MOLECULAR DYNAMICS AND SIMULATION OF INSULIN MOLECULE

ABSTRACT

Molecular dynamics (MD) is a simulation methodology that investigates the system evolution by calculating the movement of system particles over time. MD simulation can provide real geometric surprises, that is, new structures that the modeler would not have expected prior to the simulation run. Insulin is a polypeptide hormone that is essential in controlling glucose levels in higher organisms. Defects in insulin signaling can result in insulin resistance, which is a defining feature of diabetes mellitus. The Avogadro’s software was used in the MD simulation and the molecule was obtained from the PDB, the steepest descent was the default algorithm, the simulation was performed at steepest descent 1,2,3,4 and 5. the visualisation, geometric optimisation was carried out. The time taken for the simulation was taken for each steps per update and it was seen that as the number of steps per update increases, the optimization time reduces. steps per update of 2 and 3 were seen to be the best in performing optimization.