Title page for ETD etd-04132004-154150


Type of Document Master's Thesis
Author Oard, Svetlana V
Author's Email Address soard@agctr.lsu.edu
URN etd-04132004-154150
Title Parallel Molecular Dynamics Simulations of Antimicrobial Peptides
Degree Master of Science in Systems Science (M.S.S.S.)
Department Computer Science
Advisory Committee
Advisor Name Title
S. Sitharama Iyengar Committee Chair
Bijaya Karki Committee Member
John Tyler Committee Member
Keywords
  • MD simulations scaling small proteins
Date of Defense 2004-04-12
Availability unrestricted
Abstract
Molecular dynamics (MD) simulations of the wheat antimicrobial peptide -purothionin were carried out in explicit water (~14,000 atoms) using an all-atom model. The structural properties of the peptide as a function of MD simulation, temperature, and presence of the mono- and divalent metal ions were investigated. The accuracy and scalability tests of the code Peach 3.8 for our system were performed on the Intel Xeon-based Linux cluster SuperHelix at Louisiana State University (LSU). The code showed the reliable accuracy and the parallel efficiency of 0.61 for ~14,000 particles on 16 processors. The microcanonical (MC) MD simulation of -purothionin in water showed that all secondary structures were stable and exhibited normal conformation at 300 K initial temperature. Helicity of the peptide was found to depend strongly on temperature, consistent with experimental data. Analysis of the MD trajectories elucidated new details of temperature effects on purothionin. Thus, the -helix 1 displayed unusual temperature resistance. The -sheets and all four disulphide bonds were not affected by change in the range of temperature from 0 to 400 K. The residues Tyr13 and Arg30 thought to be involved in antimicrobial activity of purothionin displayed increased stability. Decrease in flexibility of the peptide largely decreased upon interaction with K+ and Mg 2+ ions. The MD simulations indicated that Mg2+ ions impaired the -helix 2 and both ions interacted with Tyr13 and Agr30, suggesting the mechanism of cation inhibition for antimicrobial activity of purothionin. Therefore, the results reported here showed that the MC MD simulations reproduced effects of temperature and metal ions on structure of purothionin. Moreover, this study provided new insights into structural properties, and effects of temperature and metal ions on structure stability and conformation of the purothionin molecule.
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