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

dc.contributor.advisorBishop, Barney
dc.contributor.authorMajul, Amr Zein Al-Abideen
dc.creatorMajul, Amr Zein Al-Abideen
dc.date2015-07-28
dc.date.accessioned2017-01-26T22:10:32Z
dc.date.available2017-01-26T22:10:32Z
dc.date.issued2017-01-26
dc.description.abstractThis 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.
dc.identifier.urihttps://hdl.handle.net/1920/10517
dc.language.isoen
dc.subjectComputational chemistry
dc.subjectPeptides
dc.subjectAMP
dc.subjectMolecular dynamics
dc.titleComparative Molecular Dynamic Simulations of 2 helical-AMPS found in snakes, ATRA-1 and ATRA-2
thesis.degree.disciplineChemistry
thesis.degree.grantorGeorge Mason University
thesis.degree.levelMaster's
thesis.degree.nameMaster of Science in Chemistry

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