ac.id/gdl/view/23361
• Institution: Institut Teknologi Bandung

Bacillus subtilis a-amylase (BSUA) is known to have different activity profile and stability within different pH condition. This research is intended to obtain understanding on what different pH condition affects conformation of BSUA using molecular dynamics (MD). This was performed under pH 3, 4, 5, 6, 7, 8 and 9. We obtain data that show BSUA has sensitivity on pH condition. Protein structure representation gives visual information on this. Changes are obvious on conformational structure. pH 7 has final conformation similar to initial structure which is showing stability. RMSD (root mean square deviation) of the final structure shows minima on pH 7 at 8 A. Largest RMSD is on pH 5 at 12 A. Hydrophobic core stability is analyzed by calculating SASA (solvent accessible surface area) of apolar amino acid residue. Minima is obtained at pH 7 (5,500 A2) which shows that this pH condition has less exposed hydrophobic core. Secondary structure (a-helix and B-sheet) tend to decrease during MD simulation and a-helix has more sensitivity to pH.