MOLECULAR DYNANMICS AND SIMULATION OF LYSOZYME USING AVOGADRO SOFTWARE

ABSTRACT

Lysozyme is a bacteriolytic enzyme commonly found in nature and one of the most abundant antimicrobial proteins in our system commonly found in bodily secretions such as tears, saliva, and milk. It function as an antimicrobial agent by cleaving the peptidoglycan component bacterial cell walls, which leads to cell death. Molecular dynamics (MD) simulations predict how every atom in a protein or other molecular system will move over time, based on a general model of the physics governing interatomic interactions. The molecule was optimize using UFF and steepest descent algorithm to obtain perfect geometry. HL has a stable energy of 3220.916 kj/mol and an average of 15,214.5secs optimization time which is about 4.2hrs. With MD simulation, the molecular properties and other necessary properties for the interaction of human lysozyme was obtain following various simulation steps,