MOLECULAR DYNAMICS AND SIMULATION OF THE MELANIN PROTEASE COMPLEX USING THE AVOGADRO SOFTWARE

ABSTRACT.

Melanin is a natural skin pigment that gives human skin hair and eyes their color, dark skinned people have more melanin in their skin than light skinned people. It is responsible for our beautiful variety of skin tones shades eye colors and hair colors. Proteinase K is a serine protease that exhibits broad cleavage activity it cleaves peptide bonds adjacent to the carboxylic group of aliphatic and aromatic amino acids. In this study we are to carry out molecular dynamics simulation of the melanin protease complex (PDB 1OYO) using the Avogadro software, by importing the molecule, visualizing, optimizing its geometry and carrying out MD simulation runs to obtain results. The results show that the minimized energy (global minimum) of the melanin protease complex (PDB1OYO) is the same regardless of steps per update used for geometry optimization. Furthermore results show that the inverse variation of steps per update and time of optimization. This study indicates the importance of molecular dynamics simulation in the study of complex molecules.