Comparative Molecular Dynamic Simulations of 2 helical-AMPS found in snakes, ATRA-1 and ATRA-2

Abstract

This thesis proposes the use of Molecular Dynamic (MD) simulations to study the two synthetic cationic antimicrobial peptides (CAMPs), ATRA-1 and ATRA-2. The peptides are based o a natural antimicrobial peptide found in the elapid snake Naja Atra [de Latour et al., 2010]. Natural AMPs can potentially serve as templates for engineering novel antibiotics. MD simulations provide a valuable resource to supplement existing experimental and database-aided prediction data. Specifically the interaction of the two aforementioned peptides with a model lipid bilayer membrane is studied. The antimicrobial potencies between the peptides di er appreciably, yet their amino acid sequences differ from each other at only 2 positions. This thesis proposes the use of MD to run simulations to extract qualitative and quantitative information on each peptide. Most other similar computational studies on peptides are done on a single type of peptide. Simulations comparing ATRA-1 and ATRA-2 are analysed in this thesis, focusing on ending various physical and chemical parameters that differentiate the two peptides. The simulations employ all atom explicit models, with a realistic non-anchored membrane. In addition, the feasibility of using MD simulations to predict and rank the effectiveness of proposed rationally designed novel antimicrobial peptides will be evaluated.