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.
