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




Majul, Amr Zein Al-Abideen

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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.



Computational chemistry, Peptides, AMP, Molecular dynamics